Search results for: genome wide association studies

Authors: Salima Kerai, Muhammad Islam, Uzma Khan, Nargis Asad, Junaid Razzak, Omrana Pasha

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Background: Pre-hospital care providers are exposed to various kinds of stressors. Their daily exposure to diverse critical and traumatic incidents can lead to stress reactions like Post-Traumatic Stress Disorder (PTSD). Consequences of PTSD in terms of work loss can be catastrophic because of its compound effect on families, which affect them economically, socially and emotionally. Therefore, it is critical to assess the association between PTSD and Work performance in Emergency Medical Service (EMS) if exist any. Methods: This prospective observational study was carried out at AMAN EMS in Karachi, Pakistan. EMS personnel were screened for potential PTSD using impact of event scale-revised (IES-R). Work performance was assessed on basis of five variables; number of late arrivals to work, number of days absent, number of days sick, adherence to protocol and patient satisfaction survey over the period of 3 months. In order to model outcomes like number of late arrivals to work, days absent and days late; negative binomial regression was used whereas logistic regression was applied for adherence to protocol and linear for patient satisfaction scores. Results: Out of 536 EMS personnel, 525 were found to be eligible, of them 518 consented. However data on 507 were included because 7 left the job during study period. The mean score of PTSD was found to be 24.0 ± 12.2. However, weak and insignificant association was found between PTSD and work performance measures: number of late arrivals (RRadj 0.99; 95% CI 0.98-1.00), days absent (RRadj 0.98; 95% CI 0.96-0.99), days sick (Rradj 0.99; 95% CI 0.98 to 1.00), adherence to protocol (ORadj 1.01: 95% CI 0.99 to 1.04) and patient satisfaction (0.001% score; 95% CI -0.03% to 0.03%). Conclusion: No association was found between PTSD and Work performance in the selected EMS population in Karachi Pakistan. Further studies are needed to explore the phenomenon of resiliency in these populations. Moreover, qualitative work is required to explore perceptions and feelings like willingness to go to work, readiness to carry out job responsibilities.

Keywords: trauma, emergency medical service, stress, pakistan

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Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Kaili Wang, Botao Zhang, Enming Zhang

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Background: Low back pain (LBP) is a common problem affecting athletes' training and competition. Although the association between a limited hip range of motion and prevalence of low back pain has been studied extensively, it has not been studied in table tennis. Aim: The main purposes of this study in table tennis players were (1) to investigate if there is a difference in hip internal rotation (HIR) and external rotation (HER) range of motion (ROM) between players with LBP and players without LBP and (2) to analyze the association between HIR and HER ROM and LBP. Methods: Forty-six table tennis players from the Chinese table tennis team were evaluated for passive maximum HIR and HER ROM. LBP was retrospectively recorded for the last 12 months before the date of ROM assessment by a physical therapist. The data were analyzed the difference in HIR and HER ROM between players with LBP and players without LBP by Mann-Whitney U test, and the association between the difference in HIR and HER ROM and LBP was analyzed via a binary logistic regression. Results: The 54% of players had developed LBP during the retrospective study period. Significant difference between LBP group and the asymptomatic group for HIR ROM (z=4.007, p<0.001) was observed. Difference between LBP group and asymptomatic group for HER ROM (z=1.117, p=0.264) was not significant. Players who had HIR ROM deficit had an increased risk of LBP compared with players without HIR ROM deficit (OR=5.344, 95%CI: 1.006-28.395, P=0.049). Conclusion: HIR ROM of a table tennis player with LBP was less than a table tennis player without LBP. Compared with player whose HIR ROM was normal, player who had HIR ROM deficit appeared to have a higher risk for LBP.

Keywords: assessment, injury prevention, low back pain, table tennis players

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Authors: Jingjie Li, Wenjie Hu

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Phraseological units in academic English texts have been a central focus in recent corpus linguistic research. A wide variety of phraseological units have been explored, including collocations, chunks, lexical bundles, patterns, semantic sequences, etc. This paper describes a special category of clause-level phraseological units, namely, Characteristic Sentence Stems (CSSs), with a view to describing their defining criteria and extraction method. CSSs are contiguous lexico-grammatical sequences which contain a subject-predicate structure and which are frame expressions characteristic of academic writing. The extraction of CSSs consists of six steps: Part-of-speech tagging, n-gram segmentation, structure identification, significance of occurrence calculation, text range calculation, and overlapping sequence reduction. Significance of occurrence calculation is the crux of this study. It includes the computing of both the internal association and the boundary independence of a CSS and tests the occurring significance of the CSS from both inside and outside perspectives. A new normalization algorithm is also introduced into the calculation of LocalMaxs for reducing overlapping sequences. It is argued that many sentence stems are so recurrent in academic texts that the most typical of them have become the habitual ways of making meaning in academic writing. Therefore, studies of CSSs could have potential implications and reference value for academic discourse analysis, English for Academic Purposes (EAP) teaching and writing.

