Search results for: genome wide association studies (GWAS)

Authors: Preeti Nakhat

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Background: Values are essential part of one's life. They are inculcated since the early years of life and shape the personality of the individual. They play a tremendous role in decision making. Teenagers are seen perplexed about the values of their life. The challenge faced by majority of the teenage population in choosing between a positive and negative value is high. The values they adopt remain throughout their life and in every decision, hence it is a crucial topic of research. Research Methodology: This research aimed at finding out the value conflict of teenagers in relations. Hypothesis of the study are: H₀- There is no significant association between the life values and value conflict of higher secondary students; H₁– There is a significant association between the life values and value conflict of higher secondary students. For the same, the standardized tool, value conflict scale by R. L. Bhardwaj has been used. The tool consists 24 questions of different life situations with multiple choice options. Findings: There is 96% variation in value conflict due to evasion vs. fortitude, dependence vs. self-reliance, selfishness vs. probity, hate vs. love, fear vs. assertion and pragmatism vs. idealism life values. There is a positive association between all the life values and value conflict of higher secondary school students. Percentages of association are: 0.17% between value conflict and evasion vs. fortitude value, 0.16% between value conflict and dependence vs. self-reliance value, 0.17% between value conflict and selfishness vs. probity value, 0.16% between value conflict and hate vs. love value, 0.17% between value conflict and fear vs. assertion, 0.17% between value conflict and pragmatism vs. idealism value. Discussions: The dilemma faced by the students regarding value conflict is high. Bewilderment of being honest or lying, of loving or hating family and friends, being pragmatic or idealistic in life decision, being selfish or selfless is seen among the students. It is the challenge for the future. Teaching of values with a practical aspect should be added in the school curriculum.

Keywords: dilemma, conflict, school, values

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Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: Faisal Nouroz, Mukaramin Mukaramin

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Of the transposable elements (TEs), the retrotransposons are the most copious elements identified from many sequenced genomes. They have played a major role in genome evolution, rearrangement, and expansions based on their copy and paste mode of proliferation. They are further divided into LTR and Non-LTR retrotransposons. The purpose of the current study was to identify the LTR REs in sequenced Phoenix dactylifera genome and to study their structural diversity. A total of 150 P. dactylifera BAC sequences with > 60kb sizes were randomly retrieved from National Center for Biotechnology Information (NCBI) database and screened for the presence of LTR retrotransposons. Seven bacterial artificial chromosomes (BAC) sequences showed full-length LTR Retrotransposons with 4 Copia and 3 Gypsy families having variable copy numbers in respective families. Reverse transcriptase (RT) domain was found as the most conserved domain among Copia and Gypsy superfamilies and was used to deduce evolutionary analysis. The amino acid residues among various RT sequences showed variability in their percentages indicating post divergence evolution. Amino acid Leucine was found in highest proportions followed by Lysine, while Methionine and Tryptophan were in lowest percentages. The phylogenetic analysis based on RT domains confirmed that although having most conserved RT regions, several evolutionary events occurred causing nucleotide polymorphisms and hence clustering of Gypsy and Copia superfamilies into their respective lineages. The study will be helpful in identification and annotation of these elements in other species and genera and their distribution patterns on chromosomes by fluorescent in situ hybridization techniques.

Keywords: transposable elements, Phoenix dactylifera, retrotransposons, phylogenetic analysis

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Authors: Yu Chen Su

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Introduction: Gestational diabetes mellitus (GDM) refers to impaired glucose tolerance in pregnant women, impacting both the mother and newborn with short and long-term effects. It increases risks of preeclampsia, hypertension, type 2 diabetes, cesarean section, and preterm birth. GDM is associated with fetal macrosomia, shoulder dystocia, neonatal hypoglycemia, and future type 2 diabetes risk. A study on 6,421 pregnant women found 12% experienced high stress, linked to maladaptive coping and depressive emotions. Women with high-risk pregnancies may experience greater stress and depression. Research suggests GDM increases depression prevalence. A study on 632 Hispanic women with GDM showed severe stress and depression tendencies. Involving 95 women with GDM, 33.4% exhibited depression symptoms. Another study compared 180 GDM women to 186 with normal glucose levels, revealing higher depression levels in GDM women. They found GDM women were 1.85 times more likely to receive antidepressants during pregnancy and 1.69 times more likely to experience postpartum depression. Maternal stress and depressive symptoms during pregnancy are significant factors. Early identification by healthcare professionals can greatly benefit GDM women, their infants, and their families. Objectives: The purpose of this study was to investigate the association between gestational diabetes mellitus (GDM) and the risk of depression. Methods: This study reviewed and analyzed relevant literature on gestational diabetes mellitus (GDM) and depression in 6,876 patients. The literature search followed PRISMA guidelines and included databases like Embase, PubMed, MEDLINE, CINAHL, and Cochrane Library. Prospective or retrospective studies with relevant risk ratios and estimates were included, using a random-effects model for the analysis of depression risk correlation. Studies without depression data or relevant risks were excluded. The search period extended until October 2022. Results: Systematic review of 7 studies (6,876 participants) found a significant association (OR = 8.77, CI: 7.98-9.64, p < 0.05) between gestational diabetes mellitus (GDM) and higher depression risk compared to healthy pregnant women. Conclusions: Pregnancy is a significant life transition involving physiological, psychological, and social changes. Gestational diabetes poses challenges to women's physical and mental well-being. Sensitive healthcare professionals identifying issues early can greatly benefit women, babies, and the family.

