Search results for: genetic testing

Authors: Rebecca Richards Steed, James Van Derslice, Ken Smith, Richard Medina, Amanda Bakian

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Elucidating gene-environment interactions for heritable disease outcomes is an emerging area of disease research, with genetic studies informing hypotheses for environment and gene interactions underlying some of the most confounding diseases of our time, like autism spectrum disorder (ASD). Geography has thus far played a key role in identifying environmental factors contributing to disease, but its use can be broadened to include genetic and environmental factors that have a synergistic effect on disease. Through the use of family pedigrees and disease outcomes with life-course residential histories, space-time clustering of generations at critical developmental windows can provide further understanding of (1) environmental factors that contribute to disease patterns in families, (2) susceptible critical windows of development most impacted by environment, (3) and that are most likely to lead to an ASD diagnosis. This paper introduces a retrospective case-control study that utilizes pedigree data, health data, and residential life-course location points to find space-time clustering of ancestors with a grandchild/child with a clinical diagnosis of ASD. Finding space-time clusters of ancestors at critical developmental windows serves as a proxy for shared environmental exposures. The authors refer to geographic life-course exposures as geographic legacies. Identifying space-time clusters of ancestors creates a bridge for researching exposures of past generations that may impact modern-day progeny health. Results from the space-time cluster analysis show multiple clusters for the maternal and paternal pedigrees. The paternal grandparent pedigree resulted in the most space-time clustering for birth and childhood developmental windows. No statistically significant clustering was found for adolescent years. These results will be further studied to identify the specific share of space-time environmental exposures. In conclusion, this study has found significant space-time clusters of parents, and grandparents for both maternal and paternal lineage. These results will be used to identify what environmental exposures have been shared with family members at critical developmental windows of time, and additional analysis will be applied.

Keywords: family pedigree, environmental exposure, geographic legacy, medical geography, transgenerational inheritance

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Authors: Ana L. Martins, Rita S. Saraiva, João C. Ferreira

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Much effort has been placed on the assessment of perceived service quality. Several models can be found in literature, but these are mainly focused on business-to-consumer (B2C) relationships. Literature on how to assess perceived quality in business-to-business (B2B) contexts is scarce both conceptually and in terms of its application. This research aims at filling this gap in literature by applying INDSERV to a case study situation. Under this scope, this research aims at analyzing the adequacy of the proposed assessment tool to other context besides the one where it was developed and by doing so analyzing the perceive quality of the advertisement service provided by a specific television network to its B2B customers. The INDSERV scale was adopted and applied to a sample of 33 clients, via questionnaires adapted to interviews. Data was collected in person or phone. Both quantitative and qualitative data collection was performed. Qualitative data analysis followed content analysis protocol. Quantitative analysis used hypotheses testing. Findings allowed to conclude that the perceived quality of the television service provided by television network is very positive, being the Soft Process Quality the parameter that reveals the highest perceived quality of the service as opposed to Potential Quality. To this end, some comments and suggestions were made by the clients regarding each one of these service quality parameters. Based on the hypotheses testing, it was noticed that only advertisement clients that maintain a connection to the television network from 5 to 10 years do show a significant different perception of the TV advertisement service provided by the company in what the Hard Process Quality parameter is concerned. Through the collected data content analysis, it was possible to obtain the percentage of clients which share the same opinions and suggestions for improvement. Finally, based on one of the four service quality parameter in a B2B context, managerial suggestions were developed aiming at improving the television network advertisement perceived quality service.

Keywords: B2B, case study, INDSERV, perceived service quality

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Authors: Petcharat Kerdonfag, Surasak Taneepanichskul, Winai Wadwongtham

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Background: Although there have not been effective treatments for Noise Induced Hearing Loss (NIHL), it can be definitely preventable with promoting the use of Hearing Protection devices (HPDs) among workers who have been exposed to excessive noise for a long period. Objectives: The objectives of this study were to explore the use of HPDs among steel industrial workers in the high noise level zone in Samut Prakan province, Thailand and to examine the relationships of the HPDs use and hearing loss. Materials and Methods: In this cross-sectional study, eligible ninety-three participants were recruited in the designated zone of higher noise (> 85dBA) of two factories, using simple random sampling. The use of HPDs was gathered by the self-record form, examined and confirmed by the researcher team. Hearing loss was assessed by the audiometric screening at the regional Samut Prakan hospital. If an average threshold level exceeds 25 dBA at high frequency (4 and 6 Hz) in each ear, participants would be lost of hearing. Data were collected from October to December, 2016. All participants were examined by the same examiners for the validity. An Audiometric testing was performed with the participants who have been exposed to high noise levels at least 14 hours from workplace. Results: Sixty participants (64.5%) had secondary level of education. The average mean score of percent time of using HPDs was 60.5% (SD = 25.34). Sixty-seven participants (72.0%) had abnormal hearing which they have still needed to increase lower percent time of using HPDs (Mean = 37.01, SD = 23.81) than those having normal hearing (Mean = 45.77, SD = 28.44). However, there was no difference in the mean average of percent time of using HPDs between these two groups.Conclusion: The findings of this study have confirmed that the steel industrial workers still need to be motivated to use HPDs regularly. Future research should pay more attentions for creating a meaningful innovation to steel industrial workers.

Keywords: hearing protection devices, noise induced hearing loss, audiometric testing, steel industry

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Authors: Navid Kaboudi, Ali Shayanfar

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Introduction: Feeding infants with safe milk from the beginning of their life is an important issue. Drugs which are used by mothers can affect the composition of milk in a way that is not only unsuitable, but also toxic for infants. Consuming permeable drugs during that sensitive period by mother could lead to serious side effects to the infant. Due to the ethical restrictions of drug testing on humans, especially women, during their lactation period, computational approaches based on structural parameters could be useful. The aim of this study is to develop mechanistic models to predict the M/P ratio of drugs during breastfeeding period based on their structural descriptors. Methods: Two hundred and nine different chemicals with their M/P ratio were used in this study. All drugs were categorized into two groups based on their M/P value as Malone classification: 1: Drugs with M/P>1, which are considered as high risk 2: Drugs with M/P>1, which are considered as low risk Thirty eight chemical descriptors were calculated by ACD/labs 6.00 and Data warrior software in order to assess the penetration during breastfeeding period. Later on, four specific models based on the number of hydrogen bond acceptors, polar surface area, total surface area, and number of acidic oxygen were established for the prediction. The mentioned descriptors can predict the penetration with an acceptable accuracy. For the remaining compounds (N= 147, 158, 160, and 174 for models 1 to 4, respectively) of each model binary regression with SPSS 21 was done in order to give us a model to predict the penetration ratio of compounds. Only structural descriptors with p-value<0.1 remained in the final model. Results and discussion: Four different models based on the number of hydrogen bond acceptors, polar surface area, and total surface area were obtained in order to predict the penetration of drugs into human milk during breastfeeding period About 3-4% of milk consists of lipids, and the amount of lipid after parturition increases. Lipid soluble drugs diffuse alongside with fats from plasma to mammary glands. lipophilicity plays a vital role in predicting the penetration class of drugs during lactation period. It was shown in the logistic regression models that compounds with number of hydrogen bond acceptors, PSA and TSA above 5, 90 and 25 respectively, are less permeable to milk because they are less soluble in the amount of fats in milk. The pH of milk is acidic and due to that, basic compounds tend to be concentrated in milk than plasma while acidic compounds may consist lower concentrations in milk than plasma. Conclusion: In this study, we developed four regression-based models to predict the penetration class of drugs during the lactation period. The obtained models can lead to a higher speed in drug development process, saving energy, and costs. Milk/plasma ratio assessment of drugs requires multiple steps of animal testing, which has its own ethical issues. QSAR modeling could help scientist to reduce the amount of animal testing, and our models are also eligible to do that.

