Search results for: genome wide association studies (GWAS)

Authors: Yugander Arra, Florence Auguy, Melissa Stiebner, Sophie Chéron, Michael M. Wudick, Van Schepler-Luu, Sébastien Cunnac, Wolf B. Frommer, Laurence Albar

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Rice yellow mottle virus (RYMV) is one of the most important diseases affecting rice in Africa. The most promising strategy to reduce yield losses is the use of highly resistant varieties. The resistance gene RYMV2 is homolog of the Arabidopsis constitutive expression of pathogenesis related protein-5 (AtCPR5) nucleoporin gene. Resistance alleles are originating from African cultivated rice Oryza glaberrima, rarely cultivated, and are characterized by frameshifts or early stop codons, leading to a non-functional or truncated protein. Rice possesses two paralogs of CPR5 and function of these genes are unclear. Here, we evaluated the role of the two rice candidate nucleoporin paralogs OsCPR5.1 (pathogenesis-related gene 5; RYMV2) and OsCPR5.2 by CRISPR/Cas9 genome editing. Despite striking sequence and structural similarity, only loss-of-function of OsCPR5.1 led to full resistance, while loss-of-function oscpr5.2 mutants remained susceptible. Short N-terminal deletions in OsCPR5.1 also did not lead to resistance. In contrast to Atcpr5 mutants, neither OsCPR5.1 nor OsCPR5.2 knock out mutants showed substantial growth defects. Taken together, the candidate nucleoporin OsCPR5.1, but not its close homolog OsCPR5.2, plays a specific role for the susceptibility to RYMV, possibly by impairing the import of viral RNA or protein into the nucleus. Whereas gene introgression from O. glaberrima to high yielding O. sativa varieties is impaired by strong sterility barriers and the negative impact of linkage drag, genome editing of OsCPR5.1, while maintaining OsCPR5.2 activity, thus provides a promising strategy to generate O. sativa elite lines that are resistant to RYMV.

Keywords: CRISPR Cas9, genome editing, knock out mutant, recessive resistance, rice yellow mottle virus

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Authors: Soumaya Mrabet, Taieb Ach, Imen Akkari, Amira Atig, Neirouz Ghannouchi, Koussay Ach, Elhem Ben Jazia

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Introduction: Celiac disease (CD) and type 1 diabetes mellitus (T1D) are complex disorders with shared genetic components. The association between CD and T1D has been reported in many pediatric series. The aim of our study is to describe the epidemiological, clinical and evolutive characteristics of adult patients presenting this association. Material and Methods: This is a retrospective study including patients diagnosed with CD and T1D, explored in Internal Medicine, Gastroenterology and Endocrinology and Diabetology Departments of the Farhat Hached University Hospital, between January 2005 and June 2016. Results: Among 57 patients with CD, 15 patients had also T1D (26.3%). There are 11 women and 4 men with a median age of 27 years (16-48). All patients developed T1D prior to the diagnosis of CD with an average duration of 47 months between the two diagnosis (6 months-5 years). CD was revealed by recurrent abdominal pain in 11 cases, diarrhea in 10 cases, bloating in 8 cases, constipation in 6 cases and vomiting in 2 cases. Three patients presented cycle disorders with secondary amenorrhea in 2 patients. Anti-Endomysium, anti-transglutaminase and Anti-gliadin antibodies were positive respectively in 57, 54 and 11 cases. The biological tests revealed anemia in 10 cases, secondary to iron deficiency in 6 cases and folate and vitamin B12 deficiency in 4 cases, hypoalbuminaemia in 4 cases, hypocalcemia in 3 cases and hypocholesterolemia in 1 patient. Upper gastrointestinal endoscopy showed an effacement of the folds of the duodenal mucosa in 6 cases and a congestive duodenal mucosa in 3 cases. The macroscopic appearance was normal in the others cases. Microscopic examination showed an aspect of villous atrophy in 57 cases, which was partial in 10 cases and total in 47 cases. After an average follow-up of 3 years 2 months, the evolution was favorable in all patients under gluten-free diet with the necessity of less important doses of insulin in 10 patients. Conclusion: In our study, the prevalence of T1D in adult patients with CD was 26.3%. This association can be attributed to overlapping genetic HLA risk loci. In recent studies, the role of gluten as an important player in the pathogenesis of CD and T1D has been also suggested.

