Search results for: genome wide association studies

Authors: Xuechen Chen

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The EU-ASEAN relations which can be dated back to 1972 represents one of the oldest group-to-group relationship in international politics. Despite a longstanding dialogue partnership, the EU and ASEAN have long been reluctant to forge deeper and substantial cooperation in political and security domains. However, the year of 2012 witnessed a salient shift in EU-ASEAN relations, with the EU significantly elevating ASEAN's profile in its external relations. Given the limited scholarly attention that has been devoted to this change in ASEAN-EU relations, this article explores why there has been a greater level of engagement and approximation between the EU and ASEAN. In particular, it asks why the EU, which had long been reluctant to recognize ASEAN as a strategic partner, has changed its policy towards ASEAN. Drawing on social constructivism, this article argues that the EU’s and ASEAN’s evolving identity-formation processes have played a significant role in reshaping their mutual perceptions, which subsequently leads to the modification of the interregional policies of both actors. The methodology of this study is based on content analysis of a wide range of official documents and policy papers from the EU and ASEAN, as well as more than 20 in-depth elite interviews with diplomats and experts working on the EU-ASEAN relationship from both organisations. Departing from the existing works which mainly adopt a Eurocentric perspective when analysing the EU-ASEAN interregionalism, this study suggests that the approximation of the EU-ASEAN relationship between 2012 and 2017 is driven by both actors’ adjustment of international identities, together with the internal dynamics and systematic changes within both regions.

Keywords: Association of Southeast Asia Nations, European Union, EU foreign policy, interregionalism

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Authors: Qi Peng

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The Chinese sport sector is currently undergoing a dramatic institutional change. A sport system that was heavily dominated by the government is starting to shift towards one that is driven by the market. During the past sixty years, the Chinese Football Association (CFA), although ostensibly a ‘non-governmental organization’, has been in fact operated under the close supervision and control of the government. The double-identity of CFA has taken most of the blame for the poor performance of the Chinese football team, especially the men’s team. In 2015, a policy initiated by the Chinese government introduced a potentially radical change to the institutional structure of CFA by delegating the power of government agency – the General Administration of Sport of China - to the organization (CFA) itself. Against such background, an overarching research question was brought up- will an organization remained institutionalized within the system change in response to the external (policy) jolt? To answer this question, three principal data collection methods were employed: document review, participant observation and semi-structured interviews. Document review provides the mapping of the structural and cultural framework in which the CFA functions during the change process. The author have had the chance to interact closely with the organization as participant observer in the organization for a period of time, long enough to collect the data, but never too long to get biased view of the situation. This stage enables the author to gain an in-depth understanding of how CFA managed to restructure the governance and legitimacy. Conducting semi-structured interviews with staff within the CFA and from staff within selected stakeholders of CFA also provided a crucial step to gain an insight into the factors for change as well as the implications of the change. A wide range of interviewees that have been and to be interviewed include: CFA members (senior officials and staff); local football associations members; senior Chinese Super League football club managers; CFA Super League Co., LTD (senior officials and staff); CSL broadcasters; Chinese Olympic Committee members. The preliminary research data shows that the CFA is currently undergoing two levels of change: although the settings of CFA has been gradually restructured (organizational framework), the organizational values and beliefs remain almost the same as the CFA before the reform. This means that the plan of shifting from a governmental agency to an autonomous association is an going process, and that organizational core beliefs and values are more difficult to change than its structural framework. This is due to the inertia of the organizational history and the effect of institutionalization. The change of Chinese Football Association is looked at as a pioneering sport organization in China to undertake the “decoupling” road. It is believed that many other sport organizations, especially sport governing bodies will follow the step of CFA in the near future. Therefore, the experience of CFA change is worthy of studying.

Keywords: Chinese Football Association, Organizational Change, Organizational Culture, Structural Framework

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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: Mohammed Al-Shalabi, Alaa Obeidat

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In any food stores, some items will be expired or destroyed because the demand on these items is infrequent, so we need a system that can help the decision maker to make an offer on such items to improve the demand on the items by putting them with some other frequent item and decrease the price to avoid losses. The system generates hundreds or thousands of patterns (offers) for each low demand item, then it uses the association rules (support, confidence) to find the interesting patterns (the best offer to achieve the lowest losses). In this paper, we propose a data mining method for determining the best offer by merging the data mining techniques with the e-commerce strategy. The task is to build a model to predict the best offer. The goal is to maximize the profits of a store and avoid the loss of products. The idea in this paper is the using of the association rules in marketing with a combination with e-commerce.

