69 research outputs found
New wave simulations to the (3+1)-dimensional modified Kdv-Zakharov-Kuznetsov equation
No full textInternational Conference on Numerical Analysis and Applied Mathematics (ICNAAM) - SEP 19-25, 2016 - Rhodes, GREECEWOS: 000410159800577In this study, we apply an effective method which is improved Bernoulli sub-equation function method (IBSEFM) to the (3+1)-dimensional modified KdV-Zakharov-Kuznetsov equation. It gives some new wave simulations such as complex and exponential structures. We check up whether all structures verify the (3+1)-dimensional modified KdV-Zakharov-Kuznetsov model. Then, we plot three and two dimensional surfaces of obtained solutions by using Wolfram Mathematica 9
Investigating Effects of Microenvironment Stiffness on Valvular Interstitial Cell Myofibroblast Activation
Get PDFAortic valve stenosis (AVS) is a progressive fibrocalcific disease characterized by the thickening and stiffening of the valve leaflets, leading to disrupted blood flow through the aorta and altered cellular phenotypes of resident valvular interstitial cells (VICs) from quiescent fibroblasts to activated myofibroblasts. Comprehending the intricate mechanisms and signaling pathways underlying the transmission and processing of microenvironmental mechanical cues leading to alterations in VICs during myofibroblast activation can facilitate the identification of key players and potential druggable targets. With this objective in mind, the present thesis intends to investigate VIC signaling in response to matrix stiffness by employing 2D PEG hydrogel systems. Gaining insights into every stage of the process, ranging from the impact of primary mechanosensors to downstream signaling pathways and global gene expression changes, can enhance our comprehension of AVS initiation and progression. We first investigate the role of mechanosensitive calcium channel Transient Receptor Potential Vanilloid type 4 (TRPV4) in stiffness induced myofibroblast activation, a channel which has been strongly linked to fibrosis development. Using live calcium imaging, we verified TRPV4 functionality in VICs during application of small molecule drugs. We show that TRPV4 regulates VIC proliferation in a microenvironment stiffness-independent manner, whereas myofibroblast activation regulation is matrix-stiffness dependent. We further identify Yes-activated protein (YAP) as a downstream target for TRPV4 activity. In addition to inhibiting molecules that are involved in promoting fibrosis like TRPV4, over-expressing protective mechanisms which promote the resolution of fibrosis could be a potential therapeutic strategy. Thus, we direct our focus towards better understanding the role of PTEN as a protector against matrix-induced myofibroblast activation in VICs. We showed that PTEN overexpression using pharmacological inducers prevented myofibroblast activation, whereas genetic and pharmacological inhibition of PTEN further activated myofibroblasts. Finally, we observed that increased nuclear PTEN localization on stiff hydrogels correlated with smaller, more condensed nuclei and a quiescent fibroblast phenotype, suggesting an additional function for nuclear PTEN in promoting quiescence. Ultimately, our data suggested that PTEN could serve as a potential pharmacological target for the treatment of AVS. To better understand the link between microenvironmental stiffness and its effects on chromatin architecture, we study gene expression and accessibility changes that occur in during myofibroblast activation using Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) and RNAseq. We compare the chromatin landscape of quiescent VICs cultured on soft hydrogels and activated VICs cultured on stiff hydrogels. We find that open chromatin regions in activated VICs were enriched for transcription factor binding motifs associated with mechanosensing pathways compared to quiescent VICs. Next, we show the open chromatin regions in activated VICs correlated with pro-fibrotic gene expression including αSMA. In contrast, chromatin remodeling genes were downregulated in activated VICs compared to quiescent VICs, indicating quiescent VICs may be protected from myofibroblast activation through epigenetic mechanisms. Small molecule inhibition of one of these remodelers, CREB Binding Protein (CREBBP), prevented quiescent VICs from activating to activated VICs. Notably, CREBBP is more abundant in valves from healthy patients compared to fibrotic valves. Our findings reveal the role of mechanical regulation in chromatin remodeling during VIC activation and quiescence and highlight one potential therapeutic target for treating AVS. Overall, these insights into the mechanistic details of VIC activation and quiescence can inform the development of targeted therapies to prevent or reverse the progression of AVS.</p
Application of the Split GFP system to Listeria monocytogenes to visualize the virulence factor InlC
Get PDFListeria monocytogenes (Lm) is an opportunistic pathogen that is able to survive in a range of environments and cell types, and therefore serves as an important model system for host-pathogen studies. Lm can enter mammalian cells and survive within these host cells by secreting a number of virulence proteins during these steps. In the literature, there are inconsistencies in the localizations of one of these effector proteins, InlC. In order to better understand the localizations of the Lm effector protein InlC in the live cell during infections, a split GFP approach is taken to fluorescently label the protein. This system has been previously used in the Gram-negative pathogen Salmonella, and the goal of this thesis project is to create the tool to establish this method in Listeria monocytogenes. To provide more clear contrast in the fluorescence assays of the localizations of protein, an Lm strain producing a red fluorescent protein was created