Keywords: logistic regression, breastfeeding, descriptors, penetration

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Authors: Zelikha Labbani

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The in vitro isolated microspore culture is the most powerful androgenic pathway to produce doubled haploid plants in the short time. To deviate a microspore toward embryogenesis, a number of factors, different for each species, must concur at the same time and place. Once induced, the microspore undergoes numerous changes at different levels, from overall morphology to gene expression. Induction of microspore embryogenesis not only implies the expression of an embryogenic program, but also a stress-related cellular response and a repression of the gametophytic program to revert the microspore to a totipotent status. As haploid single cells, microspore became a strategy to achieve various objectives particularly in genetic engineering. In this communication we would show the most recent advances in the producing haploid embryos via in vitro isolated microspore culture.

Keywords: in vitro isolated microspore culture, success, haploid cells, bioinformatics, biomedicine

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast

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Authors: Kostas Metaxiotis, Kostas Liagkouras

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This study presents an Expert System specially designed to be used with Multiobjective Evolutionary Algorithms (MOEAs) for the solution of the portfolio selection problem. The validation of the proposed hybrid System is done by using data sets from Hang Seng 31 in Hong Kong, DAX 100 in Germany and FTSE 100 in UK. The performance of the proposed system is assessed in comparison with the Non-dominated Sorting Genetic Algorithm II (NSGAII). The evaluation of the performance is based on different performance metrics that evaluate both the proximity of the solutions to the Pareto front and their dispersion on it. The results show that the proposed hybrid system is efficient for the solution of this kind of problems.

Keywords: expert systems, multi-objective optimization, evolutionary algorithms, portfolio selection

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Authors: Mohammad Moridzadeh, Mohammad Djavid, Barry Doyle

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An assessment of the long-term stability of a cavern in Chagrin shale excavated by the sequential excavation method was performed during and after construction. During the excavation of the cavern, deformations of rock mass were measured at the surface of excavation and within the rock mass by surface and deep measurement instruments. Rock deformations were measured during construction which appeared to result from the as-built excavation sequence that had potentially disturbed the rock and its behavior. Also some additional time dependent rock deformations were observed during and post excavation. Several opinions have been expressed to explain this time dependent deformation including stress changes induced by excavation, strain softening (or creep) in the beddings with and without clay and creep of the shaley rock under compressive stresses. In order to analyze and replicate rock behavior observed during excavation, including current and post excavation elastic, plastic, and time dependent deformation, Finite Element Analysis (FEA) was performed. The analysis was also intended to estimate long term deformation of the rock mass around the excavation. Rock mass behavior including time dependent deformation was measured by means of rock surface convergence points, MPBXs, extended creep testing on the long anchors, and load history data from load cells attached to several long anchors. Direct creep testing of Chagrin Shale was performed on core samples from the wall of the Pump Room. Results of these measurements were used to calibrate the FEA of the excavation. These analyses incorporate time dependent constitutive modeling for the rock to evaluate the potential long term movement in the roof, walls, and invert of the cavern. The modeling was performed due to the concerns regarding the unanticipated behavior of the rock mass as well as the forecast of long term deformation and stability of rock around the excavation.

Keywords: Cavern, Chagrin shale, creep, finite element.

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Authors: Brunno Vasques

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Due to the non-toxic nature and high performance in terms of vacuum specific impulse and density specific impulse, the combination of liquid oxygen and liquid methane have been identified as a promising option for future space vehicle systems. Applications requiring throttling capability include specific missions such as rendezvous, planetary landing and de-orbit as well as weapon systems. One key challenge in throttling liquid rocket engines is maintaining an adequate pressure drop across the injection elements, which is necessary to provide good propellant atomization and mixing as well as system stability. The potential scalability of pintle injectors, their great suitability to throttling and inherent combustion stability characteristics led to investigations using a variety of propellant combinations, including liquid oxygen and hydrogen and fluorine-oxygen and methane. Presented here are the preliminary performance and heat transfer information obtained during hot-fire testing of a pintle injector running on liquid oxygen and liquid methane propellants. The specific injector design selected for this purpose is a multi-configuration building block version with replaceable injection elements, providing flexibility to accommodate hardware modifications with minimum difficulty. On the basis of single point runs and the use of a copper/nickel segmented calorimetric combustion chamber and associated transient temperature measurement, the characteristic velocity efficiency, injector footprint and heat fluxes could be established for the first proposed pintle configuration as a function of injection velocity- and momentum-ratios. A description of the test-bench is presented as well as a discussion of irregularities encountered during testing, such as excessive heat flux into the pintle tip resulting from certain operating conditions.

Keywords: green propellants, hot-fire performance, rocket engine throttling, pintle injector

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Authors: ZhenlinJu, Christopher P. Vellano, RehanAkbani, Yiling Lu, Gordon B. Mills

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The epithelial–mesenchymal transition (EMT) is a process by which epithelial cells acquire mesenchymal characteristics, such as profound disruption of cell-cell junctions, loss of apical-basolateral polarity, and extensive reorganization of the actin cytoskeleton to induce cell motility and invasion. A hallmark of EMT is its capacity to promote metastasis, which is due in part to activation of several transcription factors and subsequent downregulation of E-cadherin. Unfortunately, current approaches have yet to uncover robust protein marker sets that can classify tumors as possessing strong EMT signatures. In this study, we utilize reverse phase protein array (RPPA) data and consensus clustering methods to successfully classify a subset of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tumors into an EMT protein signaling group (EMT group). The overall survival (OS) of patients in the EMT group is significantly worse than those in the other Hormone and PI3K/AKT signaling groups. In addition to a shrinkage and selection method for linear regression (LASSO), we applied training/test set and Monte Carlo resampling approaches to identify a set of protein markers that predicts the EMT status of CESC tumors. We fit a logistic model to these protein markers and developed a classifier, which was fixed in the training set and validated in the testing set. The classifier robustly predicted the EMT status of the testing set with an area under the curve (AUC) of 0.975 by Receiver Operating Characteristic (ROC) analysis. This method not only identifies a core set of proteins underlying an EMT signature in cervical cancer patients, but also provides a tool to examine protein predictors that drive molecular subtypes in other diseases.