Keywords: celiac disease, gluten, prevalence, type 1 diabetes

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Authors: Alvaro L. Ronco

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Background and purpose: Although our country is a developing one, it has a typical Western meat-rich dietary style. Based on estimates of heme and nonheme iron contents in representative foods, we carried out the present epidemiologic study, with the aim of accurately analyzing dietary iron and its role on CRC risk. Subjects/methods: Patients (611 CRC incident cases and 2394 controls, all belonging to public hospitals of our capital city) were interviewed through a questionnaire including socio-demographic, reproductive and lifestyle variables, and a food frequency questionnaire of 64 items, which asked about food intake 5 years before the interview. The sample included 1937 men and 1068 women. Controls were matched by sex and age (± 5 years) to cases. Food-derived nutrients were calculated from available databases. Total dietary iron was calculated and classified by heme or nonheme source, following data of specific Dutch and Canadian studies, and additionally adjusted by energy. Odds Ratios (OR) and 95% confidence intervals were calculated through unconditional logistic regression, adjusting for relevant potential confounders (education, body mass index, family history of cancer, energy, infusions, and others). A heme/nonheme (H/NH) ratio was created and the interest variables were categorized into tertiles, for analysis purposes. Results: The following risk estimations correspond to the highest tertiles. Total iron intake showed no association with CRC risk neither among men (OR=0.83, ptrend =.18) nor among women (OR=1.48, ptrend =.09). Heme iron was positively associated among men (OR=1.88, ptrend < .001) and for the overall sample (OR=1.44, ptrend =.002), however, it was not associated among women (OR=0.91, ptrend =.83). Nonheme iron showed an inverse association among men (OR=0.53, ptrend < .001) and the overall sample (OR=0.78, ptrend =.04), but was not associated among women (OR=1.46, ptrend =.14). Regarding H/NH ratio, risks increased only among men (OR=2.12, ptrend < .001) but lacked of association among women (OR=0.81, ptrend =.29). Conclusions. We have observed different types of associations between CRC risk and high dietary heme, nonheme and H/NH iron ratio. Therefore, the source of the available iron might be of importance as a link to colorectal carcinogenesis, perhaps pointing to reconsider the animal/plant proportions of this vital mineral within diet. Nevertheless, the different associations observed for each sex, demand further studies in order to clarify these points.

Keywords: chelation, colorectal cancer, heme, iron, nonheme

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Authors: Muhammad Ihsan Andi Dagong, Cece Sumantri, Ronny Rachman Noor, Rachmat Herman, Mohamad Yamin

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Calpastatin involved in various physiological processes in the body such as the protein turnover, growth, fusion and mioblast migration. Thus, allegedly Calpastatin gene diversity (CAST) have an association with growth and potential use as candidate genes for growth trait. This study aims to identify the association between the genetic diversity of CAST gene with some growth properties such as body dimention (morphometric), body weight and daily weight gain in sheep. A total of 157 heads of Thin Tail Sheep (TTS) reared intensively for fattening purposes in the uniform environmental conditions. Overall sheep used were male, and maintained for 3 months. The parameters of growth properties were measured among others: body weight gain (ADG) (g/head / day), body weight (kg), body length (cm), chest circumference (cm), height (cm). All the sheep were genotyped by using PCR-SSCP (single strand conformational polymorphism) methods. CAST gene in locus fragment intron 5 - exon 6 were amplified with a predicted length of about 254 bp PCR products. Then the sheep were stratified based on their CAST genotypes. The result of this research showed that no association were found between the CAST gene variations with morphometric body weight, but there was a significant association with daily body weight gain (ADG) in sheep observed. CAST-23 and CAST-33 genotypes has higher average daily gain than other genotypes. CAST-23 and CAST-33 genotypes that carrying the CAST-2 and CAST-3 alleles potential to be used in the selection of the nature of the growth trait of the TTS sheep.

Keywords: body weight, calpastatin, genotype, growth trait, thin tail sheep

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Authors: Pratistha Shrestha

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Background: Acrochordons (Skin tags) are common benign skin tumors usually occurring on the neck and major flexors of older people. These range in size from 1 mm to 1cm in diameter and are skin-colored or brownish. A possible association with diabetes mellitus has been suggested in previous studies, but the result is not conclusive. Objective: The aim of this study was to find out the association of diabetes mellitus with acrochordons. Material and Methods: One hundred and two patients were selected for the study. Among them, 51 (males–23 and females–28) with acrochordons were taken as cases, and 51 with other dermatologic diseases after matching age and sex were taken as controls. The patients were selected from OPD of the Department of Dermatology and Venereology in Universal College of Medical Sciences–Teaching Hospital (UCMS-TH). Blood glucose levels, including both fasting plasma glucose and 2-hour post-glucose load, were determined for both case and control and compared. Results: Patients with acrochordons had a significantly higher frequency of diabetes than the control group (p < 0.001). A total of 48.5% and 40% of patients with acrochordons having diabetes were obese and overweight, respectively. Conclusion: There is an increased risk of diabetes mellitus in patients with acrochordons. With regard to the importance of early diagnosis of diabetes, it is recommended a high level of suspicion for diabetes mellitus in patients with acrochordons.