Keywords: gestational diabetes, depression, systematic review, neta-analysis

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Authors: Sihao Lin

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Objectives: Infrared thermography (IRT) has been little documented in the objective measurement of ergonomic exposure. We aimed to examine the association between different ergonomic exposures and low back skin temperature measured by IRT. Methods: A total of 114 subjects among sedentary students, sports students and cleaning workers were selected as different ergonomic exposure levels. Low back skin temperature was measured by infrared thermography before and post ergonomic exposure. Ergonomic exposure was assessed by Quick Exposure Check (QEC) and quantitative scores were calculated on the low back. Multiple regressions were constructed to examine the possible associations between ergonomic risk exposures and the skin temperature over the low back. Results: Compared to the two student groups, clean workers had significantly higher ergonomic exposure scores on the low back. The low back temperature variations were different among the three groups. The temperature decreased significantly among students with ergonomic exposure (P < 0.01), while it increased among cleaning workers. With adjustment of confounding, the post-exposure temperature and the temperature changes after exposure showed a significantly negative association with ergonomic exposure scores. For maximum temperature, one increasing ergonomic score decreased -0.23◦C (95% CI -0.37, -0.10) of temperature after ergonomic exposure over the low back. Conclusion: There was a significant association between ergonomic exposures and infrared thermal temperature over low back. IRT could be used as an objective assessment of ergonomic exposure on the low back.

Keywords: ergonomic exposure, infrared thermography, musculoskeletal disorders, skin temperature, low back

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Authors: Mushtaq Ahmad, Bashir Rahman, Taqweem-ul-Haq, Fazal Jalil, Aftab Ali Shah

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Single nucleotide polymorphisms (SNPs) in genes coding for microRNAs (miRNAs) play a pivotal role in the progression of breast cancer (BC). We investigated the association of miR-146a rs2910164 G/C polymorphism with the risk of BC in the Pakistani population. The miR-146a rs2910164 polymorphism was genotyped in 300 BC-cases and 300 age- and gender-matched healthy controls using T-ARMS-PCR. Genotype and allele frequencies were calculated, and the association between genotypes and the risk of BC was calculated by odds ratios (OR) and confidence intervals (95%). A significant difference in genotypic frequencies (χ2=63.10; p ≤ 0.0001) and allelic frequencies (OR=0.3955 (0.3132-0.4993); p ≤ 0.0001) was observed between cases and controls. Furthermore, we also found that miR-146 rs2910164 CC homozygote increased the risk of breast cancer in the dominant (OR=0.2397 (0.1629-0.3526); p=0.0001; GG vs GC+CC) and recessive (OR=2.803 (1.865- 4.213); P ≤ 0.0001; CC vs GC+GG) inheritance models. In summary, miR-146a rs2910164 G/C is significantly associated with BC in the Pakistani population. To our knowledge, this is the first study that assessed MIR146a rs2910164 G > C SNP in Pakistani population. By analyzing the secondary structure of MIR146A variant, a significant structural modification was noted. Study with a larger sample size is needed to further confirm these findings.

Keywords: breast cancer, MIR146A, microRNA, SNP

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Authors: Nandini Mohan, Elayne Ahern

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Neurocognitive deficits, as well as psychosocial dysfunction, are typically observed in major depressive disorder (MDD). These deficits persist even after a significant reduction of symptoms and remission from MDD. These deficits have also been linked to greater relapse rates. The link between neurocognitive deficits, relapse, and psychosocial functioning in MDD, on the other hand, has received little attention. This review aimed to conduct an in-depth review of the literature on the association between neurocognitive deficits, relapse, and psychosocial functioning in MDD remission. We used search terms related to MDD, MDD remission, psychosocial functioning, neurocognitive impairments, and relapse to conduct a systematic review of English-language literature in PubMed, PsycArticles, PsycINFO, Medline, and Web of Science to identify relevant studies in the area from which 15 studies were identified for inclusion following an examination against inclusion/ exclusion criteria. Executive functioning, psychomotor speed, and memory were closely related to the psychosocial deficits in the phase of MDD remission. Similarly, Executive function, divided attention, and inhibition were closely related to the relapse in the phase of MDD remission. The limitations of the present review include limited and contradicting evidence that led to fewer studies being included. The implications of this review include an understanding of the difference between clinical and full-functional recovery. This evidence can be the basis for incorporating treatment measures that focus on neurocognitive and psychosocial deficits along with the affective symptoms of MDD.

Keywords: depression, MDD, remission, relapse, neurocognitive functioning, psychosocial deficits

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Authors: Suzan Wedyan

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Data mining is one of the main phases in the Knowledge Discovery Database (KDD) which is responsible of finding hidden and useful knowledge from databases. There are many different tasks for data mining including regression, pattern recognition, clustering, classification, and association rule. In recent years a promising data mining approach called associative classification (AC) has been proposed, AC integrates classification and association rule discovery to build classification models (classifiers). This paper surveys and critically compares several AC algorithms with reference of the different procedures are used in each algorithm, such as rule learning, rule sorting, rule pruning, classifier building, and class allocation for test cases.