Keywords: consensus clustering, TCGA CESC, Silhouette, Monte Carlo LASSO

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Authors: Aparna Lal, Ashwin Swaminathan, Teisa Holani

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Background: Clostridium difficile infections (CDIs) have been on the rise globally. In Australia, rates of CDI in all States and Territories have increased significantly since mid-2011. Identifying risk factors for CDI in the community can help inform targeted interventions to reduce infection. Methods: We examine the role of neighbourhood socio-economic status, demography, testing practices and the number of residential aged care facilities on spatial patterns in CDI incidence in the Australian Capital Territory. Data on all tests conducted for CDI were obtained from ACT Pathology by postcode for the period 1st January 2004 through 31 December 2014. Distribution of age groups and the neighbourhood Index of Relative Socio-economic Advantage Disadvantage (IRSAD) were obtained from the Australian Bureau of Statistics 2011 National Census data. A Bayesian spatial conditional autoregressive model was fitted at the postcode level to quantify the relationship between CDI and socio-demographic factors. To identify CDI hotspots, exceedance probabilities were set at a threshold of twice the estimated relative risk. Results: CDI showed a positive spatial association with the number of tests (RR=1.01, 95% CI 1.00, 1.02) and the resident population over 65 years (RR=1.00, 95% CI 1.00, 1.01). The standardized index of relative socio-economic advantage disadvantage (IRSAD) was significantly negatively associated with CDI (RR=0.74, 95% CI 0.56, 0.94). We identified three postcodes with high probability (0.8-1.0) of excess risk. Conclusions: Here, we demonstrate geographic variations in CDI in the ACT with a positive association of CDI with socioeconomic disadvantage and identify areas with a high probability of elevated risk compared with surrounding communities. These findings highlight community-based risk factors for CDI.

Keywords: spatial, socio-demographic, infection, Clostridium difficile

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Authors: Chung Danbi, Linton Oliver, Whang Yoon-Jae

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Supermodularity, or complementarity, is a popular concept in economics which can characterize many objective functions such as utility, social welfare, and production functions. Further, supermodular dominance captures a preference for greater interdependence among inputs of those functions, and it can be applied to examine which input set would produce higher expected utility, social welfare, or production. Therefore, we propose and justify a consistent testing for a useful implication of supermodular dominance. We also conduct Monte Carlo simulations to explore the finite sample performance of our test, with critical values obtained from the recentered bootstrap method, with and without the selective recentering, and the subsampling method. Under various parameter settings, we confirmed that our test has reasonably good size and power performance. Finally, we apply our test to compare the geographic and distant knowledge spillover in terms of their effects on social welfare using the National Bureau of Economic Research (NBER) patent data. We expect localized citing to supermodularly dominate distant citing if the geographic knowledge spillover engenders greater social welfare than distant knowledge spillover. Taking subgroups based on firm and patent characteristics, we found that there is industry-wise and patent subclass-wise difference in the pattern of supermodular dominance between localized and distant citing. We also compare the results from analyzing different time periods to see if the development of Internet and communication technology has changed the pattern of the dominance. In addition, to appropriately deal with the sparse nature of the data, we apply high-dimensional methods to efficiently select relevant data.

Keywords: supermodularity, supermodular dominance, stochastic dominance, Monte Carlo simulation, bootstrap, subsampling

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Authors: Mathula Thangarajh

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Duchenne muscular dystrophy (DMD) is a severe form of X-linked muscular dystrophy caused by mutations in the dystrophin gene resulting in progressive skeletal muscle weakness. Boys with DMD also have significant cognitive disabilities. The intelligence quotient of boys with DMD, compared to peers, is approximately one standard deviation below average. Detailed neuropsychological testing has demonstrated that boys with DMD have a global developmental impairment, with verbal memory and visuospatial skills most significantly affected. Furthermore, the total brain volume and gray matter volume are lower in children with DMD compared to age-matched controls. These results are suggestive of a significant structural and functional compromise to the developing brain as a result of absent dystrophin protein expression. There is also some genetic evidence to suggest that mutations in the 3’ end of the DMD gene are associated with more severe neurocognitive problems. Our working hypothesis is that (i) boys with DMD do not make gains in neurodevelopmental skills compared to typically developing children and (ii) women carriers of DMD mutations may have subclinical cognitive deficits. We also hypothesize that there may be an intergenerational vulnerability of cognition, with boys of DMD-carrier mothers being more affected cognitively than boys of non-DMD-carrier mothers. The objectives of this study are: 1. Assess the neurodevelopment in boys with DMD at 4-time points and perform baseline neuroradiological assessment, 2. Assess cognition in biological mothers of DMD participants at baseline, 3. Assess possible correlation between DMD mutation and cognitive measures. This study also explores functional brain abnormalities in people with DMD by exploring how regional and global connectivity of the brain underlies executive function deficits in DMD. Such research can contribute to a better holistic understanding of the cognition alterations due to DMD and could potentially allow clinicians to create better-tailored treatment plans for the DMD population. There are four study visits for each participant (baseline, 2-4 weeks, 1 year, 18 months). At each visit, the participant completes the NIH Toolbox Cognition Battery, a validated psychometric measure that is recommended by NIH Common Data Elements for use in DMD. Visits 1, 3, and 4 also involve the administration of the BRIEF-2, ABAS-3, PROMIS/NeuroQoL, PedsQL Neuromuscular module 3.0, Draw a Clock Test, and an optional fMRI scan with the N-back matching task. We expect to enroll 52 children with DMD, 52 mothers of children with DMD, and 30 healthy control boys. This study began in 2020 during the height of the COVID-19 pandemic. Due to this, there were subsequent delays in recruitment because of travel restrictions. However, we have persevered and continued to recruit new participants for the study. We partnered with the Muscular Dystrophy Association (MDA) and helped advertise the study to interested families. Since then, we have had families from across the country contact us about their interest in the study. We plan to continue to enroll a diverse population of DMD participants to contribute toward a better understanding of Duchenne Muscular Dystrophy.