Keywords: characteristic sentence stem, extraction method, phraseological unit, the statistical measure

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Authors: Awad A. Younis, Elise Stronberg, Shifa Noor

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Malware attacks due to end-user vulnerabilities have been noticeably increased in the past few years. Investigating the factors that make an end-user vulnerable to those attacks is critical because they can be utilized to set up proactive strategies such as awareness and education to mitigate the impacts of those attacks. Some existing studies investigated demographic, behavioral, and cultural factors that make an end-user susceptible to malware attacks. However, it has been challenging to draw more general conclusions from individual studies due to the varieties in the type of end-users and different types of malware. Therefore, we conducted a systematic literature review (SLR) of the existing research for end-user susceptibility factors to malware attacks. The results showed while some demographic factors are mostly associated with malware infection regardless of the end users' type, age, and gender are not consistent among the same and different types of end-users. Besides, the association of culture and personality factors with malware infection are consistent in most of the selected studies and for all type of end-users. Moreover, malware infection varies based on age, geographic location, and host types. We propose that future studies should carefully take into consideration the type of end-users because different end users may be exposed to different threats or be targeted based on their user domains’ characteristics. Additionally, as different types of malware use different tactics to trick end-users, taking the malware types into consideration is important.

Keywords: cybersecurity, malware, end-users, demographics, personality, culture, systematic literature review

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Authors: Mahadev Bhise, Nabanita Majumder

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Recent studies have found association between air pollutants and mortality, particularly how concentration of air pollutant explains under-five mortality across the countries. Thus, the present study evaluates the relationship between Carbon dioxide (CO2) emission and under-five mortality, while controlling other well-being determinant of Under-five mortality in 100 countries using panel unbalanced cross sectional data. We have used PCSE and GMM model for the period 1990-2011 to meet our objectives. Our findings suggest that, the positive relationship between lagged periods of carbon dioxide and under-five mortality; the percentage of rural population with access of improved water is negatively associated with under-five mortality, while in case of urban population with access of improved water, is positively related to under-five mortality. Access of sanitation facility, food production index, GDP per capita, and concentration of urban population have significant negative impact on under-five mortality. Further, total fertility rate is significantly associated (positive) with under-five mortality which indicates relative change in fertility is related to relative change in under-five mortality.

Keywords: arbon dioxide (CO2), under-five mortality (0q5), gross domestic product (GDP), urban population, food production, panel corrected standard errors (PCSE), generalized method of moments (GMM)

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Authors: Todd R. Walton

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Social media would seem to be an ideal mechanism for crisis communication, yet it has been met with varied results. Natural disasters, such as hurricanes, provide a slow moving view of how social media can be leveraged to guide stakeholders and the public through a crisis. Crisis communication managers have struggled to reach target audiences with credible messaging. This Qualitative Evidence Synthesis (QES) analyzed the findings of eight studies published in the last year to determine how organizations effectively utilize social media for crisis communication. Additionally, the evidence was analyzed to note strategies for establishing credibility in a medium fraught with misinformation. Studies indicated wide agreement on the use of multiple social media channels in addition to frequent accurate messaging in order to establish credibility. Studies indicated mixed agreement on the use of text based emergency notification systems. The findings in this QES will help crisis communication professionals plan for social media use for crisis communication.

Keywords: crisis communication, crisis management, emergency response, social media

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Authors: Adewale O. Ogunde, Olusegun Folorunso, Adesina S. Sodiya

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Most existing Distributed Association Rule Mining (DARM) systems are still facing several challenges. One of such challenges that have not received the attention of many researchers is the inability of existing systems to adapt to constantly changing databases and mining environments. In this work, an Adaptive Incremental Mining Algorithm (AIMA) is therefore proposed to address these problems. AIMA employed multiple mobile agents for the entire mining process. AIMA was designed to adapt to changes in the distributed databases by mining only the incremental database updates and using this to update the existing rules in order to improve the overall response time of the DARM system. In AIMA, global association rules were integrated incrementally from one data site to another through Results Integration Coordinating Agents. The mining agents in AIMA were made adaptive by defining mining goals with reasoning and behavioral capabilities and protocols that enabled them to either maintain or change their goals. AIMA employed Java Agent Development Environment Extension for designing the internal agents’ architecture. Results from experiments conducted on real datasets showed that the adaptive system, AIMA performed better than the non-adaptive systems with lower communication costs and higher task completion rates.

Keywords: adaptivity, data mining, distributed association rule mining, incremental mining, mobile agents

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Authors: E. Syngelaki, C. C. F. Schinkel, S. Klatt, E. Hörandl