Keywords: associative classification, classification, data mining, learning, rule ranking, rule pruning, prediction

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Authors: Teresa Smith, Farrah Jacquez

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Health-risk behaviors (e.g., smoking, poor diet) directly increase the risk for chronic disease and morbidity. There is substantial evidence of a negative association between socioeconomic status (SES) and engagement in health-risk behaviors. However, due to the complexity of SES, researchers have suggested looking beyond this factor to fully understand the mechanisms that underlie engagement in health-risk behaviors. Stress is one plausible mechanism through which SES impacts health-risk behaviors. Currently, it remains unclear how stress occurring across the life course might impact health behaviors and explain the association between SES and these behaviors. To address the gaps in the literature, 172 adults between the ages of 18-49 were surveyed about their lifetime stress exposure, sociodemographic variables, and health-risk behaviors via an online recruitment portal, Prolific. Five major findings emerged from the current study. First, SES was negatively associated with engagement in health-risk behaviors and lifetime stress above and beyond current stress and other relevant demographics. Second, lifetime stress was significantly associated with health-risk behaviors above and beyond current stress and relevant demographic variables. Third, lifetime stress fully mediated the association between SES and health-risk behaviors above and beyond current stress and other demographics. Fourth, the severity of stress experienced emerged as the most significant lifetime stress variable that explains the relation between SES and health-risk behaviors. Fifth and finally, lower SES and experiencing financial and legal/crime stressors increased the likelihood of engaging in health-risk behaviors. The current study results align with previous research and suggest that stress occurring over the lifespan impacts the relation between SES and health-risk behaviors, which are in turn known to impact health outcomes. However, our findings move the current literature forward by providing a more nuanced understanding of the specific aspects of stress that influence this association. Specifically, the severity of stress experienced across the entire lifespan was the most important aspect of stress when examining the association between SES and health-risk behaviors. Further, individuals most at risk for engaging in health-risk behaviors are those of the lowest SES and experience financial and legal/crime stressors. These findings have the potential to inform interventions and policies aimed at addressing health-risk behaviors by providing a more sophisticated understanding of the impact of stress.

Keywords: stress, health behaviors, socioeconomic status, health

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Authors: Irina S. Burashnikova, Dmitriy A. Sychev, Ruslan Y. Kazakov

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Сytochrome P450 CYP2D6 activity affects antipsychotic therapy safety. CYP2D6*4 polymorphism frequency varies among different ethnic groups. We studied CYP2D6*4 polymorphism frequency in Tatar and Russian schizophrenic patients and association of CYP2D6*4 polymorphism and extrapyramidal disorders (EPD) frequency in schizophrenic patients on haloperidol monotherapy in daily doses up to 20 mg. Results: Heterozygous CYP2D6*4 allele carrier frequency among Tatars was lower (23.8% vs 32.4% in Russians), but the differences did not reach statistical significance. CYP2D6*4 allele frequency among Tatars was also lower (11.9% vs 24.3% in Russians), but the difference was not quite significant (p=0.0592). Average daily haloperidol dose in the group without EPD was significantly higher than in the group with EPD (11.35±4.6 vs 13.87±3.3 mg, p=0.0252), but average daily haloperidol dose/weight ratios in the compared groups had no significant differences. Statistically significant association between EPD development and heterozygous CYP2D6*1/*4 genotype and CYP2D6*4 allele carrier frequency was revealed among all schizophrenic patients and among those of Tatar nationality. Further well designed pharmacogenetic studies in different Russian regions are needed to improve psychotropic therapy safety and to establish evidence-based indications for pharmacogenetic testing in clinical practice.

Keywords: antipsychotic, CYP2D6 polymorphism, ethnic differences of CYP2D6*4 allele frequency, extrapyramidal side effects/disorder, schizophrenia, pharmacogenetics, Russians, Tatars

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Authors: Pritam Kitey

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Platelets play a key role in the development of atherothrombosis, a major contributor of cardiovascular evevts. The contributor of platelets to cardiovascular events has been noted for decades. Mean paltelets volume [MPV] is a marker of platelets size that is easily determined on routine automated haemograms and routinely available at low cost. Subjects with higher MPV have larger platelets that are metabolically and enzamatically more active and have greater prothombotic potential than smaller platelets. In fact several studies have demonstrated a significant association between higher MPV and an increased incidence of cerebrovascular events and all-cause mortality.

Keywords: mean paltelets volume (MPV), platelets, cerebrovascular stroke, cardiovascular events

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Authors: Sabika Rafiq, Rubaida Mehmood, Sajid Hussain, Atia Iqbal

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Background and objectives: The pathogenesis of liver function abnormalities and cardiac dysfunction in hyperthyroid patients after I131 treatment is still unclear. This study aimed to determine the effects of radioiodine I131 on liver function parameters, lactate dehydrogenase (LDH) and low-density lipoproteins (LDL) before and after I131 therapy hyperthyroidism patients. Material & Methods: A total of 52 patients of hyperthyroidism recommended for I131were involved in this study with ages ranging from 12–65 years (mean age=38.6±14.8 & BMI=11.5±3.7). The significance of the differences between the results of 1st, 2nd and 3rd-time serum analysis was assessed by unpaired student’s t-test. Associations between the parameters were assessed by Spearman correlation analysis. Results: Significant variations were observed for thyroid profile free FT3 (p=0.04), FT4 (p=0.01), TSH (p=0.005) during the follow-up treatment. Before taking I131 (serum analyzed at 1st time), negative correlation of FT3 with AST (r=-0.458, p=0.032) and LDL (r=-0.454, p=0.039) were observed. During 2nd time (after stopping carbimazole), no correlation was assessed. Two months after the administration of I131 drops, a significant negative association of FT3 (r=-0.62, p=0.04) and FT4(r=-0.61, p=0.02) with ALB were observed. FT3(r=-0.82, p=0.00) & FT4 (r=-0.71, p=0.00) also showed negative correlation with LDL after I131 therapy. Whereas TSH showed significant positive association with ALB (r=0.61, p=0.01) and LDL (r=0.70, p=0.00) respectively. Conclusion: Current findings suggested that the association of TFTs with biochemical parameters in patients with goiter recommended for iodine therapy is an important diagnostic and therapeutic tool. The significant changes increased in transaminases and low-density lipoprotein levels after taking I131drops are alarming signs for heart and liver function abnormalities and warrant physicians' attention on an urgent basis.