Investigating Effects of Microenvironment Stiffness on Valvular Interstitial Cell Myofibroblast Activation
Get PDFAortic valve stenosis (AVS) is a progressive fibrocalcific disease characterized by the thickening and stiffening of the valve leaflets, leading to disrupted blood flow through the aorta and altered cellular phenotypes of resident valvular interstitial cells (VICs) from quiescent fibroblasts to activated myofibroblasts. Comprehending the intricate mechanisms and signaling pathways underlying the transmission and processing of microenvironmental mechanical cues leading to alterations in VICs during myofibroblast activation can facilitate the identification of key players and potential druggable targets. With this objective in mind, the present thesis intends to investigate VIC signaling in response to matrix stiffness by employing 2D PEG hydrogel systems. Gaining insights into every stage of the process, ranging from the impact of primary mechanosensors to downstream signaling pathways and global gene expression changes, can enhance our comprehension of AVS initiation and progression. We first investigate the role of mechanosensitive calcium channel Transient Receptor Potential Vanilloid type 4 (TRPV4) in stiffness induced myofibroblast activation, a channel which has been strongly linked to fibrosis development. Using live calcium imaging, we verified TRPV4 functionality in VICs during application of small molecule drugs. We show that TRPV4 regulates VIC proliferation in a microenvironment stiffness-independent manner, whereas myofibroblast activation regulation is matrix-stiffness dependent. We further identify Yes-activated protein (YAP) as a downstream target for TRPV4 activity. In addition to inhibiting molecules that are involved in promoting fibrosis like TRPV4, over-expressing protective mechanisms which promote the resolution of fibrosis could be a potential therapeutic strategy. Thus, we direct our focus towards better understanding the role of PTEN as a protector against matrix-induced myofibroblast activation in VICs. We showed that PTEN overexpression using pharmacological inducers prevented myofibroblast activation, whereas genetic and pharmacological inhibition of PTEN further activated myofibroblasts. Finally, we observed that increased nuclear PTEN localization on stiff hydrogels correlated with smaller, more condensed nuclei and a quiescent fibroblast phenotype, suggesting an additional function for nuclear PTEN in promoting quiescence. Ultimately, our data suggested that PTEN could serve as a potential pharmacological target for the treatment of AVS. To better understand the link between microenvironmental stiffness and its effects on chromatin architecture, we study gene expression and accessibility changes that occur in during myofibroblast activation using Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) and RNAseq. We compare the chromatin landscape of quiescent VICs cultured on soft hydrogels and activated VICs cultured on stiff hydrogels. We find that open chromatin regions in activated VICs were enriched for transcription factor binding motifs associated with mechanosensing pathways compared to quiescent VICs. Next, we show the open chromatin regions in activated VICs correlated with pro-fibrotic gene expression including αSMA. In contrast, chromatin remodeling genes were downregulated in activated VICs compared to quiescent VICs, indicating quiescent VICs may be protected from myofibroblast activation through epigenetic mechanisms. Small molecule inhibition of one of these remodelers, CREB Binding Protein (CREBBP), prevented quiescent VICs from activating to activated VICs. Notably, CREBBP is more abundant in valves from healthy patients compared to fibrotic valves. Our findings reveal the role of mechanical regulation in chromatin remodeling during VIC activation and quiescence and highlight one potential therapeutic target for treating AVS. Overall, these insights into the mechanistic details of VIC activation and quiescence can inform the development of targeted therapies to prevent or reverse the progression of AVS.</p
Application of the Split GFP system to Listeria monocytogenes to visualize the virulence factor InlC
Get PDFListeria monocytogenes (Lm) is an opportunistic pathogen that is able to survive in a range of environments and cell types, and therefore serves as an important model system for host-pathogen studies. Lm can enter mammalian cells and survive within these host cells by secreting a number of virulence proteins during these steps. In the literature, there are inconsistencies in the localizations of one of these effector proteins, InlC. In order to better understand the localizations of the Lm effector protein InlC in the live cell during infections, a split GFP approach is taken to fluorescently label the protein. This system has been previously used in the Gram-negative pathogen Salmonella, and the goal of this thesis project is to create the tool to establish this method in Listeria monocytogenes. To provide more clear contrast in the fluorescence assays of the localizations of protein, an Lm strain producing a red fluorescent protein was created
İnsan – mekan ilişkisi
No full textHaraçcı, Dilara (Dogus Author -- Çelik, Sönmez (Dogus Author)Yaşamda “mekân” çok farklı biçimlerde bireylerin karşına çıkmakta ve insan mekan ilişkisini oluşturmaktadır.