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Environmental influence can alter the conditions for plant development and can trigger changes in epigenetic variation. Thus, the exposure to abiotic environmental stress can lead to different DNA methylation profiles and may have evolutionary consequences for adaptation. Epigenetic control mechanisms may further influence mode of reproduction. The alpine species R. kuepferi has diploid and tetraploid cytotypes, that are mostly sexual and facultative apomicts, respectively. Hence, it is a suitable model system for studying the correlations of mode of reproduction, ploidy, and environmental stress. Diploid and tetraploid individuals were placed in two climate chambers and treated with low (+7°C day/+2°C night, -1°C cold shocks for three nights per week) and warm (control) temperatures (+15°C day/+10°C night). Subsequently, methylation sensitive-Amplified Fragment-Length Polymorphism (AFPL) markers were used to screen genome-wide methylation alterations triggered by stress treatments. The dataset was analyzed for four groups regarding treatment (cold/warm) and ploidy level (diploid/tetraploid), and also separately for full methylated, hemi-methylated and unmethylated sites. Patterns of epigenetic variation suggested that diploids differed significantly in their profiles from tetraploids independent from treatment, while treatments did not differ significantly within cytotypes. Furthermore, diploids are more differentiated than the tetraploids in overall methylation profiles of both treatments. This observation is in accordance with the increased frequency of apomictic seed formation in diploids and maintenance of facultative apomixis in tetraploids during the experiment. Global analysis of molecular variance showed higher epigenetic variation within groups than among them, while locus-by-locus analysis of molecular variance showed a high number (54.7%) of significantly differentiated un-methylated loci. To summarise, epigenetic variation seems to depend on ploidy level, and in diploids may be correlated to changes in mode of reproduction. However, further studies are needed to elucidate the mechanism and possible functional significance of these correlations.

Keywords: apomixis, cold stress, DNA methylation, Ranunculus kuepferi

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Authors: Anahita Izadyar, My Ni Van, Kayleigh Amber Rodriguez, Ilwoo Seok, Elizabeth E. Hood

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Using a recombinant enzyme derived from corn and a simple modification, we fabricated a facile, fast, and cost-beneficial biosensor to measure glucose. The Nafion/ Plant Produced Mn Peroxidase (PPMP)– glucose oxidase (GOx)- Bovine serum albumin (BSA) /Au electrode showed an excellent amperometric response to detect glucose. This biosensor is capable of responding to a wide range of glucose—20.0 µM−15.0 mM and has a lower detection limit (LOD) of 2.90µM. The reproducibility response using six electrodes is also very substantial and indicates the high capability of this biosensor to detect a wide range of 3.10±0.19µM to 13.2±1.8 mM glucose concentration. Selectivity of this electrode was investigated in an optimized experimental solution contains 10% diet green tea with citrus containing ascorbic acid (AA), and citric acid (CA) in a wide concentration of glucose at 0.02 to 14.0mM with an LOD of 3.10µM. Reproducibility was also investigated using 4 electrodes in this sample and shows notable results in the wide concentration range of 3.35±0.45µM to of 13.0 ± 0.81 mM. We also used other voltammetry methods to evaluate this biosensor. We applied linear sweep voltammetry (LSV) and this technique shows a wide range of 0.10−15.0 mM to detect glucose with a lower detection limit of 19.5µM. The performance and strength of this enzyme biosensor were the simplicity, wide linear ranges, sensitivities, selectivity, and low limits of detection. We expect that the modified biosensor has the potential for monitoring various biofluids.

Keywords: plant-produced manganese peroxidase, enzyme-based biosensors, glucose, modified gold electrode, glucose oxidase

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Barby Jennette A. Florano

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Dietary intake has been associated with the health and wellbeing of adults, and lifestyle related diseases. The aim of this study was to investigate whether nutrition knowledge, food label use, and food preference are associated with the dietary intake in a sample of San Jose Del Monte City, Bulacan (SJDM) adults. A sample of 148 adults, with a mean age of 20 years, completed a validated questionnaire related to their demographic, dietary intake, nutrition knowledge, food label use and food preference. Data were analyzed using Pearson correlation and there was no association between dietary intake and nutrition knowledge. However, there were positive relationships between dietary intake and food label use (r=0.1276, p<0.10), and dietary intake and food preference (r=0.1070, p<0.10). SJDM adults who use food label and have extensive food preference had better diet quality. This finding magnifies the role of nutrition education as a potential tool in health campaigns to promote healthy eating patterns and reading food labels among students and adults. Results of this study can give information for the design of future nutrition education intervention studies to assess the efficacy of nutrition knowledge and food label use among a similar sample population.

Keywords: dietary intake, nutrition knowledge, food preference, food label use

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Authors: Hassan Y. Kikhia, Jin P. Zhang, Khaldoon G. Albiatr

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The Enron and Arthur Andersen scandal has raised concerns internationally about auditor independence and audit quality. Furthermore, the debate continues about the relationship between audit fees, auditor tenure and audit quality in spite of extensive empirical evidence examining audit failures and earnings management. Therefore, the purpose of current research is to determine the effect of audit fee and audit tenure both partially and simultaneously on the audit quality. Using a sample of Chinese firms, an environment where we believe it provides us with an opportunity to test whether the development of market and legal institutions affects the impact of audit fees and auditor tenure on audit quality. We employ the standard deviation of residuals from regressions relating current accruals to cash flows as proxy for audit quality. The paper documents statistically significant negative association between audit fees and audit quality. These findings are consistent with economic bonding being a determinant of auditor behavior rather than auditor reputational concerns. Further, the current paper shows a positive association between auditor tenure and audit quality in the earlier years of audit tenure. These results support the proposition that when the Learning Effect dominates the Bonding Effect in the earlier years of tenure, then audit quality is likely to be higher. Taken audit fees and audit tenure together, the results suggest that there is positive association between audit fees and audit quality in the earlier years of auditor tenure. Interestingly, the findings of our study have important implications for auditors, policymakers, multinational firms, and users of financial reports. As the rapid growth of China's economy gains global recognition, the Chinese stock market is capturing the attention of international investors. To a lesser extent, our paper also differs from the prior studies in methodology and findings in the investigation of audit quality.

