Browsing by Subject "Reproducibility"
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Item Open Access Content-based retrieval of historical Ottoman documents stored as textual images(IEEE, 2004) Şaykol, E.; Sinop, A. K.; Güdükbay, Uğur; Ulusoy, Özgür; Çetin, A. EnisThere is an accelerating demand to access the visual content of documents stored in historical and cultural archives. Availability of electronic imaging tools and effective image processing techniques makes it feasible to process the multimedia data in large databases. In this paper, a framework for content-based retrieval of historical documents in the Ottoman Empire archives is presented. The documents are stored as textual images, which are compressed by constructing a library of symbols occurring in a document, and the symbols in the original image are then replaced with pointers into the codebook to obtain a compressed representation of the image. The features in wavelet and spatial domain based on angular and distance span of shapes are used to extract the symbols. In order to make content-based retrieval in historical archives, a query is specified as a rectangular region in an input image and the same symbol-extraction process is applied to the query region. The queries are processed on the codebook of documents and the query images are identified in the resulting documents using the pointers in textual images. The querying process does not require decompression of images. The new content-based retrieval framework is also applicable to many other document archives using different scripts.Item Open Access How (not) to disappear completely: pedagogical potential of research methods in international relations(Sage Publications Ltd., 2015) Mutlu, C. E.The question of research methods, and their role in the field, is a major source of contention for IR scholars. We can, however, discuss method, methodology, and innovation without revising or revisiting old debates. Methods do not have to be divisive, or disciplining. A frank discussion of research design, methods, and methodological preferences is essential to innovation and reproducibility. This intervention is a call for increased transparency in IR research outputs; IR theorists should not erase their own footprints from their publications and openly admit and discuss failures as productive moments in research. The act of disappearing, which has become the norm in the name of professionalised publications, robs the field of the productive pedagogical potential of research methods. The true impact of research rests in its pedagogical potential. As researchers, our job is thus to find a sensitive balance between not determining the outcome of the research from the get-go by making it all about our preferences and opinions, but also not making the impact of our preferences and opinions disappear completely. Building on this premise, this intervention discusses the significant pedagogical potential of research methods, reproducibility and discussion of failures in International Relations.Item Open Access A hybrid classification model for digital pathology using structural and statistical pattern recognition(Institute of Electrical and Electronics Engineers, 2013) Ozdemir, E.; Gunduz-Demir, C.Cancer causes deviations in the distribution of cells, leading to changes in biological structures that they form. Correct localization and characterization of these structures are crucial for accurate cancer diagnosis and grading. In this paper, we introduce an effective hybrid model that employs both structural and statistical pattern recognition techniques to locate and characterize the biological structures in a tissue image for tissue quantification. To this end, this hybrid model defines an attributed graph for a tissue image and a set of query graphs as a reference to the normal biological structure. It then locates key regions that are most similar to a normal biological structure by searching the query graphs over the entire tissue graph. Unlike conventional approaches, this hybrid model quantifies the located key regions with two different types of features extracted using structural and statistical techniques. The first type includes embedding of graph edit distances to the query graphs whereas the second one comprises textural features of the key regions. Working with colon tissue images, our experiments demonstrate that the proposed hybrid model leads to higher classification accuracies, compared against the conventional approaches that use only statistical techniques for tissue quantification. © 2012 IEEE.Item Open Access Injectable in situ forming microparticles: A novel drug delivery system(2012) Yapar, E. A.; Inal, Ö.; Özkan, Y.; Baykara, T.Pharmaceutical formulation research has recently been focusing on delivery systems which provide long therapeutic effects and reduced side effects, and involving simplified production stages and facilitated application process. In situ forming microparticle (ISM) systems, one of the latest approach in this field, offer a new encapsulation technique and meet the objectives stated above. Factors such as the carrier used to form the multiparticles, amount and type of drug and the vehicle type can be taken as the main performance criteria for these systems. Ongoing studies have shown that this new multiparticulate drug delivery system is suitable for achieving new implant delivery system with low risk of dose-dumping, capable of being modulated to exhibit