Keywords: hyperthyroidism, carbimazole, radioiodine I131, liver functions, low-density lipoprotein

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Authors: Hui Li, Xueying Zhao, Ke Ma, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

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Soil can often link a person or item to a crime scene, which makes it a valuable evidence in forensic casework. Several techniques have been utilized in forensic soil discrimination in previous studies. Because soil contains a vast number of microbiomes, the analyse of soil microbiomes is expected to be a potential way to characterise soil evidence. In this study, we applied massively parallel sequencing (MPS) to soil bacterial profiling on the Ion Torrent Personal Genome Machine (PGM). Soils from different regions were collected repeatedly. V-region 3 and 4 of Bacterial 16S rRNA gene were detected by MPS. Operational taxonomic units (OTU, 97%) were used to analyse soil bacteria. Several bioinformatics methods (PCoA, NMDS, Metastats, LEfse, and Heatmap) were applied in bacterial profiles. Our results demonstrate that MPS can provide a more detailed picture of the soil microbiomes and the composition of soil bacterial components from different region was individualistic. In conclusion, the utility of soil bacterial profiling via MPS of the 16S rRNA gene has potential value in characterising soil evidences and associating them with their place of origin, which can play an important role in forensic science in the future.

Keywords: bacterial profiling, forensic, massively parallel sequencing, soil evidence

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Authors: Fetah Eren, Ismail Sahin, Ismail Celik, Ahmet Oguz Akturk

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The aim of this study is to discover secondary school students’ perceptions related to information technologies and the connections between concepts in their cognitive structures. A word association test consisting of six concepts related to information technologies is used to collect data from 244 secondary school students. Concept maps that present students’ cognitive structures are drawn with the help of frequency data. Data are analyzed and interpreted according to the connections obtained as a result of the concept maps. It is determined students associate most with these concepts—computer, Internet, and communication of the given concepts, and associate least with these concepts—computer-assisted education and information technologies. These results show the concepts, Internet, communication, and computer, are an important part of students’ cognitive structures. In addition, students mostly answer computer, phone, game, Internet and Facebook as the key concepts. These answers show students regard information technologies as a means for entertainment and free time activity, not as a means for education.

Keywords: word association test, cognitive structure, information technology, secondary school

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Authors: Ahmed M. Debela, Mayreli Ortiz , Ciara K. O´Sullivan

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The completion of the human genome Project (HGP) has paved the way for mapping the diversity in the overall genome sequence which helps to understand the genetic causes of inherited diseases and susceptibility to drugs or environmental toxins. Arrayed primer extension (APEX) is a microarray based minisequencing strategy for screening disease causing mutations. It is derived from Sanger DNA sequencing and uses fluorescently dideoxynucleotides (ddNTPs) for termination of a growing DNA strand from a primer with its 3´- end designed immediately upstream of a site where single nucleotide polymorphism (SNP) occurs. The use of DNA polymerase offers a very high accuracy and specificity to APEX which in turn happens to be a method of choice for multiplex SNP detection. Coupling the high specificity of this method with the high sensitivity, low cost and compatibility for miniaturization of electrochemical techniques would offer an excellent platform for detection of mutation as well as sequencing of DNA templates. We are developing an electrochemical APEX for the analysis of SNPs found in the MYH7 gene for group of cardiomyopathy patients. ddNTPs were labeled with four different redox active compounds with four distinct potentials. Thiolated oligonucleotide probes were immobilised on gold and glassy carbon substrates which are followed by hybridisation with complementary target DNA just adjacent to the base to be extended by polymerase. Electrochemical interrogation was performed after the incorporation of the redox labelled dedioxynucleotide. The work involved the synthesis and characterisation of the redox labelled ddNTPs, optimisation and characterisation of surface functionalisation strategies and the nucleotide incorporation assays.

Keywords: array based primer extension, labelled ddNTPs, electrochemical, mutations

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Authors: S. K. M. Basha

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Pulicat Lake is the second largest brackish water lagoon after Chilika Lake of Orissa along the east coast of India. Estuaries and lagoons have brackish water which shows high biological productivity than fresh or sea water. Hence it has wide range of aquatic, terrestrial flora and fauna. The World Wide Fund for Nature declared that it is a protected area. Present study aims to explore the flora and fauna of the lagoon along with the various threats for its eco-degradation which helps to plan necessary conservation methods.

