Browsing by Subject "Meta-analysis"
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Item Open Access Aligning software engineering education with industrial needs: a meta-analysis(Elsevier, 2019) Garousi, V.; Giray, G.; Tüzün, Eray; Catal, C.; Felderer, M.Context: According to various reports, many software engineering (SE) graduates often face difficulties when beginning their careers, which is mainly due to misalignment of the skills learned in university education with what is needed in the software industry. Objective: Our objective is to perform a meta-analysis to aggregate the results of the studies published in this area to provide a consolidated view on how to align SE education with industry needs, to identify the most important skills and also existing knowledge gaps. Method: To synthesize the body of knowledge, we performed a systematic literature review (SLR), in which we systematically selected a pool of 35 studies and then conducted a meta-analysis using data extracted from those studies. Results: Via a meta-analysis and using data from 13 countries and over 4,000 data points, highlights of the SLR include: (1) software requirements, design, and testing are the most important skills; and (2) the greatest knowledge gaps are in configuration management, SE models and methods, SE process, design (and architecture), as well as in testing. Conclusion: This paper provides implications for both educators and hiring managers by listing the most important SE skills and the knowledge gaps in the industryItem Open Access The Association between familial risk and brain abnormalities Is disease specific: an ENIGMA-relatives study of schizophrenia and bipolar disorder(Elsevier, 2019) Zwarte, S. M. C.; Brouwer, R. M.; Agartz, I.; Alda, M.; Aleman, A.; Alpert, K. I.; Bearden, C. E.; Bertolino, A.; Bois, C.; Bonvino, A.; Bramon, E.; Buimer, E.; Cahn, W.; Cannon, D. M.; Cannon, T. D.; Caseras, X.; Castro-Fornieles, J.; Chen, Q.; Serna, E.; Giorgio, A. D.; Doucet, G.; Eker, M. C.; Erk, S.; Fears, S.; Foley, S.; Frangou, S.; Frankland, A.; Fullerton, J.; Glahn, D.; Goghari, V.; Goldman, A.; Gonul, A.; Gruber, O.; Haan, L.; Hajek, T.; Hawkins, E.; Heinz, A.; Hillegers, M.; Pol, H.; Hultman, C.; Ingvar, M.; Johansson, V.; Jönsson, E.; Kane, K.; Kempton, M.; Koenis, M.; Kopecek, M.; Krabbendam, L.; Krämer, B.; Lawrie, S.; Lenroot, R.; Marcelis, M.; Marsman, J-B; Mattay, V.; McDonald, C.; Meyer-Lindenberg, A.; Michielse, S.; Mitchell, P.; Moreno, D.; Murray, R.; Mwangi, B.; Najt, P.; Neilson, E.; Newport, J.; Os, J.; Overs, B.; Özerdem, A.; Picchioni, M.; Richter, A.; Roberts, G.; Aydoğan, A. S.; Schofield, P.; Şimşek, F.; Soares, J.; Sugranyes, G.; Toulopoulou, Timothea; Tronchin, G.; Walter, H.; Wang, L.; Weinberger, D.; Whalley, H.; Yalın, N.; Andreassen, O.; Ching, C.; Erp, T.; Turner, J.; Jahanshad, N.; Thompson, P.; Kahn, R.; Haren, N.Abstract Background Schizophrenia and bipolar disorder share genetic liability, and some structural brain abnormalities are common to both conditions. First-degree relatives of patients with schizophrenia (FDRs-SZ) show similar brain abnormalities to patients, albeit with smaller effect sizes. Imaging findings in first-degree relatives of patients with bipolar disorder (FDRs-BD) have been inconsistent in the past, but recent studies report regionally greater volumes compared with control subjects. Methods We performed a meta-analysis of global and subcortical brain measures of 6008 individuals (1228 FDRs-SZ, 852 FDRs-BD, 2246 control subjects, 1016 patients with schizophrenia, 666 patients with bipolar disorder) from 34 schizophrenia and/or bipolar disorder family cohorts with standardized methods. Analyses were repeated with a correction for intracranial volume (ICV) and for the presence of any psychopathology in the relatives and control subjects. Results FDRs-BD had significantly larger ICV (d = +0.16, q < .05 corrected), whereas FDRs-SZ showed smaller thalamic volumes than control subjects (d = −0.12, q < .05 corrected). ICV explained the enlargements in the brain measures in FDRs-BD. In FDRs-SZ, after correction for ICV, total brain, cortical gray matter, cerebral white matter, cerebellar gray and white matter, and thalamus volumes were significantly smaller; the cortex was thinner (d < −0.09, q < .05 corrected); and third ventricle was larger (d = +0.15, q < .05 corrected). The findings were not explained by psychopathology in the relatives or control subjects. Conclusions Despite shared genetic liability, FDRs-SZ and FDRs-BD show a differential pattern of structural brain abnormalities, specifically a divergent effect in ICV. This may imply that the neurodevelopmental trajectories leading to brain anomalies in schizophrenia or bipolar disorder are distinct.Item Open Access CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer(Springer, 2021-04) Shehwana, Huma; Keskus, Ayse Gokce; Ozdemir, E. Sila; Acikgöz, Azer Aylin; Biyik-Sit, Rumeysa; Cagnan, I.; Gunes, Damla; Jahja, Ermira; Cingir-Koker, Sahika; Olmezer, Gizem; Sucularli, Ceren; Konu, OzlenCholinergic signals can be important modulators of cellular signaling in cancer. We recently have shown that knockdown of nicotinic acetylcholine receptor subunit alpha 5, CHRNA5, diminishes the proliferative potential of breast cancer cells. However, modulation of CHRNA5 expression in the context of estrogen signaling and its prognostic implications in breast cancer remained unexplored.Item Open Access Development of novel tools for cancer diagnosis, prognosis and treatment using intra- or inter-species transcriptome