Keywords: audit quality, accruals quality, audit fees, auditor tenure

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Authors: Mohamad Farhat, Bal Virdee

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This paper present a compact Microstrip Bandpass filter exhibiting a very wide stop band and high selectivity. The filter comprises of asymmetric resonator structures, which are interconnected by an inter-digital capacitor to enable the realization of a wide bandwidth with high rejection level. High selectivity is obtained by optimizing the parameters of the interdigital capacitor. The filter has high out-of-band rejection (> 30 dB), less than 0.6 dB of insertion-loss, up to 5.5 GHz spurii free, and about 18 dB of return-loss. Full-wave electromagnetic simulator ADSTM (Mom) is used to analyze and optimize the prototype bandpass filter. The proposed technique was verified practically to validate the design methodology. The experimental results of the prototype circuit are presented and a good agreement was obtained comparing with the simulation results. The dimensions of the proposed filter are 32 x 24 mm2.The filter’s characteristics and compact size make it suitable for wireless communication systems.

Keywords: asymmetric resonator, bandpass filter, microstrip, spurious suppression, ultra-wide stop band

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Authors: Azizah Nurdin, Trika Irianta, Mardiah Tahir, Maisuri T. Chalid

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Background: Studies of anal incontinence in the general population are rare however its financial healthcare cost is significant. Women attended Hasanuddin University Teaching Hospital and its networking in Makassar, Indonesia was surveyed between February to April 2015 about their obstetrical and gynecological history. Aims: To establish obstetrical risk factor of anal incontinence among women in Makassar. Methods: In a cross sectional face to face interview study, 135 women aged 30 years or more were selected randomly. Participants were asked to complete an anal incontinence questionnaire. Results: From a total sample of 135 respondents, 42,2 % reported has flatulence incontinence. Parity, history of anal sphincter laceration, history of having large baby, history of assisted vaginal delivery were shown have no significant association with anal incontinence, while history of episiotomy was shown have a significant association with anal incontinence (p value < 0.05). The risk of flatulence incontinence was higher among women with history of episiotomy (OR : 2,85, 95 % CI = 1,58- 5,13) Conclusions: This study has confirmed that fecal incontinence is a fairly common symptom. Flatulence incontinence is the most frequent even. An obstetrical factor like episiotomy is one of risk factor that could be avoided in order to prevent anal incontinence.

Keywords: anal incontinence, flatulence incontinence, obstetrical risk factor, women

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Authors: Rumman M. D. Raihanuzzaman, Lee Chang Chuan, Zonghan Xie, Reza Ghomashchi

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Cemented carbides, owing to their excellent mechanical properties, have been of immense interest in the field of hard materials for the past few decades. A number of processing techniques have been developed to obtain high quality carbide tools, with a wide range of grain size depending on the application and requirements. Microwave sintering is one of the heating processes, which has been used on a wide range of materials including ceramics. The complete understanding of microwave sintering and its contribution towards control of grain growth and on deformation of the resulting carbide materials needs further studies and attention. In addition, the effect of binder materials and their behaviour as a function of microwave sintering is another area that requires clear understanding. This review aims to focus on microwave sintering, providing information of how the process works and what type of materials it is best suited for. In addition, a closer look at some microwave sintered Tungsten Carbide-Cobalt samples will be taken and discussed, addressing some of the key issues and challenges faced in the research.

Keywords: cemented carbides, consolidation, microwave sintering, mechanical properties

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Authors: Sreelekha Prakash, Yulong Gu

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Background: About 61% of adults surveyed across 25 states reported they had experienced at least one type of Adverse Childhood Experience (ACE) before 18 years of age. Relationships between ACEs and a variety of substance-related behaviors and behavioral health have been reported in previous studies. ACEs can have lasting, negative effects on health, well-being, as well as life opportunities such as education and job potential. Objectives: For the current research, the aim was to assess the factors affecting substance use behavior in young adults. The further onset of drug use and its association was analyzed with ACEs and mental health. Method: The young adults from a county in the north-eastern United States were invited to participate in an online questionnaire survey with prior consent through an IRB approved study. The Survey included questions related to social determinants of health, 10 item ACE questionnaire, and substance use related to Alcohol, Marijuana, Opioids, Stimulants, and other drugs. PHQ-9 questionnaire was used to assess cognitive health. Results: Data was analyzed for the 244 completed surveys {68% (165) were females, and 78% (190) were Whites}. The average age of the participants was 26.7 years, and approximately 80% were lifelong residents of the county or year-round residents. Of the respondents, 50% (122) were high school graduates with some college education, and 56% (136) had a full-time jobs. Past 30-day usage for alcohol was 76% (72), and marijuana was 28.4% (27). The data showed that the higher the ACE scores, the younger they start using any substance (p < 0.0001). The data for PHQ-9 and ACE scores showed that the higher the ACE score, the higher the PHQ-9 score, with a significant p-value (p 0.0001). The current data also showed a significant association with other drugs; marijuana use showed significance for 30 days of use (p 0.0001), stimulant use (0.0008), prescription drug misuse (0.01), and opioids (0.01). Conclusion: These findings further support the association between ACEs and initiation of drug use and its correlation with mental health symptoms. Promoting a safe and supportive environment for children and youth in their earlier ages can prevent the youth and young adults from the effects of drug use and create healthy living habits for young adults.