Keywords: neurology, Duchenne muscular dystrophy, muscular dystrophy, cognition, neurodevelopment, x-linked disorder, DMD, DMD gene

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Authors: Othmane Touri, Sanaa El Filali, El Habib Benlahmar

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Natural Language Processing (NLP) has gained significant attention lately. It has proved its ability to analyze and extract insights from unstructured text data in various languages. It is found that one of the most popular NLP applications is sentiment analysis which aims to identify the sentiment expressed in a piece of text, such as positive, negative, or neutral, in multiple languages. While there are several multilingual NLP models available for sentiment analysis, there is a need to investigate their effectiveness in different contexts and applications. In this study, we aim to investigate the effectiveness of different multilingual NLP models for sentiment analysis on a dataset of online product reviews in multiple languages. The performance of several NLP models, including Google Cloud Natural Language API, Microsoft Azure Cognitive Services, Amazon Comprehend, Stanford CoreNLP, spaCy, and Hugging Face Transformers are being compared. The models based on several metrics, including accuracy, precision, recall, and F1 score, are being evaluated and compared to their performance across different categories of product reviews. In order to run the study, preprocessing of the dataset has been performed by cleaning and tokenizing the text data in multiple languages. Then training and testing each model has been applied using a cross-validation approach where randomly dividing the dataset into training and testing sets and repeating the process multiple times has been used. A grid search approach to optimize the hyperparameters of each model and select the best-performing model for each category of product reviews and language has been applied. The findings of this study provide insights into the effectiveness of different multilingual NLP models for Multilingual Sentiment Analysis and their suitability for different languages and applications. The strengths and limitations of each model were identified, and recommendations for selecting the most performant model based on the specific requirements of a project were provided. This study contributes to the advancement of research methods in multilingual NLP and provides a practical guide for researchers and practitioners in the field.

Keywords: NLP, multilingual, sentiment analysis, texts

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Authors: Danni Cheng

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Background: Preclinical and epidemiological studies have reported potential protective effects of low-density lipoprotein cholesterol (LDL-C) lowering drugs on head and neck squamous cell cancer (HNSCC) survival, but the causality was not consistent. Genetic variants associated with LDL-C lowering drug targets can predict the effects of their therapeutic inhibition on disease outcomes. Objective: We aimed to evaluate the causal association of genetically proxied cholesterol-lowering drug targets and circulating lipid traits with cancer survival in HNSCC patients stratified by human papillomavirus (HPV) status using two-sample Mendelian randomization (MR) analyses. Method: Single-nucleotide polymorphisms (SNPs) in gene region of LDL-C lowering drug targets (HMGCR, NPC1L1, CETP, PCSK9, and LDLR) associated with LDL-C levels in genome-wide association study (GWAS) from the Global Lipids Genetics Consortium (GLGC) were used to proxy LDL-C lowering drug action. SNPs proxy circulating lipids (LDL-C, HDL-C, total cholesterol, triglycerides, apoprotein A and apoprotein B) were also derived from the GLGC data. Genetic associations of these SNPs and cancer survivals were derived from 1,120 HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) and 2,570 non-HPV-driven HNSCC patients in VOYAGER program. We estimated the causal associations of LDL-C lowering drugs and circulating lipids with HNSCC survival using the inverse-variance weighted method. Results: Genetically proxied HMGCR inhibition was significantly associated with worse overall survival (OS) in non-HPV-drive HNSCC patients (inverse variance-weighted hazard ratio (HR IVW), 2.64[95%CI,1.28-5.43]; P = 0.01) but better OS in HPV-positive OPSCC patients (HR IVW,0.11[95%CI,0.02-0.56]; P = 0.01). Estimates for NPC1L1 were strongly associated with worse OS in both total HNSCC (HR IVW,4.17[95%CI,1.06-16.36]; P = 0.04) and non-HPV-driven HNSCC patients (HR IVW,7.33[95%CI,1.63-32.97]; P = 0.01). A similar result was found that genetically proxied PSCK9 inhibitors were significantly associated with poor OS in non-HPV-driven HNSCC (HR IVW,1.56[95%CI,1.02 to 2.39]). Conclusion: Genetically proxied long-term HMGCR inhibition was significantly associated with decreased OS in non-HPV-driven HNSCC and increased OS in HPV-positive OPSCC. While genetically proxied NPC1L1 and PCSK9 had associations with worse OS in total and non-HPV-driven HNSCC patients. Further research is needed to understand whether these drugs have consistent associations with head and neck tumor outcomes.

Keywords: Mendelian randomization analysis, head and neck cancer, cancer survival, cholesterol, statin

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Authors: Valerii Dashuk

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The usage of the confidence intervals in economics and econometrics is widespread. To be able to investigate a random variable more thoroughly, joint tests are applied. One of such examples is joint mean-variance test. A new approach for testing such hypotheses and constructing confidence sets is introduced. Exploring both the value of the random variable and its deviation with the help of this technique allows checking simultaneously the shift and the probability of that shift (i.e., portfolio risks). Another application is based on the normal distribution, which is fully defined by mean and variance, therefore could be tested using the introduced approach. This method is based on the difference of probability density functions. The starting point is two sets of normal distribution parameters that should be compared (whether they may be considered as identical with given significance level). Then the absolute difference in probabilities at each 'point' of the domain of these distributions is calculated. This measure is transformed to a function of cumulative distribution functions and compared to the critical values. Critical values table was designed from the simulations. The approach was compared with the other techniques for the univariate case. It differs qualitatively and quantitatively in easiness of implementation, computation speed, accuracy of the critical region (theoretical vs. real significance level). Stable results when working with outliers and non-normal distributions, as well as scaling possibilities, are also strong sides of the method. The main advantage of this approach is the possibility to extend it to infinite-dimension case, which was not possible in the most of the previous works. At the moment expansion to 2-dimensional state is done and it allows to test jointly up to 5 parameters. Therefore the derived technique is equivalent to classic tests in standard situations but gives more efficient alternatives in nonstandard problems and on big amounts of data.