Keywords: data mining, association rules, confidence, online stores

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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: 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: 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: 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: Soojin Kim, Yongjae Kim

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Continuous economic downturn and ongoing budget cuts poses higher education with profound challenges which has a direct impact on the collegiate athletic programs. In response to the ever-changing landscape of the fiscal environment, universities seek to boost revenues, resorting to alternative sources of funding. In particular, athletic programs have become increasingly dependent on financial support from their alumni and boosters, which is how athletic departments attempt to offset budget shortfalls and make capital improvements. Although there currently exists three major divisions within National Collegiate Athletic Association (NCAA), the majority of the sport management studies on college sport tend to focus on Division I level. Particularly within the donor motivation literature, a plethora of donor motivation studies exist, but mainly on NCAA Division I athletic programs. Since each athletic department functions differently in a number of different dimensions, while institutional difference can also have a huge impact on athletic donor motivations, the current study attempts to fill this gap that exists in the literature. As such, the purpose of this study was to (I) reexamine the factor structure of the Athletic Donor motivation scale; and (II) identify the prominent athletic donor motives in a NCAA Division II athletic program. For the purpose of this study, a total of 232 actual donors were used for analysis. A confirmatory factor analysis (CFA) was employed to test construct validity, and the reliability of the scale was assessed using Composite Reliability. To identify the prominent motivational factors, the means and standard deviations were examined. Results of this study indicated that Vicarious Achievement, Philanthropy, and Commitment are the three primary motivational factors, while Tangible Benefits, was consistently found as an important motive in prior studies was found low. Such findings highlight the key difference and suggest different salient motivations exist that are specific to the context.

Keywords: college athletics, donor, motivation, NCAA

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Authors: Vito Telesca, Giuseppina A. Giorgio

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The earth system is subject to a wide range of human activities that have changed the ecosystem more rapidly and extensively in the last five decades. These global changes have a large impact on human health. The relationship between extreme weather events and mortality are widely documented in different studies. In particular, a number of studies have investigated the relationship between climatological variations and the cardiovascular and respiratory system. The researchers have become interested in the evaluation of the effect of environmental variations on the occurrence of different diseases (such as infarction, ischemic heart disease, asthma, respiratory problems, etc.) and mortality. Among changes in weather conditions, the heat waves have been used for investigating the association between weather conditions and cardiovascular events and cerebrovascular, using thermal indices, which combine air temperature, relative humidity, and wind speed. The effects of heat waves on human health are mainly found in the urban areas and they are aggravated by the presence of atmospheric pollution. The consequences of these changes for human health are of growing concern. In particular, meteorological conditions are one of the environmental aspects because cardiovascular diseases are more common among the elderly population, and such people are more sensitive to weather changes. In addition, heat waves, or extreme heat events, are predicted to increase in frequency, intensity, and duration with climate change. In this context, are very important public health and climate change connections increasingly being recognized by the medical research, because these might help in informing the public at large. Policy experts claim that a growing awareness of the relationships of public health and climate change could be a key in breaking through political logjams impeding action on mitigation and adaptation. The aims of this study are to investigate about the importance of interactions between weather variables and your effects on human health, focusing on Italy. Also highlighting the need to define strategies and practical actions of monitoring, adaptation and mitigation of the phenomenon.

Keywords: climate change, illness, Italy, temperature, weather

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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: 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: 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: 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: 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: 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: 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: Asif Mahmood, Shama Shama, Hao Ni, Hao Wang, Yu Ling, Hui Xu, Shixing Yang, Qais Ahmad Naseer, Wen Zhang

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Cardiovirus is a genus of viruses belonging to the family Picornaviridae. Here, we used viral metagenomic techniques to detect the viral nucleic acid in the fecal samples from wild rats in Zhenjiang city in China. Fecal samples were collected from 20 wild rats and pooled into four sample pools and then subjected to libraries construction which were then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline. A novel cardiovirus from feces of a wild rat was identified, named amzj-2018, of which the complete genome was acquired. Phylogenetic analysis based on the complete amino acid sequence of polyprotein revealed that amzj-2018 formed a separate branch located between clusters of Saffold virus and Rat Theilovirus 1 (RTV-1). Phylogenetic analysis based on different regions of the polyproteins, including P1, P2, P3, and P2+P3, respectively, showed discordant trees, where the tree based on P3 region indicated that amzj-2018 clustered separately between Theiler's murine encephalomyelitis virus and RTV-1. The complete genome of a cardiovirus was determined from the feces of wild rats which belonged to a novel type of cardiovirus based on phylogenetic analysis. Whether it is associated with disease needs further investigation.

Keywords: cardiovirus, viral metagenomics, genomic organization, phylogenetic analysis

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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: 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: 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: 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: 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

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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

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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

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

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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

Procedia PDF Downloads 172