Keywords: subtance use, young adults, adverse childhood experience, PHQ-9

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Authors: Ghada Badr, Manar Hosny, Nuha Bintayyash, Eman Albilali, Souad Larabi Marie-Sainte

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The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms.

Keywords: median problem, phylogenetic tree, permutation, genetic algorithm, beam search, genome rearrangement distance

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Authors: Angela Maria Fenu

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The aim of this study was to better characterize the nature of word association responses in people with aphasia. The participants selected for the experimental group were 4 individuals with mild Broca’s aphasia. The control group consisted of 51 cognitively intact age- and gender-matched individuals. The participants were asked to perform a word association task in which they had to say the first word they thought of when hearing each cue. The cue words (n= 16) were the translation in Italian of the set of English cue words of a published study. The participants from the experimental group were administered the word association test every two weeks for a period of two months when they received speech-language therapy A combination of analytical approaches to measure the data was used. To analyse different patterns of word association responses in both groups, the nature of the relationship between the cue and the response was examined: responses were divided into five categories of association. To investigate the similarity between aphasic and non-aphasic subjects, the stereotypy of responses was examined.While certain stimulus words (nouns, adjectives) elicited responses from Broca’s aphasics that tended to resemble those made by non-aphasic subjects; others (adverbs, verbs) showed the tendency to elicit responses different from the ones given by normal subjects. This suggests that some mechanisms underlying certain types of associations are degraded in aphasics individuals, while others display little evidence of disruption. The high number of paradigmatic associations given in response to a noun or an adjective might imply that the mechanisms, largely semantic, underlying paradigmatic associations are relatively preserved in Broca’s aphasia, but it might also mean that some words are more easily processed depending on their grammatical class (nouns, adjectives). The most significant variation was noticed when the grammatical class of the cue word was an adverb. Unlike the normal individuals, the experimental subjects gave the most idiosyncratic associations, which are often produced when the attempt to give a paradigmatic response fails. In turn, the failure to retrieve paradigmatic responses when the cue is an adverb might suggest that Broca’s aphasics are more sensitive to this grammatical class.The findings from this study suggest that, from research on word associations in people with aphasia, important data can arise concerning the specific lexical retrieval impairments that characterize the different types of aphasia and the various treatments that might positively influence the kinds of word association responses affected by language disruption.

Keywords: aphasia therapy, clinical linguistics, word-association behaviour, mental lexicon

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Authors: Dwipa Rizki Utama, Hanief Ibrahim

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The development of industry retail in Indonesia is very fast, various strategy was undertaken to boost the customer satisfaction and the productivity purchases to boost the profit, one of which is implementing strategies layout. The purpose of this study is to determine the layout of Qita supermarket, a retail industry in Indonesia, in order to improve customer satisfaction and to maximize the rate of products’ sale as a whole, so as the infrequently purchased products will be purchased. This research uses a literature study method, and one of the data mining methods is association rule which applied in market basket analysis. Data were tested amounted 100 from 160 after pre-processing data, so then the distribution department and 26 departments corresponding to the data previous layout will be obtained. From those data, by the association rule method, customer behavior when purchasing items simultaneously can be studied, so then the layout of the supermarket based on customer behavior can be determined. Using the rapid miner software by the minimal support 25% and minimal confidence 30% showed that the 14th department purchased at the same time with department 10, 21st department purchased at the same time with department 13, 15th department purchased at the same time with department 12, 14th department purchased at the same time with department 12, and 10th department purchased at the same time with department 14. From those results, a better supermarket layout can be arranged than the previous layout.