Keywords: confidence set, cumulative distribution function, hypotheses testing, normal distribution, probability density function

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Authors: Mark Kennedy, E. Bantugon, Noruane A. Daileg

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Leaks arising from aircraft fuel tanks is a protracted problem for the aircraft manufacturers, operators, and maintenance crews. It principally arises from stress, structural defects, or degraded sealants as the aircraft age. It can be ignited by different sources, which can result in catastrophic flight and consequences, exhibiting a major drain both on time and budget. In order to mitigate and eliminate this kind of problem, the researcher produced an experimental sealant having a base material of natural tree resin, the Pili Tree Resin. Aside from producing an experimental sealant, the main objective of this research is to analyze its physical, chemical, mechanical, thermal, and rheological properties, which is beneficial and effective for specific aircraft parts, particularly the integral fuel tank. The experimental method of research was utilized in this study since it is a product invention. This study comprises two parts, specifically the Optimization Process and the Characterization Process. In the Optimization Process, the experimental sealant was subjected to the Flammability Test, an important test and consideration according to 14 Code of Federal Regulation Appendix N, Part 25 - Fuel Tank Flammability Exposure and Reliability Analysis, to get the most suitable formulation. Followed by the Characterization Process, where the formulated experimental sealant has undergone thirty-eight (38) different standard testing including Organoleptic, Instrumental Color Measurement Test, Smoothness of Appearance Test, Miscibility Test, Boiling Point Test, Flash Point Test, Curing Time, Adhesive Test, Toxicity Test, Shore A Hardness Test, Compressive Strength, Shear Strength, Static Bending Strength, Tensile Strength, Peel Strength Test, Knife Test, Adhesion by Tape Test, Leakage Test), Drip Test, Thermogravimetry-Differential Thermal Analysis (TG-DTA), Differential Scanning Calorimetry, Calorific Value, Viscosity Test, Creep Test, and Anti-Sag Resistance Test to determine and analyze the five (5) material properties of the sealant. The numerical values of the mentioned tests are determined using product application, testing, and calculation. These values are then used to calculate the efficiency of the experimental sealant. Accordingly, this efficiency is the means of comparison between the experimental and commercial sealant. Based on the results of the different standard testing conducted, the experimental sealant exceeded all the data results of the commercial sealant. This result shows that the physicochemical-mechanical, thermal, and rheological properties of the experimental sealant are far more effective as an aircraft integral fuel tank sealant alternative in comparison to the commercial sealant. Therefore, Pili Tree possesses a new role and function: a source of ingredients in sealant production.

Keywords: Aircraft Integral Fuel Tank, Physicochemi-mechanical, Pili Tree Resin, Properties, Rheological, Sealant, Thermal

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Authors: Devender Sharma, Shweta Goyal

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Sustainable development is a key to protect the environment for a secure future. Accelerated carbonation curing is a comparatively new technique for curing of concrete which involves sequestration of carbon dioxide gas into the precast concrete, resulting in improvement of the properties of concrete. This paper presents the results of a study to evaluate the effect of carbonation curing on cement mortars incorporating cement kiln dust (CKD) as partial replacement of cement. The mortar specimens were prepared by replacing cement with CKD in varying percentages of 0-50% by the weight of cement. The specimens were subjected to 12 hour carbonation curing, followed by sealed packing till testing age. The results were compared with the normal curing procedure, in which the specimens were water cured till the testing age. Compressive strength and microstructure of the mix were studied. It was noted that on increasing the percentage of CKD up to 10% by the weight of the cement, no considerable change was observed in the compressive strength. But as the percentage of CKD was further increased, there was a decrease in compressive strength, with strength decreasing up to 40% when 50% of the cement was replaced with CKD. The decrease in strength is due to the lesser lime content in CKD as compared to cement. High ettringite formation was observed in mixes with high percentages of CKD, thus indicating a decrease in the compressive strength. With carbonation curing, an early age strength gain was observed in mortars, even with higher percentages of CKD. The early strength of the carbonation cured mixes was found to be greater than water cured mixes irrespective of the percentage of CKD. 7 days and 28 days compressive strength of the mix was comparable for both the carbonation cured and water cured specimen. The increase in compressive strength can be attributed to the conversion of unstable Ca(OH)2 into stable CaCO3, which causes densification of the mix. CaCO3 precipitation and greater CSH gel formation was clearly observed in the SEM images of carbonation cured specimen, indicating higher compressive strength. Thus, carbonation curing can be used as an efficient method to enhance the properties of concrete.

Keywords: carbonation, cement kiln dust, compressive strength, microstructure

Procedia PDF Downloads 220

Authors: Dipti Chand, Riya Saboo

Abstract:

OBJECTIVES: Early and correct diagnosis may present a significant clinical challenge in diagnosis of patients presenting to Emergency Department with Acute Dyspnoea. The common cause of acute dyspnoea and respiratory distress in Emergency Department are Decompensated Heart Failure (HF), Chronic Obstructive Pulmonary Disease (COPD), Asthma, Pneumonia, Acute Respiratory Distress Syndrome (ARDS), Pulmonary Embolism (PE), and other causes like anaemia. The aim of the study was to measure NT-pro Brain Natriuretic Peptide (BNP) and exhaled End-Tidal Carbon dioxide (ETCO2) in patients presenting with dyspnoea. MATERIAL AND METHODS: This prospective, cross-sectional and observational study was performed at the Government Medical College and Hospital, Nagpur, between October 2019 and October 2021 in patients admitted to the Medicine Intensive Care Unit. Three groups of patients were compared: (1) HFrelated acute dyspnoea group (n = 52), (2) pulmonary (COPD/PE)-related acute dyspnoea group (n = 31) and (3) sepsis with ARDS-related dyspnoea group (n = 13). All patients underwent initial clinical examination with a recording of initial vital parameters along with on-admission ETCO2 measurement, NT-proBNP testing, arterial blood gas analysis, lung ultrasound examination, 2D echocardiography, chest X-rays, and other relevant diagnostic laboratory testing. RESULTS: 96 patients were included in the study. Median NT-proBNP was found to be high for the Heart Failure group (11,480 pg/ml), followed by the sepsis group (780 pg/ml), and pulmonary group had an Nt ProBNP of 231 pg/ml. The mean ETCO2 value was maximum in the pulmonary group (48.610 mmHg) followed by Heart Failure (31.51 mmHg) and the sepsis group (19.46 mmHg). The results were found to be statistically significant (P < 0.05). CONCLUSION: NT-proBNP has high diagnostic accuracy in differentiating acute HF-related dyspnoea from pulmonary (COPD and ARDS)-related acute dyspnoea. The higher levels of ETCO2 help in diagnosing patients with COPD.