Keywords: acrochordons, diabetes mellitus, obesity, skin tags

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Authors: Ines Zemni, Maher Slimane, Jamel Ben Hassouna, Khaled Rahal

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Background: Neurofibromatosis type 1 (NF1) is a genetic disease, which is associated with an increased risk of developing different malignancies including breast cancer. The association between NF1 band breast sarcoma is a rare entity. Herein we present a 25-year-old woman with NF1 who had fibrosarcoma of the left breast. Case presentation: The patient has multiple thoraco-abdominal 'café au lait' spots. Clinical examination showed a lump of the left breast measuring 9 cm of diameter, which was noticed for 6 months. There was a left inguinal mass of 6 cm of diameter. The patient underwent first a left lumpectomy. Histopathological exam revealed a high-grade fibrosarcoma of the left breast measuring 7.5 cm. Three months later, the patient underwent a left mastectomy and excision of the inguinal mass, which was a neurofibroma. An adjuvant chemotherapy and radiation therapy were indicated, but not applied because of the timeout. The patient is now alive after a follow up of 6 years, with no loco-regional recurrence or metastasis. Conclusion: The relationship between NF1 and breast cancer need to be more clarified by further studies. Establishing a specific screening program of these patients may help to make an earlier diagnosis of breast cancer.

Keywords: neurofibromatosis, breast, sarcoma, cancer

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Authors: O. Zlatkin-Troitschanskaia, J. Fischer, C. Lautenbach, H. A. Pant

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In 21st century higher education (HE), the diversity among students has increased in recent years due to the internationalization and higher mobility. Offering and providing equal and fair opportunities based on students’ individual skills and abilities instead of their social or cultural background is one of the major aims of HE. In this context, valid, objective and transparent assessments of students’ preconditions and academic competencies in HE are required. However, as analyses of the current states of research and practice show, a substantial research gap on assessment practices in HE still exists, calling for the development of effective solutions. These demands lead to significant conceptual and methodological challenges. Funded by the German Federal Ministry of Education and Research, the research program 'Modeling and Measuring Competencies in Higher Education – Validation and Methodological Challenges' (KoKoHs) focusses on addressing these challenges in HE assessment practice by modeling and validating objective test instruments. Including 16 cross-university collaborative projects, the German-wide research program contributes to bridging the research gap in current assessment research and practice by concentrating on practical and policy-related challenges of assessment in HE. In this paper, we present a differentiated overview of existing assessments of HE at the national and international level. Based on the state of research, we describe the theoretical and conceptual framework of the KoKoHs Program as well as results of the validation studies, including their key outcomes. More precisely, this includes an insight into more than 40 developed assessments covering a broad range of transparent and objective methods for validly measuring domain-specific and generic knowledge and skills for five major study areas (Economics, Social Science, Teacher Education, Medicine and Psychology). Computer-, video- and simulation-based instruments have been applied and validated to measure over 20,000 students at the beginning, middle and end of their (bachelor and master) studies at more than 300 HE institutions throughout Germany or during their practical training phase, traineeship or occupation. Focussing on the validity of the assessments, all test instruments have been analyzed comprehensively, using a broad range of methods and observing the validity criteria of the Standards for Psychological and Educational Testing developed by the American Educational Research Association, the American Economic Association and the National Council on Measurement. The results of the developed assessments presented in this paper, provide valuable outcomes to predict students’ skills and abilities at the beginning and the end of their studies as well as their learning development and performance. This allows for a differentiated view of the diversity among students. Based on the given research results practical implications and recommendations are formulated. In particular, appropriate and effective learning opportunities for students can be created to support the learning development of students, promote their individual potential and reduce knowledge and skill gaps. Overall, the presented research on competency assessment is highly relevant to national and international HE practice.

Keywords: 21st century skills, academic competencies, innovative assessments, KoKoHs

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Authors: Maryum Nawaz

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Purpose: To determine the frequency of refractive errors in squinting eyes of children from 4 to 16 years presenting at tertiary care hospital. Study Design: A descriptive cross-sectional study was done. Place and Duration: The study was conducted in Pediatric Ophthalmology, Hayatabad Medical Complex, Peshawar. Materials and Methods: The sample size was 146 keeping 41.45%5 proportion of refractive errors in children with squinting eyes, 95% confidence interval and 8% margin of error under WHO sample size calculations. Non-probability consecutive sampling was done. Result: Mean age was 8.57±2.66 years. Male were 89 (61.0%) and female were 57 (39.0%). Refractive error was present in 56 (38.4%) and was not present in 90 (61.6%) of patients. There was no association of gender, age, parent refractive errors, or early usage of electric equipment with the refractive errors. Conclusion: There is a high prevalence of refractive errors in a patient with strabismus. There is no association of age, gender, parent refractive errors, or early usage of electric equipment in the occurrence of refractive errors. Further studies are recommended for confirmation of these.