Keywords: phytodiversity, Pulicat Lake, threats, conservation

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Authors: Douglas F. Prawitt, Nathan Y. Sharp, David A. Wood

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Consistent with prior experimental and survey studies, we find that IAFs that spend more time directly assisting the external auditor is associated with lower external audit fees. Interestingly, we do not find evidence that external auditors reduce fees based on work previously performed by the IAF. We also find that the time spent assisting the external auditor has a greater negative effect on external audit fees than the time spent performing tasks upon which the auditor may rely but that are not performed as direct assistance to the external audit. Our results also show that previous proxies used to measure this relation is either not associated with or are negatively associated with our direct measures of how the IAF can contribute to the external audit and are highly positively associated with the size and the complexity of the organization. Thus, we conclude the disparate experimental and archival results may be attributable to issues surrounding the construct validity of measures used in previous archival studies and that when measures similar to those used in experimental studies are employed in archival tests, the archival results are consistent with experimental findings. Our research makes four primary contributions to the literature. First, we provide evidence that internal auditing contributes to a reduction in external audit fees. Second, we replicate and provide an explanation for why previous archival studies find that internal auditing has either no association with external audit fees or is associated with an increase in those fees: prior studies generally use proxies of internal audit contribution that do not adequately capture the intended construct. Third, our research expands on survey-based research (e.g., Oil Libya sh.co.) by separately examining the impact on the audit fee of the internal auditors’ work, indirectly assisting external auditors and internal auditors’ prior work upon which external auditors can rely. Finally, we extend prior research by using a new, independent data source to validate and extend prior studies. This data set also allows for a sample of examining the impact of internal auditing on the external audit fee and the use of a more comprehensive external audit fee model that better controls for determinants of the external audit fee.

Keywords: internal audit, contribution, external audit, function

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Authors: Chamilani Nikapitiya, Mahanama De Zoysa, Jehee Lee

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Most of the bacterial diseases are associated with high mortalities in aquaculture species and causing huge economic losses. Different approaches have been taken to prevent or control of bacterial diseases including use of vaccines, probiotics, chemotherapy, water quality management, etc. Antibiotics are widely applying as chemotherapy to control bacterial diseases, however, it has been shown that frequent use of antibiotics is favored to develop multi-drug resistance bacteria. Therefore, phages and phage encoded lytic proteins are known to be one of the most promising alternatives for antibiotics to avoid the emergence of antibiotic-resistant bacteria. We isolated and characterized the two lytic phages, namely pAh-1 and pAs-1 against pathogenic Aeromonas hydrophila and Aeromonas salmonicida, respectively. Morphological characteristics were analyzed by Transmission electron microscopy (TEM) and host strain specificities were tested with Aeromonas and other closely related bacterial strains. TEM analysis revealed that both pAh-1 and pAsm-1 are composed of an icosahedral head and a segmented tail, and we suggest that, they are new members of Myoviridae family. Genome sizes of isolated phages were estimated by restriction enzyme digestion of genomic DNA using selected endonucleases followed by agarose gel electrophoresis. Estimated genome size of pAh-1 and pAs-1 were approximately 64 Kbp and 120 Kbp, respectively. Both pAh-1 and pAs-1 have shown narrow host specificity. Moreover, protective effects of phage therapy against fish pathogenic A. hydrophila were investigated in zebrafish model. The survival rate was 40% higher when zebrafish received intra-peritoneal injection (i.p.) of pAh-1 were simultaneously challenge A. hydrophila (2 x 106 CFU/fish) compared to that without phage treatment. Overall results suggest that both pAh-1 and pAs-1 can be used as a potential phage therapy to control Aeromonas infections in aquaculture.

Keywords: Aeromonas infections, antibiotic resistance, bacteriophage, bio-control, lytic phage

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Authors: Nurunnahar Akter, Elena Kulinskaya, Nicholas Steel, Ilyas Bakbergenuly

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Although Hormone Replacement Therapy (HRT) is an effective treatment in ameliorating menopausal symptoms, it has mixed effects on different health outcomes, increasing, for instance, the risk of breast cancer. Because of this, many symptomatic women are left untreated. Untreated menopausal symptoms may result in other health issues, which eventually put an extra burden and costs to the health care system. All-cause mortality analysis may explain the net benefits and risks of the HRT therapy. However, it received far less attention in HRT studies. This study investigated the impact of HRT on all-cause mortality using electronically recorded primary care data from The Health Improvement Network (THIN) that broadly represents the female population in the United Kingdom (UK). The study entry date for this study was the record of the first HRT prescription from 1984, and patients were followed up until death or transfer to another GP practice or study end date, which was January 2017. 112,354 HRT users (cases) were matched with 245,320 non-users by age at HRT initiation and general practice (GP). The hazards of all-cause mortality associated with HRT were estimated by a parametric Weibull-Cox model adjusting for a wide range of important medical, lifestyle, and socio-demographic factors. The multilevel multiple imputation techniques were used to deal with missing data. This study found that during 32 years of follow-up, combined HRT reduced the hazard ratio (HR) of all-cause mortality by 9% (HR: 0.91; 95% Confidence Interval, 0.88-0.94) in women of age between 46 to 65 at first treatment compared to the non-users of the same age. Age-specific mortality analyses found that combined HRT decreased mortality by 13% (HR: 0.87; 95% CI, 0.82-0.92), 12% (HR: 0.88; 95% CI, 0.82-0.93), and 8% (HR: 0.92; 95% CI, 0.85-0.98), in 51 to 55, 56 to 60, and 61 to 65 age group at first treatment, respectively. There was no association between estrogen-only HRT and women’s all-cause mortality. The findings from this study may help to inform the choices of women at menopause and to further educate the clinicians and resource planners.