Keywords: NT PRO BNP, ETCO2, dyspnoea, lung USG

Procedia PDF Downloads 68

Authors: Ramin Javadzadeh

Abstract:

The particle swarm optimization are Meta heuristic optimization method, which are used for clustering and pattern recognition applications are abundantly. These algorithms in multimodal optimization problems are more efficient than genetic algorithms. A major drawback in these algorithms is their slow convergence to global optimum and their weak stability can be considered in various running of these algorithms. In this paper, improved Particle swarm optimization is introduced for the first time to overcome its problems. The fuzzy cellular automata is used for improving the algorithm efficiently. The credibility of the proposed approach is evaluated by simulations, and it is shown that the proposed approach achieves better results can be achieved compared to the Particle swarm optimization algorithms.

Keywords: cellular automata, cellular learning automata, local search, optimization, particle swarm optimization

Procedia PDF Downloads 591

Authors: Boris Blostotsky, Elia Efraim

Abstract:

The phenomenon of buckling of structural elements under compression is revealed in many cases of loading and found consideration in many structures and mechanisms. In the present work the method and results of dynamic test for buckling of bar loaded by a compression force directed towards the pole are considered. Experimental determination of critical force for such system has not been made previously. The tested object is a bar with semi-rigid connection to the base at one of its ends, and with a hinge moving along a circle at the other. The test includes measuring the natural frequency of the bar at different values of compression load. The lateral stiffness is calculated based on natural frequency and reduced mass on the bar's movable end. The critical load is determined by extrapolation the values of lateral stiffness up to zero value. For the experimental investigation the special test-bed was created that allows the stability testing at positive and negative curvature of the movable end's trajectory, as well as varying the rotational stiffness of the other end connection. Decreasing a friction at the movable end allows extend the diapason of applied compression force. The testing method includes: - Methodology of the experiment planning, that allows determine the required number of tests under various loads values in the defined range and the type of extrapolating function; - Methodology of experimental determination of reduced mass at the bar's movable end including its own mass; - Methodology of experimental determination of lateral stiffness of uncompressed bar rotational semi-rigid connection at the base. For planning the experiment and for comparison of the experimental results with the theoretical values of critical load, the analytical dependencies of lateral stiffness of the bar with defined end conditions on compression load. In the particular case of perfectly rigid connection of the bar to the base, the critical load value corresponds to solution by S.P. Timoshenko. Correspondence of the calculated and experimental values was obtained.

Keywords: non-destructive test, buckling, dynamic method, semi-rigid connections

Procedia PDF Downloads 348

Authors: Julian Sandoval, Philipp Schober

Abstract:

Lahar sand (lahars) is a material that originates from volcanic debris flows. During and after a volcano eruption, the lahars can move at speeds up to 22 meters per hour or more, so they can easily cover extensive areas and destroy any structure in their path. Mount Pinatubo eruption (1991) brought lahars to its vicinities, and its use has been a matter of research ever since. Lahars are often disposed of for land reclamation projects in the Manila Bay, Philippines. After reclamation, some deep loss deposits may still present and they are prone to liquefaction. To mitigate the risk of liquefaction of such deposits, Vibro compaction has been proposed and used as a ground improvement technique. Cone penetration testing (CPT) campaigns are usually initiated to monitor the effectiveness of the ground improvement works by vibro compaction. The CPT cone resistance is used to analyses the in-situ relative density of the reclaimed sand before and after compaction. Available correlations between the CPT cone resistance and the relative density are only valid for non-crushable sands. Due to the partially crushable nature of lahars, the CPT data requires to be adjusted to allow for a correct interpretation of the CPT data. The objective of this paper is to characterize the chemical and mechanical properties of the lahar sands used for an ongoing project in the Port of Manila, which comprises reclamation activities using lahars from the east of Mount Pinatubo, it investigates their effect in the proposed correction factor. Additionally, numerous CPTs were carried out in a test trial and during the execution of the project. Based on this data, the influence of the grid spacing, compaction steps and the holding time on the compaction results are analyzed. Moreover, the so-called “aging effect” of the lahars is studied by comparing the results of the CPT testing campaign at different times after the vibro compaction activities. A considerable increase in the tip resistance of the CPT was observed over time.

Keywords: vibro compaction, CPT, lahar sands, correction factor, chemical composition

Procedia PDF Downloads 202

Authors: Abiodun Olayinka, Daniel Dzidzienyo, Pangirayi Tongoona, Samuel Offei, Edwige Gaby Nkouaya Mbanjo, Chiedozie Egesi, Ismail Yusuf Rabbi

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Cassava (Manihot esculenta Crantz) is a major source of starch for various industrial applications. However, the traditional cultivation and harvesting methods of cassava are labour-intensive and inefficient, limiting the supply of fresh cassava roots for industrial starch production. To achieve improved productivity and quality of fresh cassava roots through mechanized cultivation, cassava cultivars with compact plant architecture and moderate plant height are needed. Plant architecture-related traits, such as plant height, harvest index, stem diameter, branching angle, and lodging tolerance, are critical for crop productivity and suitability for mechanized cultivation. However, the genetics of cassava plant architecture remain poorly understood. This study aimed to identify the genetic bases of the relationships between plant architecture traits and productivity-related traits, particularly starch content. A panel of 453 clones developed at the International Institute of Tropical Agriculture, Nigeria, was genotyped and phenotyped for 18 plant architecture and productivity-related traits at four locations in Nigeria. A genome-wide association study (GWAS) was conducted using the phenotypic data from a panel of 453 clones and 61,238 high-quality Diversity Arrays Technology sequencing (DArTseq) derived Single Nucleotide Polymorphism (SNP) markers that are evenly distributed across the cassava genome. Five significant associations between ten SNPs and three plant architecture component traits were identified through GWAS. We found five SNPs on chromosomes 6 and 16 that were significantly associated with shoot weight, harvest index, and total yield through genome-wide association mapping. We also discovered an essential candidate gene that is co-located with peak SNPs linked to these traits in M. esculenta. A review of the cassava reference genome v7.1 revealed that the SNP on chromosome 6 is in proximity to Manes.06G101600.1, a gene that regulates endodermal differentiation and root development in plants. The findings of this study provide insights into the genetic basis of plant architecture and yield in cassava. Cassava breeders could leverage this knowledge to optimize plant architecture and yield in cassava through marker-assisted selection and targeted manipulation of the candidate gene.