Keywords: strabismus, refractive error, myopia, hypermetropia, astigmatism

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Authors: Carolinda Douglass

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Institutional Effectiveness (IE) is the purposeful integration of functions that foster student success and support institutional performance. IE is growing rapidly within higher education as it is increasingly viewed by higher education administrators as a beneficial approach for promoting data-informed decision-making in campus-wide strategic planning and execution of strategic initiatives. Specific IE tools, including, but not limited to, project management; impactful collaboration and communication; commitment to continuous quality improvement; and accountability through rigorous evaluation; are gaining momentum under the auspices of IE. This research utilizes a case study approach to examine the use of these IE tools, highlight successes of this use, and identify areas for improvement in the implementation of IE tools within higher education. The research includes three case studies: (1) improving upon academic program review processes including the assessment of student learning outcomes as a core component of program quality; (2) revising an institutional vision, mission, and core values; and (3) successfully navigating an institution-wide re-accreditation process. Several methods of data collection are embedded within the case studies, including surveys, focus groups, interviews, and document analyses. Subjects of these methods include higher education administrators, faculty, and staff. Key findings from the research include areas of success and areas for improvement in the use of IE tools associated with specific case studies as well as aggregated results across case studies. For example, the use of case management proved useful in all of the case studies, while rigorous evaluation did not uniformly provide the value-added that was expected by higher education decision-makers. The use of multiple IE tools was shown to be consistently useful in decision-making when applied with appropriate awareness of and sensitivity to core institutional culture (for example, institutional mission, local environments and communities, disciplinary distinctions, and labor relations). As IE gains a stronger foothold in higher education, leaders in higher education can make judicious use of IE tools to promote better decision-making and secure improved outcomes of strategic planning and the execution of strategic initiatives.

Keywords: accreditation, data-informed decision-making, higher education management, institutional effectiveness tools, institutional mission, program review, strategic planning

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Authors: Kamyar Moradi

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Background: There is mixed evidence regarding the association between recreational cannabinoid use and memory performance. One of the major reasons for the present controversy is different cannabinoid use-related covariates that influence the cognitive status of an individual. Adjustment of these confounding variables provides accurate insight into the real effects of cannabinoid use on memory status. In this study, we sought to investigate the association between recent recreational cannabinoid use and memory performance while correcting the model for other possible covariates such as demographic characteristics and duration, and amount of cannabinoid use. Methods: Cannabinoid users were assigned to two groups based on the results of THC urine drug screen test (THC+ group: n = 110, THC- group: n = 410). THC urine drug screen test has a high sensitivity and specificity in detecting cannabinoid use in the last 3-4 weeks. The memory domain of NIH Toolbox battery and brain MRI volumetric measures were compared between the groups while adjusting for confounding variables. Results: After Benjamini-Hochberg p-value correction, the performance in all of the measured memory outcomes, including vocabulary comprehension, episodic memory, executive function/cognitive flexibility, processing speed, reading skill, working memory, and fluid cognition, were significantly weaker in THC+ group (p values less than 0.05). Also, volume of gray matter, left supramarginal, right precuneus, right inferior/middle temporal, right hippocampus, left entorhinal, and right pars orbitalis regions were significantly smaller in THC+ group. Conclusions: this study provides evidence regarding the acute effect of recreational cannabis use on memory performance. Further studies are warranted to confirm the results.

Keywords: brain MRI, cannabis, memory, recreational use, THC urine test

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to reassess the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high gene support confidence with confidence intervals exceeding 95%, high internode certainty, and high gene concordance factor. The evidence stems from two datasets containing recently deciphered whole genomes of two lungfish species, as well as five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa diminishes the number of orthologues and leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction (LBA) and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: gene support confidence (GSC), origin of land vertebrates, coelacanth, two whole genomes of lungfishes, confidence intervals

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Authors: Narin Salehiyan

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The later sequencing of the complete genomes of Mycoplasma genitalium and M. pneumoniae has pulled in significant consideration to the atomic science of mycoplasmas, the littlest self-replicating living beings. It shows up that we are presently much closer to the objective of defining, in atomic terms, the complete apparatus of a self-replicating cell. Comparative genomics based on comparison of the genomic cosmetics of mycoplasmal genomes with those of other microbes, has opened better approaches of looking at the developmental history of the mycoplasmas. There's presently strong hereditary bolster for the speculation that mycoplasmas have advanced as a department of gram-positive microbes by a handle of reductive advancement. Amid this prepare, the mycoplasmas misplaced significant parcels of their ancestors’ chromosomes but held the qualities basic for life. In this way, the mycoplasmal genomes carry a tall rate of preserved qualities, incredibly encouraging quality comment. The critical genome compaction that happened in mycoplasmas was made conceivable by receiving a parasitic mode of life. The supply of supplements from their has clearly empowered mycoplasmas to lose, amid advancement, the qualities for numerous assimilative forms. Amid their advancement and adjustment to a parasitic mode of life, the mycoplasmas have created different hereditary frameworks giving a profoundly plastic set of variable surface proteins to avoid the have safe framework.