metaanalysis(Bilkent University, 2017-08) Shehwana, HumaIn the past decades, a considerable number of studies have performed meta-analysis on large data collections to prioritize sets of genes, pathways or types/categories of disease focusing on either differential expression, survival analysis, or co-expression networks. However, not many web applications or databases have been developed from these studies thus findings largely remained restricted to the addressed questions and it was not possible for other researchers to use the collected data for the evaluation of novel hypotheses. In this thesis, transcriptomic meta-analysis strategies have been applied to untangle complexities in multiple aspects of cancer research including treatment, diagnosis, and prognosis. Furthermore, three different web-tools have been developed which are not limited to a single type of meta-analysis. In this context, in addition to interesting cancer related findings, novel methodologies have been proposed and tested in the field of meta-analysis and cancer research. First chapter of the thesis presented a general introduction on the concepts of the thesis. Second chapter focused on a pathway comparison strategy based on meta-analysis that was used to reveal concordant/discordant aspects of rapamycin-mediation on transcriptomes of zebrafish and mouse. Analysis has shown that ribosomal terms were significantly upregulated while proteasome was downregulated in both species. Zebrafish has undergone a whole-genome duplication event; I also found out that rapamycin treatment resulted in largely concordant behavior of duplicated gene pairs. In addition, an online database, CompariZome, was developed to evaluate the duplicate zebrafish gene pairs in multiple GEO datasets in zebrafish in comparison to respective human expression datasets. In the third chapter of this thesis, I focused on identification of correlation between a trio of genes, CDH1, HNF4A, and GRHL3, using Cancer Cell Line Encyclopedia (CCLE) dataset to reveal the significance of association between these genes in different cancers, including breast and other epithelial cancers. The findings indicated correlation within the module and has demonstrated the power of meta-analysis using CCLE dataset. In the fourth chapter of this thesis, I focused on understanding the association of CHRNA5, a subunit of cholinergic receptors, with epithelial-to-mesenchymal transition (EMT) as well as epithelial differentiation, TP53 induction, and estrogen (E2) signaling with respect to breast cancer. Meta-analysis of invitro and in-vivo microarray expression datasets showed that CHRNA5, itself, and its positively co-expressed neighbors, were likely secondary targets of E2-signaling; overexpressed in ER- breast cancer patients; and indicators of worse prognosis. Functional annotation revealed that CHRNA5 and its co-expression network was indeed associated with proliferation related pathways. Based on meta-analysis of different cohorts processed in the study, an online database E2S (Estrogen (E2) to Survival) was developed that can facilitate user to query any gene for evaluation of E2-mediated effects, regulation by estrogen receptor (ER), prognostic importance and co-expression network along with functional annotations. In the fifth chapter of this thesis I focused on deciphering the correlation and deregulation between a human parolog pair of genes, i.e., mineralocorticoid and glucocorticoid receptors (MR and GR, respectively) in breast cancer. Meta-analysis of a separate normal/tumor cohort revealed that both genes were downregulated in breast cancer and their expressions were highly positively correlated. However, deregulation analysis predicted that expression of MR and GR was more tightly regulated in normal breast hence its regulation might be lost with the onset of tumorigenesis. Another Shiny database, DualExpBC, was developed to evaluate differential expression of a gene in breast cancer as well as correlation and deregulation of expression between any two input genes in the breast normal/cancer expression cohort. With this thesis, I have developed novel tools and approaches for intra- and inter-species comparative transcriptomics and meta-analysis providing potential diagnostic, prognostic and therapeutic biomarkers.Item Open Access Functional genomics in translational cancer research: focus on breast cancer(Oxford University Press, 2008) Yulug, I. G.; Gur-Dedeoglu, B.Conventional molecular and genetic methods for studying cancer are limited to the analysis of one locus at a time. A cluster of genes that are regulated together can be identified by DNA microarray, and the functional relationships can uncover new aspects of cancer biology. Breast cancer can be used to provide a model to demonstrate the current approaches to the molecular analysis of cancer. Meta-analysis is an important tool for the identification and validation of differentially expressed genes to increase power in clinical and biological studies across different sets of data. Recently, meta-analysis approaches have been applied to large collections of microarray datasets to investigate molecular commonalities of multiple cancer types not only to find the common molecular pathways in tumour development but also to compare the individual datasets to other cancer datasets to identify new sets of genes. Several investigators agree that microarray results should be validated. One commonly used method is quantitative reverse transcription PCR (qRT-PCR) to validate the expression profiles of the target genes obtained through