Keywords: Manihot esculenta Crantz, plant architecture, DArtseq, SNP markers, genome-wide association study

Procedia PDF Downloads 56

Authors: Ehsan Mehryaar, Seyed Armin Motahari Tabari

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Coarse-grained soils are known and commonly used in a wide range of geotechnical projects, including high earth dams or embankments for their high shear strength. The most important engineering property of these soils is friction angle which represents the interlocking between soil particles and can be applied widely in designing and constructing these earth structures. Friction angle and dilative behavior of coarse-grained soils can be estimated from empirical correlations with in-situ testing and physical properties of the soil or measured directly in the laboratory performing direct shear or triaxial tests. Unfortunately, large-scale testing is difficult, challenging, and expensive and is not possible in most soil mechanic laboratories. So, it is common to remove the large particles and do the tests, which cannot be counted as an exact estimation of the parameters and behavior of the original soil. This paper describes a new methodology to simulate particles grading distribution of a well-graded gravel sample to a smaller scale sample as it can be tested in an ordinary direct shear apparatus to estimate the stress-strain behavior, friction angle, and dilative behavior of the original coarse-grained soil considering its confining pressure, and relative density using a machine learning method. A total number of 72 direct shear tests are performed in 6 different sizes, 3 different confining pressures, and 4 different relative densities. Multivariate Adaptive Regression Spline (MARS) technique was used to develop an equation in order to predict shear strength and dilative behavior based on the size distribution of coarse-grained soil particles. Also, an uncertainty analysis was performed in order to examine the reliability of the proposed equation.

Keywords: MARS, coarse-grained soil, shear strength, uncertainty analysis

Procedia PDF Downloads 155

Authors: Amessalu Atenafu Gelaw, Nele Rath

Abstract:

Currently, laser hardening process is becoming among the most efficient and effective hardening technique due to its significant advantages. The source where heat is generated, the absence of cooling media, self-quenching property, less distortion nature due to localized heat input, environmental friendly behavior and less time to finish the operation are among the main benefits to adopt this technology. This day, a variety of injection machines are used in plastic, textile, electrical and mechanical industries. Due to the fast growing of composite technology, fiber reinforced polymer matrix becoming optional solution to use in these industries. Due, to the abrasion nature of fiber reinforced polymer matrix composite on the injection components, many parts are outdated before the design period. Niko, a company specialized in injection molded products, suffers from the short lifetime of the injection nozzles of the molds, due to the use of fiber reinforced and, therefore, more abrasive polymer matrix. To prolong the lifetime of these molds, hardening the susceptible component like the injecting nozzles was a must. In this paper, the laser hardening process is investigated on Unimax, a type of stainless steel. The investigation to get optimal results for the nozzle-case was performed in three steps. First, the optimal parameters for maximum possible hardenability for the investigated nozzle material is investigated on a flat sample, using experimental testing as well as thermal simulation. Next, the effect of an inclination on the maximum temperature is analyzed both by experimental testing and validation through simulation. Finally, the data combined and applied for the nozzle. This paper describes possible strategies and methods for laser hardening of the nozzle to reach hardness of at least 720 HV for the material investigated. It has been proven, that the nozzle can be laser hardened to over 900 HV with the option of even higher results when more precise positioning of the laser can be assured.

Keywords: absorptivity, fiber reinforced matrix, laser hardening, Nd:YAG laser

Procedia PDF Downloads 146

Authors: Elia Efraim, Boris Blostotsky

Abstract:

The phenomenon of buckling of structural elements under compression is revealed in many cases of loading and found consideration in many structures and mechanisms. In the present work the method and results of dynamic test for buckling of bar loaded by a compression force directed towards the pole are considered. Experimental determination of critical force for such system has not been made previously. The tested object is a bar with semi-rigid connection to the base at one of its ends, and with a hinge moving along a circle at the other. The test includes measuring the natural frequency of the bar at different values of compression load. The lateral stiffness is calculated based on natural frequency and reduced mass on the bar's movable end. The critical load is determined by extrapolation the values of lateral stiffness up to zero value. For the experimental investigation the special test-bed was created that allows the stability testing at positive and negative curvature of the movable end's trajectory, as well as varying the rotational stiffness of the other end connection. Decreasing a friction at the movable end allows extend the diapason of applied compression force. The testing method includes : - methodology of the experiment planning, that allows determine the required number of tests under various loads values in the defined range and the type of extrapolating function; - methodology of experimental determination of reduced mass at the bar's movable end including its own mass; - methodology of experimental determination of lateral stiffness of uncompressed bar rotational semi-rigid connection at the base. For planning the experiment and for comparison of the experimental results with the theoretical values of critical load, the analytical dependencies of lateral stiffness of the bar with defined end conditions on compression load. In the particular case of perfectly rigid connection of the bar to the base, the critical load value corresponds to solution by S.P. Timoshenko. Correspondence of the calculated and experimental values was obtained.

Keywords: buckling, dynamic method, end-fixity factor, force directed towards a pole

Procedia PDF Downloads 342

Authors: Markandeya Kunchi

Abstract:

Usability testing (UT) is one of the vital steps in the User-centred design (UCD) process when designing a product. In an e-commerce ecosystem, UT becomes primary as new products, features, and services are launched very frequently. And, there are losses attached to the company if an unusable and inefficient product is put out to market and is rejected by customers. This paper tries to answer why UT is important in the product life-cycle of an E-commerce ecosystem. Secondary user research was conducted to find out work patterns, development methods, type of stakeholders, and technology constraints, etc. of a typical E-commerce company. Qualitative user interviews were conducted with product managers and designers to find out the structure, project planning, product management method and role of the design team in a mid-level company. The paper tries to address the usual apprehensions of the company to inculcate UT within the team. As well, it stresses upon factors like monetary resources, lack of usability expert, narrow timelines, and lack of understanding of higher management as some primary reasons. Outsourcing UT to vendors is also very prevalent with mid-level e-commerce companies, but it has its own severe repercussions like very little team involvement, huge cost, misinterpretation of the findings, elongated timelines, and lack of empathy towards the customer, etc. The shortfalls of the unavailability of a UT process in place within the team and conducting UT through vendors are bad user experiences for customers while interacting with the product, badly designed products which are neither useful and nor utilitarian. As a result, companies see dipping conversions rates in apps and websites, huge bounce rates and increased uninstall rates. Thus, there was a need for a more lean UT system in place which could solve all these issues for the company. This paper highlights on optimizing the UT process with a collaborative method. The degree of optimization and structure of collaborative method is the highlight of this paper. Collaborative method of UT is one in which the centralised design team of the company takes for conducting and analysing the UT. The UT is usually a formative kind where designers take findings into account and uses in the ideation process. The success of collaborative method of UT is due to its ability to sync with the product management method employed by the company or team. The collaborative methods focus on engaging various teams (design, marketing, product, administration, IT, etc.) each with its own defined roles and responsibility in conducting a smooth UT with users In-house. The paper finally highlights the positive results of collaborative UT method after conducting more than 100 In-lab interviews with users across the different lines of businesses. Some of which are the improvement of interaction between stakeholders and the design team, empathy towards users, improved design iteration, better sanity check of design solutions, optimization of time and money, effective and efficient design solution. The future scope of collaborative UT is to make this method leaner, by reducing the number of days to complete the entire project starting from planning between teams to publishing the UT report.