Keywords: mycoplasma, plasma, pathogen, genome

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Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: Alieh Farshbaf, Tayyeb Bahrami

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Introduction: Cc-chemokine receptor-5 (CCR5) is known as a main co-receptor in human immunodeficiency virus type-1 (HIV-1) infection. Many studies showed 32bp deletion (Δ32) in CCR5 gene, provide natural resistance to HIV-1 infection in homozygous individuals. Inducing the resistance mechanism by CCR5 in HIV-1 infected patients eliminated many problems of highly-active-anti retroviral therapy (HAART) drugs like as low safety, side-effects and virus rebounding from latent reservoirs. New treatments solved some restrictions that are based on gene modification and cell therapy. Literature review: The stories of the “Berlin and Boston patients” showed autologous hematopoietic stem cells transplantation (HSCT) could provide effective cure of HIV-1 infected patients. Furthermore, gene modification by zinc finger nuclease (ZFN) demonstrated another successful result again. Despite the other studies for gene therapy by ∆32 genotype, there is another mutation -CCR5 ∆32/m303- that provides HIV-1 resistant. It is a heterozygote genotype for ∆32 and T→A point mutation at nucleotide 303. These results approved the key role of CCR5 gene. Conclusion: Recent studies showed immune gene therapy and cell therapy could provide effective cure for refractory disease like as HIV. Eradication of HIV-1 from immune system was not observed by HAART, because of reloading virus genome from latent reservoirs after stopping them. It is showed that CCR5 could induce natural resistant to HIV-1 infection by the new approaches based on stem cell transplantation and gene modifying.

Keywords: CCR5, HIV-1, stem cell, immune gene therapy, gene modification

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Authors: Jenan Shakoor

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Obesity prevalence is increasing worldwide. University life is a challenging period especially for students who have to leave their familiar surroundings and settle in a new environment. The current study aimed to assess the diet and exercise habits and their association with body mass index (BMI) among nursing college students living at Kirkuk University residence. This was a descriptive study. A non-probability (purposive) sample of 101 students living in Kirkuk University residence was recruited during the period from the 15^th November 2015 to the 5^th May 2016. A questionnaire was constructed for the purpose of the study which consisted of four parts: the demographic characteristics of the study sample, eating habits, eating at college and healthy habits. The data were collected by interviewing the study sample and the weight and height were measured by a trained researcher at the college. Descriptive statistical analysis was undertaken. Data were prepared, organized and entered into the computer file; the Statistical Package for Social Science (SPSS 20) was used for data analysis. A p value≤ 0.05 was accepted as statistical significant. A total of 63 (62.4%) of the sample were aged20-21with a mean age of 22.1 (SD±0.653). A third of the sample 38 (37.6%) were from level four at college, 67 (66.3%) were female and 46 45.5% of participants were from a middle socio-economic status. 14 (13.9%) of the study sample were overweight (BMI =25-29.9kg/m²) and 6 (5.9%) were obese (BMI≥30kg/m²) compared to 73 (72.3%) were of normal weight (BMI =18.5-24.9kg/m²). With regard to eating habits and exercise, 42 (41.6%) of the students rarely ate breakfast, 79 (78.2%) eat lunch at university residence, 77 (78.2%) of the students reported rarely doing exercise and 62 (61.4%) of them were sleeping for less than eight hours. No significant association was found between the variables age, sex, level of college and socio-economic status and BMI, while there was a significant association between eating lunch at university and BMI (p =0.03). No significant association was found between eating habits, healthy habits and BMI. The prevalence of overweight and obesity among the study sample was 19.8% with female students being more obese than males. Further studies are needed to identify BMI among residence students in other colleges and increasing the awareness of undergraduate students to healthy food habits.

Keywords: body mass index, diet, obesity, university residence

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Authors: Ahmed Mohammed Alsalama

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Recommendation systems are widely used in e-commerce applications. The engine of a current recommendation system recommends items to a particular user based on user preferences and previous high ratings. Various recommendation schemes such as collaborative filtering and content-based approaches are used to build a recommendation system. Most of the current recommendation systems were developed to fit a certain domain such as books, articles, and movies. We propose a hybrid framework recommendation system to be applied on two-dimensional spaces (User x Item) with a large number of Users and a small number of Items. Moreover, our proposed framework makes use of both favorite and non-favorite items of a particular user. The proposed framework is built upon the integration of association rules mining and the content-based approach. The results of experiments show that our proposed framework can provide accurate recommendations to users.

Keywords: data mining, association rules, recommendation systems, hybrid systems

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Authors: Wei Tian, Jie Liang, Hammad Naveed

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Beta-barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. They carry out diverse biological functions, including pore formation, membrane anchoring, enzyme activity, and bacterial virulence. In addition, beta-barrel membrane proteins increasingly serve as scaffolds for bacterial surface display and nanopore-based DNA sequencing. Due to difficulties in experimental structure determination, they are sparsely represented in the protein structure databank and computational methods can help to understand their biophysical principles. We have developed a novel computational method to predict the 3D structure of beta-barrel membrane proteins using evolutionary coupling (EC) constraints and a reduced state space. Combined with an empirical potential function, we can successfully predict strand register at > 80% accuracy for a set of 49 non-homologous proteins with known structures. This is a significant improvement from previous results using EC alone (44%) and using empirical potential function alone (73%). Our method is general and can be applied to genome-wide structural prediction.