Mekân oluşturmak, eylemlere yanıt veren yapay ortamların elde edilmesi ile tanımlanmakta ve zaman içindeki evrelerde ihtiyaçlara bağlı olarak değişiklik göstermektedir.
Mekân yaratmak, insanoğlunun algılayabildiği doğal çevre sınırları kapsamında belirlenen alanları sınırlamaları ve kendi yararlarına kullanmalarına uygun düzenlemeleridir.
Mekânlar, insanların yaşamlarına yön veren özellik ve ilkeleri içermelidir. Toplumların oluşturdukları mekan biçimleri, tasarım dönemlerine özgü malzemeleri ve uygulamalarını da ambiyans ve konfor olarak düzenlemelere yansıtmaktadır.ÖNSÖZ, III -- ÖZET, V -- ABSTRACT, VII -- BÖLÜM 1. , İNSAN VE MEKAN, 1 -- TANIMLAR, 1 -- İnsanın tanımı, 1 -- Mekanın tanımı, 8 -- MEKAN KİMLİĞİNİN BELİRLENMESİ, 9 -- Mekan kimliğini etkileyen nedenler, 16 -- Mekan kimliğinin değişim nedenleri, 24 -- MEKAN ÇEŞİTLERİ, 26 -- İÇ MEKAN TASARIMINDA GEREÇ KULLANIMI, 33 -- MEKANDA GRAFİK TASARIM KULLANILMASI, 37 -- İNSAN-MEKAN İLİŞKİSİ, 41 -- İnsan ve Mekan İlişkisinde İnsanın Antropometrik Ölçülerinin Önemi, 49 -- MEKANLARDA İÇMİMARIN ROLÜ, 54 -- BÖLÜM 2., İÇ VE DIŞ MEKANLAR, 61 -- İÇ MEKAN TANIMLARI VE ÖZELLİKLERİ, 66 -- İÇ MEKAN ÇEŞİTLERİ VE DONATILARI, 73 -- DIŞ MEKAN TANIMLARI VE ÖZELLİKLERİ, 80 -- BÖLÜM 3., ÇEVRE, 95 -- ÇEVRE TANIMLARI VE BİLEŞENLERİ, 96 -- Fiziksel çevre, 98 -- Doğal çevre, 99 -- Yapay çevre, 102 -- Sosyal Çevre, 105 -- KAYNAKÇA, 10
Erratum: In vitro comparison of the erosive potential of four different wines on human dental enamel (vol. 26, br. 1, str. 41-46, 2022)
No full textIn the article that appeared on pages 41-46 of the March 2022 issue of the Balkan Journal of Dental Medicine the name of first author was miswritten, and it should be Dilara Şeyma Alpkılıç. The publisher regret this error
"Högläsning av skönlitteratur ger eleverna ett rikt ordförråd" : En kvalitativ undersökning av hur mellanstadielärare arbetar med skönlitterär högläsning relaterat till ordförrådsutveckling
No full textAbstract Title: “Reading aloud fiction gives students a rich vocabulary”Author: Dilara AkcaySupervisor: Jenny MagnussonThe purpose of this study is to find out how teachers work with students' vocabulary development in reading aloud activities in fiction within the subject of Swedish.Furthermore, the purpose is to find out how teachers’ reason about their work to develop students' vocabulary in fiction reading aloud. The study’s questions are the following: What strategies do teachers use when reading fiction aloud in the Swedish subject to develop the students' vocabulary? How do the teachers reason about their work of developing students' vocabulary in fiction reading aloud?The material was analyzed based on Beck et al.'s (2013) teaching model on strategies for vocabulary development. This study is based on a qualitative method for answering the questions. A qualitative method is relevant to the study because the study examines what strategies teachers use to develop students' vocabulary in fiction reading aloud. To find out this, it is essential to observe and interview teachers. Semi-structured interviews were conducted with three teachers from three different schools.The results of the observations showed that the two teachers, Jessica and Tina used the strategy of asking questions to the students and explaining words using everyday language. Jessica also worked with the strategy that the students are allowed to use the word themselves. In addition, Tina uses visual aids to deepen students' understanding of words and she uses body language and exemplifies the word by changing her voice, so the pupils get a better understanding of the words. Jessica uses visual aids to help students gain a deeper understanding of the word.The third teacher, Katarina, does not explain any words to the students, despite the fact that there were some difficult words in the book that could have been explained. Strategies such as pronouncing words and presenting words in new contexts did not appear in the observations. The teachers say in the interviews that they work on vocabulary development in fiction reading aloud. The strategies teachers use in reading aloud are to ask students questions about the meaning of the word and define the word in everyday language. Tina uses visual support to give students a deeper understanding of the word. Jessica uses a lot of body language to shape some difficult words, and Katarina says that she works with the three-cup method, where students find synonyms for the word. Tina and Jessica talk about how important reading aloud is for students' vocabulary development, and they read aloud for students to learn new words. Katarina believes that reading aloud is more for them to be a cozy moment for the students. Keywords: Vocabulary development, middle school, Swedish teaching, reading aloud. Nyckelord: Ordförrådsutveckling, mellanstadiet, svenskundervisning, högläsning.