Keywords: industry retail, strategy, association rule, supermarket

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Authors: Chimuanya Osuji, Kido Uyamasi, Morgan Bradley

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Introduction: Obesity is a major risk factor for many chronic diseases, with higher rates occurring among certain populations. Even though disparities in obesity rates exist for those with disabilities, few studies have assessed the association between disability and obesity status. This study aims to examine the association between type of disability and obesity status among US adults during the Covid-19 pandemic (2019-2021). Methods: Data for this cross-sectional study was obtained from the 2019, 2020 and 2021 NHIS. Multinomial logistic regressions were used to assess the relationship between each type of disability and obesity status (reference= normal/underweight). Each model adjusted for demographic, health status and health-related quality of life variables. Statistical analyses were conducted using SAS version 9.4. Results: Of the 82,632 US adults who completed the NHIS in 2019, 2020, and 2021. 8.9% (n= 7,354) reported at least 1 disability-related condition. Respondents reported having a disability across vision (1.5%), hearing (1.5%), mobility (5.3%), communication (0.8%), cognition (2.4%) and self-care (1.1%) domains. After adjusting for covariates, adults with at least 1 disability-related condition were about 30% more likely to have moderate-severe obesity (AOR=1.3; 95% CI=1.11, 1.53). Mobility was the only disability category positively associated with mild obesity (AOR=1.16; 95% CI=1.01, 1.35) and moderate/severe obesity (AOR=1.6; 95% CI=1.35, 1.89). Individuals with vision disability were about 35% less likely to have mild obesity (AOR=0.66; 95% CI=0.51, 0.86) and moderate-severe obesity (AOR=0.66; 95% CI= 0.48, 0.9). Individuals with hearing disability were 28% less likely to have mild obesity (AOR=0.72; 95% CI= 0.56, 0.94). Individuals with communication disability were about 30% less likely to be overweight (AOR=0.66; 95% CI=0.47, 0.93) and 50% less likely to have mild obesity (AOR=0.45; 95% CI= 0.29, 0.71). Individuals with cognitive disability were about 25% less likely to have mild obesity and about 35% less likely to have moderate-severe obesity. Individuals with self-care disability were about 30% less likely to be overweight. Conclusion: Mobility-related disabilities are significantly associated with obesity status among adults residing in the United States. Researchers and policy makers should implement obesity intervention methods that can address the gap in obesity prevalence rates among those with and without disabilities.

Keywords: cognition, disability, mobility, obesity

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Authors: Majdi M. Alomari, Nafesah I. Alshdaifat, Mohammad S. Widyan

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Different countries have introduced different schemes and policies to counter global warming. The rationale behind the proposed policies and the potential barriers to successful implementation of the policies adopted by the countries were analyzed and estimated based on different models. It is argued that these models enhance the transparency and provide a better understanding to the policy makers. However, these models are underpinned with several structural and baseline assumptions. These assumptions, modeling features and future prediction of emission reductions and other implication such as cost and benefits of a transition to a low-carbon economy and its economy wide impacts were discussed. On the other hand, there are potential barriers in the form political, financial, and cultural and many others that pose a threat to the mitigation options.

Keywords: energy models, environmental policy instruments, mitigating CO2 emission, economic wide impact

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Authors: Ahmed Bahieldin, Ahmed Atef, Jamal S. M. Sabir, Nour O. Gadalla, Sherif Edris, Ahmed M. Alzohairy, Nezar A. Radhwan, Mohammed N. Baeshen, Ahmed M. Ramadan, Hala F. Eissa, Sabah M. Hassan, Nabih A. Baeshen, Osama Abuzinadah, Magdy A. Al-Kordy, Fotouh M. El-Domyati, Robert K. Jansen

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Wild salt-tolerant barley (Hordeum spontaneum) is the ancestor of cultivated barley (Hordeum vulgare or H. vulgare). Although the cultivated barley genome is well studied, little is known about genome structure and function of its wild ancestor. In the present study, RNA-Seq analysis was performed on young leaves of wild barley treated with salt (500 mM NaCl) at four different time intervals. Transcriptome sequencing yielded 103 to 115 million reads for all replicates of each treatment, corresponding to over 10 billion nucleotides per sample. Of the total reads, between 74.8 and 80.3% could be mapped and 77.4 to 81.7% of the transcripts were found in the H. vulgare unigene database (unigene-mapped). The unmapped wild barley reads for all treatments and replicates were assembled de novo and the resulting contigs were used as a new reference genome. This resultedin94.3 to 95.3%oftheunmapped reads mapping to the new reference. The number of differentially expressed transcripts was 9277, 3861 of which were uni gene-mapped. The annotated unigene- and de novo-mapped transcripts (5100) were utilized to generate expression clusters across time of salt stress treatment. Two-dimensional hierarchical clustering classified differential expression profiles into nine expression clusters, four of which were selected for further analysis. Differentially expressed transcripts were assigned to the main functional categories. The most important groups were ‘response to external stimulus’ and ‘electron-carrier activity’. Highly expressed transcripts are involved in several biological processes, including electron transport and exchanger mechanisms, flavonoid biosynthesis, reactive oxygen species (ROS) scavenging, ethylene production, signaling network and protein refolding. The comparisons demonstrated that mRNA-Seq is an efficient method for the analysis of differentially expressed genes and biological processes under salt stress.