Keywords: beta-barrel membrane proteins, structure prediction, evolutionary constraints, reduced state space

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Authors: Rofida Gamal, Mostafa Mohammed, Mariam Adel, Marwa Gamal, Marwa kamal, Ayat Saber, Maha Mamdouh, Amira Emad, Mai Ramadan

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Lynch Syndrome is an inherited genetic condition associated with an increased risk of colorectal and other cancers. Detecting Lynch Syndrome in individuals is crucial for early intervention and preventive measures. This study proposes a computational pipeline for Lynch Syndrome detection by integrating alignment, variant calling, and annotation. The pipeline leverages popular tools such as FastQC, Trimmomatic, BWA, bcftools, and ANNOVAR to process the input FASTQ file, perform quality trimming, align reads to the reference genome, call variants, and annotate them. It is believed that the computational pipeline was applied to a dataset of Lynch Syndrome cases, and its performance was evaluated. It is believed that the quality check step ensured the integrity of the sequencing data, while the trimming process is thought to have removed low-quality bases and adaptors. In the alignment step, it is believed that the reads were accurately mapped to the reference genome, and the subsequent variant calling step is believed to have identified potential genetic variants. The annotation step is believed to have provided functional insights into the detected variants, including their effects on known Lynch Syndrome-associated genes. The results obtained from the pipeline revealed Lynch Syndrome-related positions in the genome, providing valuable information for further investigation and clinical decision-making. The pipeline's effectiveness was demonstrated through its ability to streamline the analysis workflow and identify potential genetic markers associated with Lynch Syndrome. It is believed that the computational pipeline presents a comprehensive and efficient approach to Lynch Syndrome detection, contributing to early diagnosis and intervention. The modularity and flexibility of the pipeline are believed to enable customization and adaptation to various datasets and research settings. Further optimization and validation are believed to be necessary to enhance performance and applicability across diverse populations.

Keywords: Lynch Syndrome, computational pipeline, alignment, variant calling, annotation, genetic markers

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Authors: Maurizio E. Picarella, Ludovica Fumelli, Francesca Siligato, Andrea Mazzucato

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Studies on reproductive dynamics in crops subjected to heat stress are crucial to breed more tolerant cultivars. In tomato, cultivars, breeding lines, and wild species have been thoroughly evaluated for the response to heat stress in several studies. Here, we address the reaction to temperature stress in a panel of selected landraces representing genotypes cultivated before the advent of professional varieties that usually show high adaptation to local environments. We adopted an experimental design with two open field trials, where transplanting was spaced by one month. In the second field, plants were thus subjected to mild stress with natural temperature fluctuations. The genotypes showed wide variation for both vegetative (plant height) and reproductive (stigma exsertion, pollen viability, number of flowers per inflorescence, and fruit set) traits. On average, all traits were affected by heat conditions; except for the number of flowers per inflorescence, the “G*E” interaction was always significant. In agreement with studies based on different materials, estimated broad sense heritability was high for plant height, stigma exsertion, and pollen viability and low for the number of flowers per inflorescence and fruit set. Despite the interaction, traits recorded in control and in heat conditions were positively correlated. The first two principal components estimated by multivariate analysis explained more than 50% of the total variability. The study indicated that landraces present a wide variability for the response of reproductive traits to temperature stress and that such variability could be very informative to dissect the traits with higher heritability and identify new QTL useful for breeding more resilient varieties.

Keywords: fruit set, heat stress, solanum lycopersicum L., style exsertion, tomato

Procedia PDF Downloads 101

Authors: Manasse Elusma, Thung-Hong Lin, Chun-yin Lee

Abstract:

The relationship between hunger and war or conflict remains to be discussed. Do wars or conflicts cause hunger and food scarcity, or is the reverse relationship is true? As the world becomes more peaceful and wealthier, some countries are still suffered from hunger and food shortage. So, eradicating hunger calls for a more comprehensive understanding of the relationship between conflict and hunger. Several studies are carried out to detect the importance of conflict or war on food security. Most of these studies, however, perform only descriptive analysis and largely use food security indicators instead of the global hunger index. Few studies have employed cross-country panel data to explicitly analyze the association between conflict and chronic hunger, including hidden hunger. Herein, this study addresses this issue and the knowledge gap. We combine global datasets to build a new panel dataset including 143 countries from 1989 to 2020. This study examines the effect of conflict on hunger with fixed effect models, and the results show that the increase of conflict frequency deteriorates hunger. Peacebuilding efforts and war prevention initiative are required to eradicate global hunger.