microarray experiments. qRT-PCR is attractive for clinical use, since it can be automated and performed on fresh or archived formalin-fixed, paraffin-embedded tissue samples. The outcome of these analyses might accelerate the application of basic research findings into daily clinical practice through translational research and may have an impact on foreseeing the clinical outcome, predicting tumour response to specific therapy, identification of new prognostic biomarkers, discovering targets for the development of novel therapies and providing further insights into tumour biology. © The Author 2008. Published by Oxford University Press.Item Open Access Functionally conserved effects of rapamycin exposure on zebrafish(Spandidos Publications, 2016-03) Sucularli, C.; Shehwana, H.; Kuscu, C.; Dungul, D. C.; Ozdag, H.; Konu, O.Mechanistic target of rapamycin (mTOR) is a conserved serine/threonine kinase important in cell proliferation, growth and protein translation. Rapamycin, a well-known anti-cancer agent and immunosuppressant drug, inhibits mTOR activity in different taxa including zebrafish. In the present study, the effect of rapamycin exposure on the transcriptome of a zebrafish fibroblast cell line, ZF4, was investigated. Microarray analysis demonstrated that rapamycin treatment modulated a large set of genes with varying functions including protein synthesis, assembly of mitochondrial and proteasomal machinery, cell cycle, metabolism and oxidative phosphorylation in ZF4 cells. A mild however, coordinated reduction in the expression of proteasomal and mitochondrial ribosomal subunits was detected, while the expression of numerous ribosomal subunits increased. Meta-analysis of heterogeneous mouse rapamycin microarray datasets enabled the comparison of zebrafish and mouse pathways modulated by rapamycin, using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathway analysis. The analyses demonstrated a high degree of functional conservation between zebrafish and mice in response to rapamycin. In addition, rapamycin treatment resulted in a marked dose-dependent reduction in body size and pigmentation in zebrafish embryos. The present study is the first, to the best of our knowledge, to evaluate the conservation of rapamycin-modulated functional pathways between zebrafish and mice, in addition to the dose-dependent growth curves of zebrafish embryos upon rapamycin exposure.Item Open Access Meta-analysis and systematic review for the treatment of perpetrators of intimate partner violence(Elsevier, 2019) Karakurt, G.; Koç, E.; Çetinsaya, Ezgi Elif; Ayluçtarhan, Zozan; Bolen, S.Aim of this study is to investigate the effectiveness of different batterer intervention programs in reducing violence for male IPV perpetrators. The Cochrane Handbook for Systemic Reviews of Interventions guidelines for the process of conducting systematic reviews and meta-analysis were followed. Pooled together, overall these various intervention programs are effective in reducing violence for male perpetrators of IPV comparing post to pre-intervention [(pooled estimate = -0.85; 95% Confidence Interval (CI) (-1.02 to -0.69)]. Exploratory subgroup analysis revealed that incorporating substance abuse or trauma components to the interventions yielded better results (substance abuse: CI = -3.20 to -1.08 and trauma: CI = -2.63 to -0.30) as compared to programs that did not have these components. Gender-role based batterer intervention programs yielded mixed results. Analysis of the three controlled studies with 223 participants comparing batterer programs to a minimal control group showed mixed effects. In conclusion, treatment strategies that are addressing highly comorbid issues such as substance abuse and trauma issues may work more effectively in preventing violence.Item Open Access Meta-analysis on the effect of enrichment programs on the academic achievement of gifted and talented students(Bilkent University, 2022-08) Tosun, Ayten SengüMuch research has been conducted about gifted education recently. One of the most applied interventions in gifted education is enrichment. Enrichment is the teaching and learning process that increases the depth and complexity of typical school subjects. In this thesis, the effects of enrichment on the academic achievement of gifted and talented students, was examined. The meta-analytic procedure was used to determine the overall effect size. The researcher used Education Resources Information Center database (ERIC), the most comprehensive database on education literature, Bilkent online library, and Google Scholar to detect relevant studies. The studies were filtered to the studies published between 2013 and 2021. After applying the inclusion and exclusion criteria, 22 studies were determined to be included in this meta-analysis. The pooled effect size was estimated under the random-effects model using the R statistical software. The effect size measure used was Hedges’ g. The findings showed that enrichment programs had a positive moderate effect (g= 0.68, 95% CI [0.31, 1.05]) on students’ academic achievement. To investigate the robustness of the findings, heterogeneity analyses were conducted and publication bias was investigated through the funnel plot. High heterogeneity (I2=84.6%) of the findings supports the use of a random-effects model. Also, the funnel plot showed an asymmetry which might be the reason for this heterogeneity and/or a possible publication bias found in the literature. In addition, subgroup analyses were performed to check for possible reasons for this high heterogeneity.