Keywords: hormone replacement therapy, multiple imputations, primary care data, the health improvement network (THIN)

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Authors: Panyarat Panthong

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This research paper was conducted to examine the association between demographic, professional and social characteristics, and self-leadership of personnel who worked at Sub-District Administrative Organization Offices in Muang District, Udon Thani Province, and to identify the degree level of self-leadership of the selected samples in relation with the study variables. A total of 89 samples were collected from the 15 Sub-District Administrative Organization Offices. The paper employed both quantitative and qualitative methods using the Chi- Square and Cramer’s V statistics for the data analysis. The findings unveiled that constructive thought strategies showed a significant existence followed by behavior- focused strategies and natural reward strategies. Moreover, the research found that the respondents’ length of time working in the position and the respondents’ self- leadership presented a significant association in terms of the behavior-focused and constructive thought strategies. On the other hand, the respondents’ demographic characteristics placed no association with the level of self-leadership in behavior-focused strategies, natural reward strategies and constructive thought strategies. It is hoped that this finding will provide informative and practical guidance for the Ministry of Interior of Thailand and Department of Local Administration of the studied province.

Keywords: demographic characteristics, professional characteristics, self- leadership, social characteristics

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Authors: Vijay Kumar Singh, Pooja Kushwaha, Prabhat Ranjan, Krishna Kumar Ojha, Jitendra Kumar

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Present day high-throughput genomic technologies, NGS/microarrays, are producing large volume of data that require improved analysis methods to make sense of the data. The correlation between genes and samples has been regularly used to gain insight into many biological phenomena including, but not limited to, co-expression/co-regulation, gene regulatory networks, clustering and pattern identification. However, presence of outliers and violation of assumptions underlying Pearson correlation is frequent and may distort the actual correlation between the genes and lead to spurious conclusions. Here, we report a method to measure the strength of association between genes. The method assumes that the expression values of a gene are Bernoulli random variables whose outcome depends on the sample being probed. The method considers the two genes as uncorrelated if the number of sample with same outcome for both the genes (Ns) is equal to certainly expected number (Es). The extent of correlation depends on how far Ns can deviate from the Es. The method does not assume normality for the parent population, fairly unaffected by the presence of outliers, can be applied to qualitative data and it uses the binomial distribution to assess the significance of association. At this stage, we would not claim about the superiority of the method over other existing correlation methods, but our method could be another way of calculating correlation in addition to existing methods. The method uses binomial distribution, which has not been used until yet, to assess the significance of association between two variables. We are evaluating the performance of our method on NGS/microarray data, which is noisy and pierce by the outliers, to see if our method can differentiate between spurious and actual correlation. While working with the method, it has not escaped our notice that the method could also be generalized to measure the association of more than two variables which has been proven difficult with the existing methods.

Keywords: binomial distribution, correlation, microarray, outliers, transcriptome

Procedia PDF Downloads 385

Authors: Farah Naja, Romy Abi Fadel, Yasmin Aridi, Aya Zarif, Dania Hariri, Mohammad Alameddine, Anas Mugharbel, Maya Khalil, Zeina Nahleh, Arafat Tfayli

Abstract:

The objective of this study is to assess the prevalence and determinants of CAM use among breast cancer patients in Beirut, Lebanon. A secondary objective is to evaluate the association between CAM use and quality of life (QOL). A cross-sectional survey was conducted on 180 breast cancer patients recruited from two major referral centers in Beirut. In a face to face interview, participants completed a questionnaire comprised of three sections: socio-demographic and lifestyle characteristics, breast cancer condition, and CAM use. The assessment of QOL was carried using the FACT-B Arabic version. Prevalence of CAM use since diagnosis was 40%. CAM use was negatively associated with age, treatment at a philanthropic hospital and positively associated with having an advanced stage of disease. The most commonly used CAM was ‘Special food’ followed by ‘Herbal teas’. Only 4% of CAM users cited health care professionals as influencing their choice of CAM. One in four patients disclosed CAM use to their treating physician. There was no significant association between CAM use and QOL. The use of CAM therapies among breast cancer patients is prevalent in Lebanon. Efforts should be dedicated at educating physicians to discuss CAM use with their patients and advising patients to disclose of their use with their physicians.

Keywords: breast cancer , complementary medicine, alternative medicine, lebanon , quality of life

Procedia PDF Downloads 492

Authors: Janos Juhasz, Sandor Pongor, Balazs Ligeti

Abstract:

Next-generation sequencing, especially whole genome shotgun sequencing, is becoming a common approach to gain insight into the microbiomes in a culture-independent way, even in clinical practice. It does not only give us information about the species composition of an environmental sample but opens the possibility to detect antimicrobial resistance and novel, or currently unknown, pathogens. Accurately and reliably detecting the microbial strains is a challenging task. Here we present a sensitive approach for detecting pathogens in metagenomics samples with special regard to detecting novel variants of known pathogens. We have developed a pipeline that uses fast, short read aligner programs (i.e., Bowtie2/BWA) and comprehensive nucleotide databases. Taxonomic binning is based on the lowest common ancestor (LCA) principle; each read is assigned to a taxon, covering the most significantly hit taxa. This approach helps in balancing between sensitivity and running time. The program was tested both on experimental and synthetic data. The results implicate that our method performs as good as the state-of-the-art BLAST-based ones, furthermore, in some cases, it even proves to be better, while running two orders magnitude faster. It is sensitive and capable of identifying taxa being present only in small abundance. Moreover, it needs two orders of magnitude less reads to complete the identification than MetaPhLan2 does. We analyzed an experimental anthrax dataset (B. anthracis strain BA104). The majority of the reads (96.50%) was classified as Bacillus anthracis, a small portion, 1.2%, was classified as other species from the Bacillus genus. We demonstrate that the evaluation of high-throughput sequencing data is feasible in a reasonable time with good classification accuracy.