Keywords: armed conflict, food scarcity, hidden hunger, hunger, malnutrition

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Authors: Samarpreet Singh, Gerald Giesbrecht

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Both c-section and antibiotic exposure are linked to gut microbiota imbalance in infants. Such disturbance is associated with the Hypothalamic-Pituitary-Adrenal (HPA) axis function. However, the literature only has contradicting evidence for the association between c-sections and the HPA axis. Therefore, this study aims to test if the mode of delivery and antibiotics exposure is associated with the HPA axis. Also, whether exposure to both interacts with the HPA-axis. It was hypothesized that associations and interactions would be observed. Secondary data analysis was used for this co-relational study. Data for the mode of delivery and antibiotics exposure variables were documented from hospital records or self-questionnaires. In addition, cortisol levels (Area under the curve with respect to increasing (AUCi) and Area under the curve with respect to ground (AUCg)) were based on saliva collected from three months old during the infant’s visit to the lab and after drawing blood. One-way and between-subject ANOVA analyses were run on data. No significant association between delivery mode and infant cortisol level was found, AUCi and AUCg, p > .05. Only the infant’s AUCg was found to be significantly higher if there were antibiotics exposure at delivery (p = .001) or their mothers were exposed during pregnancy (p < .05). Infants born by c-section and exposed to antibiotics at three months had higher AUCi than those born vaginally, p < .02. These results imply that antibiotic exposure before three months is associated with an infant’s stress response. The association might increase if antibiotic exposure occurs three months after a c-section birth. However, more robust and causal evidence in future studies is needed, given a variable group’s statistically weak sample size. Nevertheless, the results of this study still highlight the unintended consequences of antibiotic exposure during delivery and pregnancy.

Keywords: HPA-axis, antibiotics, c-section, gut-microbiota, development, stress

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Authors: Parag Katira, Frederika Rentzeperis, Zuzanna Nowicka, Giada Fiandaca, Thomas Veith, Jack Farinhas, Noemi Andor

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Resource limitations shape the outcome of competitions between genetically heterogeneous pre-malignant cells. One example of such heterogeneity is in the ploidy (DNA content) of pre-malignant cells. A whole-genome duplication (WGD) transforms a diploid cell into a tetraploid one and has been detected in 28-56% of human cancers. If a tetraploid subclone expands, it consistently does so early in tumor evolution, when cell density is still low, and competition for nutrients is comparatively weak – an observation confirmed for several tumor types. WGD+ cells need more resources to synthesize increasing amounts of DNA, RNA, and proteins. To quantify resource limitations and how they relate to ploidy, we performed a PAN cancer analysis of WGD, PET/CT, and MRI scans. Segmentation of >20 different organs from >900 PET/CT scans were performed with MOOSE. We observed a strong correlation between organ-wide population-average estimates of Oxygen and the average ploidy of cancers growing in the respective organ (Pearson R = 0.66; P= 0.001). In-vitro experiments using near-diploid and near-tetraploid lineages derived from a breast cancer cell line supported the hypothesis that DNA content influences Glucose- and Oxygen-dependent proliferation-, death- and migration rates. To model how subpopulations with variable DNA content compete in the resource-limited environment of the human brain, we developed a stochastic state-space model of the brain (S3MB). The model discretizes the brain into voxels, whereby the state of each voxel is defined by 8+ variables that are updated over time: stiffness, Oxygen, phosphate, glucose, vasculature, dead cells, migrating cells and proliferating cells of various DNA content, and treat conditions such as radiotherapy and chemotherapy. Well-established Fokker-Planck partial differential equations govern the distribution of resources and cells across voxels. We applied S3MB on sequencing and imaging data obtained from a primary GBM patient. We performed whole genome sequencing (WGS) of four surgical specimens collected during the 1ˢᵗ and 2ⁿᵈ surgeries of the GBM and used HATCHET to quantify its clonal composition and how it changes between the two surgeries. HATCHET identified two aneuploid subpopulations of ploidy 1.98 and 2.29, respectively. The low-ploidy clone was dominant at the time of the first surgery and became even more dominant upon recurrence. MRI images were available before and after each surgery and registered to MNI space. The S3MB domain was initiated from 4mm³ voxels of the MNI space. T1 post and T2 flair scan acquired after the 1ˢᵗ surgery informed tumor cell densities per voxel. Magnetic Resonance Elastography scans and PET/CT scans informed stiffness and Glucose access per voxel. We performed a parameter search to recapitulate the GBM’s tumor cell density and ploidy composition before the 2ⁿᵈ surgery. Results suggest that the high-ploidy subpopulation had a higher Glucose-dependent proliferation rate (0.70 vs. 0.49), but a lower Glucose-dependent death rate (0.47 vs. 1.42). These differences resulted in spatial differences in the distribution of the two subpopulations. Our results contribute to a better understanding of how genomics and microenvironments interact to shape cell fate decisions and could help pave the way to therapeutic strategies that mimic prognostically favorable environments.