varying release patterns, reproducible, easily applicable and welltolerated compared with classically surgical implants.Item Open Access Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal(American Association for the Advancement of Science (A A A S), 2013) Gao J.; Aksoy, B. A.; Dogrusoz, U.; Dresdner, G.; Gross, B.; Sumer, S. O.; Sun, Y.; Jacobsen, A.; Sinha, R.; Larsson, E.; Cerami, E.; Sander, C.; Schultz, N.The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics. © 2013 American Association for the Advancement of Science.Item Open Access On genomic repeats and reproducibility(Oxford University Press, 2016) Firtina, C.; Alkan C.Results: Here, we present a comprehensive analysis on the reproducibility of computational characterization of genomic variants using high throughput sequencing data. We reanalyzed the same datasets twice, using the same tools with the same parameters, where we only altered the order of reads in the input (i.e. FASTQ file). Reshuffling caused the reads from repetitive regions being mapped to different locations in the second alignment, and we observed similar results when we only applied a scatter/gather approach for read mapping - without prior shuffling. Our results show that, some of the most common variation discovery algorithms do not handle the ambiguous read mappings accurately when random locations are selected. In addition, we also observed that even when the exact same alignment is used, the GATK HaplotypeCaller generates slightly different call sets, which we pinpoint to the variant filtration step. We conclude that, algorithms at each step of genomic variation discovery and characterization need to treat ambiguous mappings in a deterministic fashion to ensure full replication of results. Availability and Implementation: Code, scripts and the generated VCF files are available at DOI:10.5281/zenodo.32611.Item Open Access A photometric investigation of ultra-efficient LEDs with high color rendering index and high luminous efficacy employing nanocrystal quantum dot luminophores(Optical Society of America, 2009-12-24) Erdem, T.; Nizamoglu, S.; Sun, X. W.; Demir, Hilmi VolkanWe report a photometric study of ultra-efficient light emitting diodes (LEDs) that exhibit superior color rendering index (CRI) and luminous efficacy of optical radiation (LER) using semiconductor quantum dot nanocrystal (NC) luminophores. Over 200 million systematically varied NC-LED designs have been simulated to understand feasible performance in terms of CRI vs. LER. We evaluated the effects of design parameters including peak emission wavelength, full-width-at-half-maximum, and relative amplitudes of each NC color component on LED performance. Warm-white LEDs with CRI >90 and LER >380 lm/W at a correlated color temperature of 3000 K are shown to be achieved using nanocrystal luminophores. (C) 2009 Optical Society of AmericaItem Open Access A resampling-based meta-analysis for detection of differential gene expression in breast cancer(BioMed Central, 2008) Gur-Dedeoglu, B.; Konu, O.; Kir, S.; Ozturk, A. R.; Bozkurt, B.; Ergul, G.; Yulug, I.G.Background: Accuracy in the diagnosis of breast cancer and classification of cancer subtypes has improved over the years with the development of well-established immunohistopathological criteria. More recently, diagnostic gene-sets at the mRNA expression level have been tested as better predictors of disease state. However, breast cancer is heterogeneous in nature; thus extraction of differentially expressed gene-sets that stably distinguish normal tissue from various pathologies poses challenges. Meta-analysis of high-throughput expression data using a collection of statistical methodologies leads to the identification of robust tumor gene expression signatures. Methods: A resampling-based meta-analysis strategy, which involves the use of resampling and application of distribution statistics in combination to assess the degree of significance in differential expression between sample classes, was developed. Two independent microarray datasets that contain normal breast, invasive ductal carcinoma (IDC), and invasive lobular carcinoma (ILC) samples were used for the meta-analysis. Expression of the genes, selected from the gene list for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes were tested on 10 independent primary IDC samples and matched non-tumor controls by real-time qRT-PCR. Other existing breast cancer microarray datasets were used in support of the resampling-based meta-analysis. Results: The two independent microarray studies were found to be comparable, although differing in their experimental methodologies (Pearson correlation coefficient, R = 0.9389 and R = 0.8465 for ductal and lobular samples, respectively). The resampling-based meta-analysis has led to the identification of a highly stable set of genes for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes. The expression results of the selected genes obtained through real-time qRT-PCR supported the meta-analysis results. Conclusion: The proposed meta-analysis approach has the ability to detect a set of differentially expressed genes with the least amount of within-group variability, thus providing highly stable gene lists for class prediction. Increased statistical power and stringent filtering criteria used in the present study also make identification of novel candidate genes possible and may provide further insight to improve our understanding of breast cancer development.