Keywords: metagenomics, taxonomy binning, pathogens, microbiome, B. anthracis

Procedia PDF Downloads 112

Authors: Yung-Feng Yen, Yun-Ju Lai

Abstract:

Background: Animal studies have shown that alcohol exposure may cause immunosuppression and increase the susceptibility to tuberculosis (TB) infection. However, the temporality of alcohol consumption with subsequent TB development remains unclear. This nationwide population-based cohort study aimed to investigate the impact of alcohol exposure on TB development in Taiwanese adults. Methods: We included 46 196 adult participants from three rounds (2001, 2005, 2009) of the Taiwan National Health Interview Survey. Alcohol consumption was classified into heavy, regular, social, or never alcohol use. Heavy alcohol consumption was defined as intoxication at least once/week. Alcohol consumption and other covariates were collected by in-person interviews at baseline. Incident cases of active TB were identified from the National Health Insurance database. Multivariate logistic regression was used to estimate the association between alcohol consumption and active TB, with adjustment for age, sex, smoking, socioeconomic status, and other covariates. Results: A total of 279 new cases of active TB occurred during the study follow-up period. Heavy (adjusted odds ratio [AOR], 5.21; 95% confident interval [CI], 2.41-11.26) and regular alcohol use (AOR, 1.73; 95% CI, 1.26-2.38) were associated with higher risks of incident TB after adjusting for the subject demographics and comorbidities. Moreover, a strong dose-response effect was observed between increasing alcohol consumption and incident TB (AOR, 2.26; 95% CI, 1.59-3.21; P <.001). Conclusion: Heavy and regular alcohol consumption were associated with higher risks of active TB. Future TB control programs should consider strategies to lower the overall level of alcohol consumption to reduce the TB disease burden.

Keywords: alcohol consumption, tuberculosis, risk factor, cohort study

Procedia PDF Downloads 207

Authors: Umairah Natasya Binti Mohd Omeershffudin, Suresh Kumar

Abstract:

Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. Particular concern is the global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae. Characterization of antibiotic resistance determinants at the genomic level plays a critical role in understanding, and potentially controlling, the spread of multidrug-resistant (MDR) pathogens. In this study, drug-resistant Klebsiella pneumoniae strain 825795-1 was investigated with extensive computational approaches aimed at identifying novel drug targets among hypothetical proteins. We have analyzed 1099 hypothetical proteins available in genome. We have used in-silico genome subtraction methodology to design potential and pathogen-specific drug targets against Klebsiella pneumoniae. We employed bioinformatics tools to subtract the strain-specific paralogous and host-specific homologous sequences from the bacterial proteome. The sorted 645 proteins were further refined to identify the essential genes in the pathogenic bacterium using the database of essential genes (DEG). We found 135 unique essential proteins in the target proteome that could be utilized as novel targets to design newer drugs. Further, we identified 49 cytoplasmic protein as potential drug targets through sub-cellular localization prediction. Further, we investigated these proteins in the DrugBank databases, and 11 of the unique essential proteins showed druggability according to the FDA approved drug bank databases with diverse broad-spectrum property. The results of this study will facilitate discovery of new drugs against Klebsiella pneumoniae.

Keywords: pneumonia, drug target, hypothetical protein, subtractive genomics

Procedia PDF Downloads 157

Authors: Jaemyoung Lee

Abstract:

We propose a wide view camera scheme for automobile's black box. The proposed scheme uses the commercially available camera lenses of which view angles are about 120°}^{\circ}°. In the proposed scheme, we extend the view angle to approximately 200° ^{\circ}° using two cameras at the front side instead of three lenses with conventional black boxes.

Keywords: camera, black box, view angle, automobile

Procedia PDF Downloads 388

Authors: Farah Naja, Romy Abi Fadel, Yasmin Aridi, Aya Zarif, Dania Hariri, Mohammad Alameddine, Anas Mugharbel, Maya Khalil, Zeina Nahleh, Arafat Tfayli

Abstract:

The objective of this study is to assess the prevalence and determinants of CAM use among breast cancer patients in Beirut, Lebanon. A secondary objective is to evaluate the association between CAM use and quality of life (QOL). A cross-sectional survey was conducted on 180 breast cancer patients recruited from two major referral centers in Beirut. In a face to face interview, participants completed a questionnaire comprised of three sections: socio-demographic and lifestyle characteristics, breast cancer condition, and CAM use. The assessment of QOL was carried using the FACT-B Arabic version. Prevalence of CAM use since diagnosis was 40%. CAM use was negatively associated with age, treatment at a philanthropic hospital and positively associated with having an advanced stage of disease. The most commonly used CAM was ‘Special food’ followed by ‘Herbal teas’. Only 4% of CAM users cited health care professionals as influencing their choice of CAM. One in four patients disclosed CAM use to their treating physician. There was no significant association between CAM use and QOL. The use of CAM therapies among breast cancer patients is prevalent in Lebanon. Efforts should be dedicated at educating physicians to discuss CAM use with their patients and advising patients to disclose of their use with their physicians.