Keywords: electron transport, flavonoid biosynthesis, reactive oxygen species, rnaseq

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Authors: Wafa Toumi, Alessandro Ripalti, Luigi Ricciardiello, Dalila Gargouri, Jamel Kharrat, Abderraouf Cherif, Ahmed Bouhafa, Slim Jarboui, Mohamed Zili, Ridha Khelifa

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Background & aims: Colorectal cancer (CRC) is one of the most common malignancies throughout the world. Several risk factors, both genetic and environmental, including viral infections, have been linked to colorectal carcinogenesis. A few studies report the detection of human polyomavirus JC (JCV) DNA and transformation antigen (T-Ag) in a fraction of the colorectal tumors studied and suggest an association of this virus with CRC. In order to investigate whether such an association of JCV with CRC will hold in a different epidemiological setting, we looked for the presence of JCV DNA and T-Ag expression in a group of Tunisian CRC patients. Methods: Fresh colorectal mucosa biopsies were obtained from 17 healthy volunteers and from both colorectal tumors and adjacent normal tissues of 47 CRC patients. DNA was extracted from fresh biopsies or from formalin-fixed, paraffin-embedded tissue sections using the Invitrogen Purelink Genomic DNA mini Kit. A simple PCR and a nested PCR were used to amplify a region of the T-Ag gene. The obtained PCR products revealed a 154 bp and a 98 bp bands, respectively. Specificity was confirmed by sequencing of the PCR products. T-Ag expression was determined by immunohistochemical staining using a mouse monoclonal antibody (clone PAb416) directed against SV40 T-Ag that cross reacts with JCV T-Ag. Results: JCV DNA was found in 12 (25%) and 22 (46%) of the CRC tumors by simple PCR and by nested PCR, respectively. All paired adjacent normal mucosa biopsies were negative for viral DNA. Sequencing of the DNA amplicons obtained confirmed the authenticity of T-Ag sequences. Immunohistochemical staining showed nuclear T-Ag expression in all 22 JCV DNA- positive samples and in 3 additional tumor samples which appeared DNA-negative by PCR. Conclusions: These results suggest an association of JCV with a subpopulation of Tunisian colorectal tumors.

Keywords: colorectal cancer, immunohistochemistry, Polyomavirus JC, PCR

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Authors: Yantao Li, Jun Zheng

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Food poison caused by consumption of contaminated food, especially seafood, is one of most serious public health threats worldwide. Vibrio parahaemolyticus is emerging bacterial pathogen and the leading cause of human gastroenteritis associated with food poison, especially in the southern coastal region of China. To successfully cause disease in host, bacterial pathogens need to overcome the host-derived stresses encountered during infection. One of the toxic chemical species elaborated by the host is nitric oxide (NO). NO is generated by acidified nitrite in the stomach and by enzymes of the inducible NO synthase (iNOS) in the host cell, and is toxic to bacteria. Bacterial pathogens have evolved some mechanisms to battle with this toxic stress. Such mechanisms include genes to sense NO produced from immune system and activate others to detoxify NO toxicity, and genes to repair the damage caused by toxic reactive nitrogen species (RNS) generated during NO toxic stress. However, little is known about the NO resistance in V. parahaemolyticus. In this study, a transposon coupled with next generation sequencing (Tn-seq) technology will be utilized to identify genes for NO resistance in V. parahaemolyticus. Our strategy will include construction the saturating transposon insertion library, transposon library challenging with NO, next generation sequencing (NGS), bioinformatics analysis and verification of the identified genes in vitro and in vivo.

Keywords: vibrio parahaemolyticus, nitric oxide, tn-seq, virulence

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Authors: Harinder Singh

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The paper sheds light on the perceptions of the uninsured workers employed in the urban informal sector of India, towards the health insurance. In addition to this, it also explores the association of the identified perceptions with household decisions to enroll for health insurance schemes in India. Firstly the data taken from the primary survey of the uninsured workers employed in the urban informal sector was analyzed using exploratory factor analysis to evaluate the perceptions. Thereafter, logistic regression was employed to determine the association of the identified perceptions regarding the enrollment. Our study identifies twelve perceptions related to the health insurance enrollment of the uninsured workers employed in the urban informal sector of India. The study demonstrates that perceptions have the strongest association with the voluntary enrollment. These specifically relate to the lack of awareness about the need to buy health insurance; comprehensive coverage; income constraint; future contingencies and social obligations; lack of information; availability of subsidized government health care; linkage with government hospitals and preference for government schemes. Conclusions: Along with the food security, health security has become a crying need of the workers employed in the informal sector and the time has come to scale up the health insurance schemes for them in the country. Policy makers or marketers of health insurance policies should recognize the household perceptions as a potential barrier and try to develop a health insurance package as per the actual needs of the informal sector (low income) in India.

Keywords: association, enrollment, health insurance, informal sector, perceptions, uninsured

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Authors: Fatemeh Nokhodchi Bonab

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Bioinformatics, in its broad sense, involves application of computer processes to solve biological problems. A wide range of computational tools are needed to effectively and efficiently process large amounts of data being generated as a result of recent technological innovations in biology and medicine. A number of computational tools have been developed or adapted to deal with the experimental riches of complex and multivariate data and transition from data collection to information or knowledge. These bioinformatics tools are being evaluated and applied in various medical areas including early detection, risk assessment, classification, and prognosis of cancer. The goal of these efforts is to develop and identify bioinformatics methods with optimal sensitivity, specificity, and predictive capabilities. The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems.