Keywords: collaborative method, e-commerce, product management method, usability testing

Procedia PDF Downloads 107

Authors: Nikolai Bertelsen, Robert A. Alphinas, Klaus B. Orskov

Abstract:

The shortest possible tool stickout has been the traditional go-to approach with expectations of increased stability and productivity. However, experimental studies at Danish Advanced Manufacturing Research Center (DAMRC) have proven that for some tool stickout lengths, there exist local productivity optimums when utilizing the Stability Lobe Diagrams for chatter avoidance. This contradicts with traditional logic and the best practices taught to machinists. This paper explores the vibrational characteristics and behaviour of a milling system over the tool stickout length. The experimental investigation has been conducted by tap testing multiple endmills where the tool stickout length has been varied. For each length, the modal parameters have been recorded and mapped to visualize behavioural tendencies. Furthermore, the paper explores the correlation between the modal parameters and the Stability Lobe Diagram to outline the influence and importance of each parameter in a multi-mode system. The insights are conceptualized into a tool tuning approximation solution. It builds on an almost linear change in the natural frequencies when amending tool stickout, which results in changed positions of the Chatter-free Stability Lobes. Furthermore, if the natural frequency of two modes become too close, it will onset of the dynamic absorber effect phenomenon. This phenomenon increases the critical stable depth of cut, allowing for a more stable milling process. Validation tests on the tool tuning approximation solution have shown varying success of the solution. This outlines the need for further research on the boundary conditions of the solution to understand at which conditions the tool tuning approximation solution is applicable. If the conditions get defined, the conceptualized tool tuning approximation solution outlines an approach for quick and roughly approximating tool stickouts with the potential for increased stiffness and optimized productivity.

Keywords: milling, modal parameters, stability lobes, tap testing, tool tuning

Procedia PDF Downloads 141

Authors: Shraddha Rane, Richard Warren, Stephen Eyre

Abstract:

L-23 is a pro-inflammatory molecule that signals T cells to release cytokines such as IL-17A and IL-22. Psoriasis is driven by a dysregulated immune response, within which IL-23 is now thought to play a key role. Genome-wide association studies (GWAS) have identified a number of genetic risk loci that support the involvement of IL-23 signalling in psoriasis; in particular a robust susceptibility locus at a gene encoding a subunit of the IL-23 receptor (IL23R) (Stuart et al., 2015; Tsoi et al., 2012). The lead psoriasis-associated SNP rs9988642 is located approximately 500 bp downstream of IL23R but is in tight linkage disequilibrium (LD) with a missense SNP rs11209026 (R381Q) within IL23R (r2 = 0.85). The minor (G) allele of rs11209026 is present in approximately 7% of the population and is protective for psoriasis and several other autoimmune diseases including IBD, ankylosing spondylitis, RA and asthma. The psoriasis-associated missense SNP R381Q causes an arginine to glutamine substitution in a region of the IL23R protein between the transmembrane domain and the putative JAK2 binding site in the cytoplasmic portion. This substitution is expected to affect the receptor’s surface localisation or signalling ability, rather than IL23R expression. Recent studies have also identified a psoriatic arthritis (PsA)-specific signal at IL23R; thought to be independent from the psoriasis association (Bowes et al., 2015; Budu-Aggrey et al., 2016). The lead PsA-associated SNP rs12044149 is intronic to IL23R and is in LD with likely causal SNPs intersecting promoter and enhancer marks in memory CD8+ T cells (Budu-Aggrey et al., 2016). It is therefore likely that the PsA-specific SNPs affect IL23R function via a different mechanism compared with the psoriasis-specific SNPs. It could be hypothesised that the risk allele for PsA located within the IL23R promoter causes an increase IL23R expression, relative to the protective allele. An increased expression of IL23R might then lead to an exaggerated immune response. The independent genetic signals identified for psoriasis and PsA in this locus indicate that different mechanisms underlie these two conditions; although likely both affecting the function of IL23R. It is very important to further characterise these mechanisms in order to better understand how the IL-23 receptor and its downstream signalling is affected in both diseases. This will help to determine how psoriasis and PsA patients might differentially respond to therapies, particularly IL-23 biologics. To investigate this further we have developed an in vitro model using CD4 T cells which express either wild type IL23R and IL12Rβ1 or mutant IL23R (R381Q) and IL12Rβ1. Model expressing different isotypes of IL23R is also underway to investigate the effects on IL23R expression. We propose to further investigate the variants for Ps and PsA and characterise key intracellular processes related to the variants.

Keywords: IL23R, psoriasis, psoriatic arthritis, SNP

Procedia PDF Downloads 153

Authors: Dawit Assefa, Kassaye Tekie, Gebrie Alebachew, Degefu Beyene, Bikila Alemu, Naji Mohammed, Asnakech Agegnehu, Seble Tsehay, Geremew Tasew

Abstract:

Background: Implementation of a Laboratory Quality Management System (LQMS) is critical to ensure accurate, reliable, and efficient laboratory testing of antimicrobial resistance (AMR). However, limited LQMS implementation and progress toward accreditation in the AMR surveillance laboratory testing setting exist in Ethiopia. By addressing non-conformances (NCs) and working towards accreditation, microbiology laboratories can improve the quality of their services, increase staff competence, and contribute to mitigate the spread of AMR. Methods: Using standard ISO 15189 horizontal and vertical assessment checklists, certified assessors identified NCs at Hawassa and Jimma Hospital microbiology laboratories. The Ethiopian Public Health Institute AMR mentors and IDDS staff prioritized closing the NCs through the implementation of an intensified mentorship program that included ISO 15189 orientation training, resource allocation, and action plan development. Results: For the two facilities to clear their NCs, an intensified mentorship approach was adopted by providing ISO 15189 orientation training, provision of buffer reagents, controls, standards, and axillary equipment, and facilitating equipment maintenance and calibration. Method verification and competency assessment were also conducted along with the implementation of standard operating procedures and recommended corrective actions. This approach enhanced the laboratory's readiness for accreditation. After addressing their NCs, the two laboratories applied to Ethiopian Accreditation Services for ISO 15189 accreditation. Conclusions: Clearing NCs through the implementation of intensified mentorship was crucial in preparing the two laboratories for accreditation and improving quality laboratory test results. This approach can guide other microbiology laboratories’ accreditation attainment efforts.

Keywords: non-conformance clearance, intensified mentorship, accreditation, ISO 15189

Procedia PDF Downloads 69