Keywords: breast cancer, complementary and aLternative medicine, Lebanon, quality of life

Procedia PDF Downloads 574

Authors: M. Mydlárová Blaščáková, J. Poráčová, Z. Tomková, Ľ. Blaščáková, M. Nagy, M. Konečná, E. Petrejčíková, Z. Gogaľová, V. Sedlák, J. Mydlár, M. Zahatňanská, K. Hricová

Abstract:

Osteoporosis is a multifactorial disease that results in reduced quality of life, causes decreased bone strength, and changes in their microarchitecture. Mostly postmenopausal women are at risk. In our study, we measured anthropometric parameters of postmenopausal women (104 women of control group – CG and 105 women of osteoporotic group - OG) and determined TSH hormone levels and PTH as well as mineral elements - Ca, P, Mg and enzyme alkaline phosphatase. Through the correlation analysis in CG, we have found association based on age and BMI, P and Ca, as well as Mg and Ca; in OG we determined interdependence based on an association of age and BMI, age and Ca. Using the Student's t test, we found significantly important differences in biochemical parameters of Mg (p ˂ 0,001) and TSH (p ˂ 0,05) between CG and OG.

Keywords: factors, bone mass density, Central Europe, biomarkers

Procedia PDF Downloads 171

Authors: O. Berriche, R. Ben Othmen, H. Sfar, H. Abdesslam, S. Bou Meftah, S. Bhouri, F. Mahjoub, C. Amrouche, H. Jamoussi

Abstract:

Introduction: Although current evidence emphasizes a high prevalence of vitamin D deficiency and an inverse association between serum 25-hydroxyvitamin D (25-OHD) concentration and obesity, no studies have been conducted in Tunisian obese. The objectives of our study were to estimate the vitamin D deficiency in obese, identify risk factors for vitamin D deficiency, demonstrating a possible association between vitamin D levels and metabolic parameters. Methods: This was a descriptive study of 100 obese 18-65 year-old. Anthropometric measurements were determined. Fasting blood samples were assessed for the following essays : serum calcium, 25 OH vitamin D, inorganic phosphorus, fasting glucose, HDL, LDL cholesterol and triglyceride. Insulin resistance was evaluated by fasting insulin, HOMA-IR and HOMA-ß. Consumption of foods riche in vitamin D, sunscreen use, wearing protective clothes and exposed surface were assessed through applied questionnaires. Results: The deficit of vitamin D (< 30 ng/ml) among obese was 98,8%. Half of them had a rate < 10ng/ml. Environmental factors involved in vitamin D deficiency are : the veil (p = 0,001), wearing protective clothes (p = 0,04) and the exposed surface (p = 0,011) and dietary factors are represented by the daily caloric intake (p = 0,0001). The percent of fat mass was negatively related to vitamin D levels (p = 0,01) but not with BMI (p = 0,11) or waist circumference (p = 0,88). Similarly, lipid and glucose profile had no link with vitamin D. We found no relationship between Insulin resistance and vitamin D levels. Conclusion: At the end of our study, we have identified a very important vitamin D deficiency among obese. Dosage and systematic supplementation should be applied and for that physician awareness is needed.

Keywords: insulinresistance, risk factors, obesity, vitamin D

Procedia PDF Downloads 631

Authors: Susan Thurstans, Natalie Sessions, Carmel Dolan, Kate Sadler, Bernardette Cichon, Shelia Isanaka, Dominique Roberfroid, Heather Stobagh, Patrick Webb, Tanya Khara

Abstract:

For many years, wasting and stunting have been viewed as separate conditions without clear evidence supporting this distinction. In 2014, the Emergency Nutrition Network (ENN) examined the relationship between wasting and stunting and published a report highlighting the evidence for linkages between the two forms of undernutrition. This systematic review aimed to update the evidence generated since this 2014 report to better understand the implications for improving child nutrition, health and survival. Following PRISMA guidelines, this review was conducted using search terms to describe the relationship between wasting and stunting. Studies related to children under five from low- and middle-income countries that assessed both ponderal growth/wasting and linear growth/stunting, as well as the association between the two, were included. Risk of bias was assessed in all included studies using SIGN checklists. 45 studies met the inclusion criteria- 39 peer reviewed studies, 1 manual chapter, 3 pre-print publications and 2 published reports. The review found that there is a strong association between the two conditions whereby episodes of wasting contribute to stunting and, to a lesser extent, stunting leads to wasting. Possible interconnected physiological processes and common risk factors drive an accumulation of vulnerabilities. Peak incidence of both wasting and stunting was found to be between birth and three months. A significant proportion of children experience concurrent wasting and stunting- Country level data suggests that up to 8% of children under 5 may be both wasted and stunted at the same time, global estimates translate to around 16 million children. Children with concurrent wasting and stunting have an elevated risk of mortality when compared to children with one deficit alone. These children should therefore be considered a high-risk group in the targeting of treatment. Wasting, stunting and concurrent wasting and stunting appear to be more prevalent in boys than girls and it appears that concurrent wasting and stunting peaks between 12- 30 months of age with younger children being the most affected. Seasonal patterns in prevalence of both wasting and stunting are seen in longitudinal and cross sectional data and in particular season of birth has been shown to have an impact on a child’s subsequent experience of wasting and stunting. Evidence suggests that the use of mid-upper-arm circumference combined with weight-for-age Z-score might effectively identify children most at risk of near-term mortality, including those concurrently wasted and stunted. Wasting and stunting frequently occur in the same child, either simultaneously or at different moments through their life course. Evidence suggests there is a process of accumulation of nutritional deficits and therefore risk over the life course of a child demonstrates the need for a more integrated approach to prevention and treatment strategies to interrupt this process. To achieve this, undernutrition policies, programmes, financing and research must become more unified.

Keywords: Concurrent wasting and stunting, Review, Risk factors, Undernutrition

Procedia PDF Downloads 101