Keywords: methods, applications, transcriptional regulatory systems, techniques

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Authors: Beatrice Adeoye

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Studies have associated social and demographic characteristics as strong determinants of utilization of health care services; however, not much has been done to explore the dynamics of these variables in Nigeria. This empirical study explores the link between demographic factors and the future use of health care services in Nsukka, southeast Nigeria. A total of 543 respondents were selected using multi-stage sampling technique. The findings of the study showed that majority (56.9%) of the respondents were female while 43.1% were male. More of the respondents were married (50.3%) while 41.80/0 of the respondents were between ages 26-35. Testing the demographic characteristics regarding where people will prefer to go first for treatment with multiple regression, It is only Sex as a demographic variable that indicates positive association for future occurrence to where people will prefer to go first for treatment with 0.08 significance. Age and education indicates no association considering their level of significance. This result shows that sex is one of the determinant factors of where and when people will go for treatment. This is pointing out the realities regarding African society where in the family setting, it is the father that dictates the cause of action. Also to buttress these findings, cross tabulating age with who determines where and when to go for treatment, findings show that majority (58.9%) within age 26-35 said their spouses decide on where and when to go for treatment. Findings showed that patriarchy still plays an important role in the utilization of health care delivery among the people studied.

Keywords: Demographic characters, Determinant, Health Care, treatment, self-medication, symptom,

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Authors: Usha Barahmand, Ruhollah Heydari Sheikh Ahmad

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Distress refers to an unpleasant metal state or emotional suffering marked by negative affect such as depression (e.g., lost interest; sadness; hopelessness), anxiety (e.g., restlessness; feeling tense). These negative affect have been mostly suggested to be concomitant of metal disorders such as positive psychosis symptoms and also of proneness to psychotic features in non-clinical population. Psychotic features proneness including hallucination, delusion and schizotypal traits, have been found to be associated with metacognitive beliefs. Metacognition has been conceptualized as ‘thinking about thoughts, monitoring and controlling of cognitive processes’. The aim of the current study was to investigate the role of psychosis proneness in the association of metacognitions and distress. We predicted psychosis proneness would mediate the association of metacognitive beliefs and the distress. A sample of 420 university students was randomly recruited to endorse questionnaires of the study that consisted of DASS-21questionnaire for assessing levels of distress, Cartwright–Hatton & Wells, Meta-cognitions Questionnaire (MCQ-30) for assessing metacognitive beliefs, Launay-Slade Hallucination Scale-revised (LSHS-R), Peters et al. Delusions Inventory, Schizotypal Personality Questionnaire-Brief. Conducting a bootstrapping approach in order to investigate our hypothesis, the result showed that there was no a direct association between metacognitive dimensions and psychological distress and psychosis proneness significantly mediated the association. Finding suggested that individuals with dysfunctional metacognitive beliefs experience high levels of distress if they are prone to psychosis symptoms. In other words, psychosis proneness is a path through which individuals with dysfunctional metacognitions experience high levels of psychological distress.

Keywords: metacognition, non-clinical population, psychological distress, psychosis proneness

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Authors: Caio E. G. Reis, Jose G. Dórea, Teresa H. M. da Costa

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Objective: Epidemiological data shows an inverse association of coffee consumption with risk of type 2 diabetes mellitus. However, the clinical effects of coffee consumption on the glucose metabolism biomarkers remain controversial. Thus, this paper reviews clinical trials that evaluated the effects of coffee consumption on glucose metabolism. Research Design and Methods: We identified studies published until December 2014 by searching electronic databases and reference lists. We included randomized clinical trials which the intervention group received caffeinated and/or decaffeinated coffee and the control group received water or placebo treatments and measured biomarkers of glucose metabolism. The Jadad Score was applied to evaluate the quality of the studies whereas studies that scored ≥ 3 points were considered for the analyses. Results: Seven clinical trials (total of 237 subjects) were analyzed involving adult healthy, overweight and diabetic subjects. The studies were divided in short-term (1 to 3h) and long-term (2 to 16 weeks) duration. The results for short-term studies showed that caffeinated coffee consumption may increase the area under the curve for glucose response, while for long-term studies caffeinated coffee may improve the glycemic metabolism by reducing the glucose curve and increasing insulin response. These results seem to show that the benefits of coffee consumption occur in the long-term as has been shown in the reduction of type 2 diabetes mellitus risk in epidemiological studies. Nevertheless, until the relationship between long-term coffee consumption and type 2 diabetes mellitus is better understood and any mechanism involved identified, it is premature to make claims about coffee preventing type 2 diabetes mellitus. Conclusion: The findings suggest that caffeinated coffee may impairs glucose metabolism in short-term but in the long-term the studies indicate reduction of type 2 diabetes mellitus risk. More clinical trials with comparable methodology are needed to unravel this paradox.

Keywords: coffee, diabetes mellitus type 2, glucose, insulin

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