Keywords: tumor evolution, intra-tumor heterogeneity, whole-genome doubling, mathematical modeling

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Authors: Omneya M. Helmy, Mona T. Kashef

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Aminoglycosides are used in treating a wide range of infections caused by both Gram-negative and Gram positive bacteria. The presence of 16S rRNA methyl transferases (16S-RMTase) is among the newly discovered resistance mechanisms that confer high resistance to clinically useful aminoglycosides. Cephalosporins are the most commonly used antimicrobials in Egypt; therefore, this study was conducted to determine the isolation frequency of 16S rRNA methyl transferases among third generation cephalosporin-resistant clinical isolates in Egypt. One hundred and twenty three cephalosporin resistant Gram-negative clinical isolates were screened for aminoglycoside resistance by the Kirby Bauer disk diffusion method and tested for possible production of 16S-RMTase. PCR testing and sequencing were used to confirm the presence of 16S-RMTase and the associated antimicrobial resistance determinants, as well as the genetic region surrounding the armA gene. Out of 123 isolates, 66 (53.66%) were resistant to at least one aminoglycoside antibiotic. Only one Escherichia coli isolate (E9ECMO) which was totally resistant to all tested aminoglycosides, was confirmed to have the armA gene in association with blaTEM-1, blaCTX-M-15, blaCTX-M-14 and aac(6)-Ib genes. The armA gene was found to be carried on a large A/C plasmid. Genetic mapping of the armA surrounding region revealed, for the first time, the association of armA with aac(6)-Ib on the same transposon. In Conclusion, the isolation frequency of 16S-RMTase was low among the tested cephalosporin-resistant clinical samples. However, a novel composite transposon has been detected conferring high-level aminoglycosides resistance.

Keywords: aminoglcosides, armA gene, β lactmases, 16S rRNA methyl transferases

Procedia PDF Downloads 259

Authors: Chu Wai Ching, Kan Chi Wai

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Fashion industry is fast moving with intense competitions; it is hard for fashion retailers to stand out among their peers. In order to promote and enhance uniqueness, fashion retailers have collaborated with different brands or celebrity in their marketing campaign recently. As brand-celebrity collaboration is a growing phenomenon in the Hong Kong fashion industry, this research aims to investigate the effect of celebrity on altering consumer’s brand association and the overall attitude towards the co-branded products. One of the popular celebrity-collaborated fashion brands was chosen for this study and a survey was conducted among university students in Hong Kong which yielded 222 responses. By using factor analysis, linear regression and bootstrap test for the mediation, the results show that three celebrity attributes namely “expertise”, “trustworthiness” and “attractiveness” affect the evaluation of the co-branded products. In addition, the change in the association of the brand and co-branded product attributes mediates the relationship between the characteristics of the celebrity and the overall attitude of the co-branded product. The result shows “expertise” of the celebrity has a perfect mediation, while “trustworthiness” and “attractiveness” of the celebrity have partial mediation. This implies that expertise of the celebrity is capable in altering the association towards both the brand and core product attributes and bringing a positive attitude towards the co-brand. The trustworthiness and the attractiveness of the celebrity are able to alter the consumer association towards the brand, but do not guarantee a complete positive attitude towards the co-branded product. This means that change in brand attributes is not a definite mediator as direct relationship may happen or there may be other factors that can affect the relationship between the celebrity’s persuasiveness and the overall attitude towards the co-branded collection.

Keywords: brand attribute, brand-celebrity collaborations, co-branding, fashion industry

Procedia PDF Downloads 300

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

Procedia PDF Downloads 308

Authors: K. Doi, T. Nishimura, H. Fujimoto, Y. Hoshikawa, T. Wada

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Japanese industrial standard (JIS) association established one JIS (JIS S 0021) regarding packaging accessible design for people with visual impairments and elderly people in 2000. Recently, tactile symbol on shampoo bottle has been known as one of package accessible design and more effectively used. However, it has been said that people with visual impairment have been not been in trouble with difficulty of identifying body soap bottle between three bottles such as body soap bottle, shampoo bottle, and conditioner bottle. Japanese low vision association asked JIS association to solve this problem. JIS association and Japan cosmetic industry association constituted one review team for solving the problem. The review team asked our research team to make a proposal regarding new tactile symbol on body soap bottle. We conducted user survey and maker survey regarding tactile symbol on body soap bottle with easily identification. Seven test tactile symbol marks were elected in our proposed tactile symbols. In this study, we evaluate easily identification of tactile symbol on body soap bottle. Six visual impaired subjects were participated in our experiment. These subjects were asked to identify body soap bottle between three bottles such as body soap bottle, shampoo bottle, and conditioner bottle. The test tactile symbol on body soap were presented in random order. The test tactile symbols were produced by use of our originally developed 3D raised equipment. From our study, test tactile symbol marks with easily identification were made a short list of our proposed tactile symbols. This knowledge will be helpful in revision of ISO 11156.

Keywords: tactile symbol, easily identification, body soap, people with visual impairments

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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: 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

Procedia PDF Downloads 139

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: 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

Procedia PDF Downloads 88