"Högläsning av skönlitteratur ger eleverna ett rikt ordförråd" : En kvalitativ undersökning av hur mellanstadielärare arbetar med skönlitterär högläsning relaterat till ordförrådsutveckling
No full textAbstract Title: “Reading aloud fiction gives students a rich vocabulary”Author: Dilara AkcaySupervisor: Jenny MagnussonThe purpose of this study is to find out how teachers work with students' vocabulary development in reading aloud activities in fiction within the subject of Swedish.Furthermore, the purpose is to find out how teachers’ reason about their work to develop students' vocabulary in fiction reading aloud. The study’s questions are the following: What strategies do teachers use when reading fiction aloud in the Swedish subject to develop the students' vocabulary? How do the teachers reason about their work of developing students' vocabulary in fiction reading aloud?The material was analyzed based on Beck et al.'s (2013) teaching model on strategies for vocabulary development. This study is based on a qualitative method for answering the questions. A qualitative method is relevant to the study because the study examines what strategies teachers use to develop students' vocabulary in fiction reading aloud. To find out this, it is essential to observe and interview teachers. Semi-structured interviews were conducted with three teachers from three different schools.The results of the observations showed that the two teachers, Jessica and Tina used the strategy of asking questions to the students and explaining words using everyday language. Jessica also worked with the strategy that the students are allowed to use the word themselves. In addition, Tina uses visual aids to deepen students' understanding of words and she uses body language and exemplifies the word by changing her voice, so the pupils get a better understanding of the words. Jessica uses visual aids to help students gain a deeper understanding of the word.The third teacher, Katarina, does not explain any words to the students, despite the fact that there were some difficult words in the book that could have been explained. Strategies such as pronouncing words and presenting words in new contexts did not appear in the observations. The teachers say in the interviews that they work on vocabulary development in fiction reading aloud. The strategies teachers use in reading aloud are to ask students questions about the meaning of the word and define the word in everyday language. Tina uses visual support to give students a deeper understanding of the word. Jessica uses a lot of body language to shape some difficult words, and Katarina says that she works with the three-cup method, where students find synonyms for the word. Tina and Jessica talk about how important reading aloud is for students' vocabulary development, and they read aloud for students to learn new words. Katarina believes that reading aloud is more for them to be a cozy moment for the students. Keywords: Vocabulary development, middle school, Swedish teaching, reading aloud. Nyckelord: Ordförrådsutveckling, mellanstadiet, svenskundervisning, högläsning.
Wikipedia based semantic smoothing for Twitter sentiment classification
No full textTorunoğlu, Dilara (Dogus Author)Sentiment classification is one of the important and popular application areas of text classification in which texts are labeled as positive and negative. Moreover, Naive Bayes (NB) is one of the mostly used algorithms in this area. NB having several advantages on lower complexity and simpler training procedure, it suffers from zero probability problems (Rish, 2001). Smoothing methods are employed for this problem; mostly Laplace Smoothing is used; however in this paper we propose Wikipedia based semantic smoothing approach. Our semantic smoothing formulation is based on the work in (Zhou, 2008). We extend this study by employing Wikipedia to extract topic signatures. Moreover, we also incorporated semantic knowledge in Wikipedia such as categories and redirects. To be more precise, we use Wikipedia article titles that exist in documents, categories and redirects of these articles as topic signatures to enrich the dataset. We apply our approach to sentiment classification of tweets. Results of the extensive experiments show that our approach improves the performance of NB and even can exceed the accuracy of SVM on Twitter Sentiment 140 dataset.Anlamsal sınıflandırma, metin sınıflandırma alanında kullanılan en önemli ve en popüler sınıflandırma yaklaşımlarından biridir ki bu yaklaşımda metinler pozitif ve negatif olarak sınıflandırılmaktadır. Dahası, Naive Bayes (NB) bu alanda en çok kullanılan algoritmadır. NB algoritmasının düşük karmaşıklık, basit öğrenme prosedürü gibi avantajlarının yanında, sıfır olasılık problemiyle uğraşmaktadır (Rish, 2001). Yumuşatma metodları bu probleme uygulanmaktadır, çoğunlukla da Laplace yumuşatması kullanılır; ancak bu çalışmada biz Vikipedi tabanlı anlamsal yumuşatma algoritmasını önermekteyiz. Bizim anlamsal yumuşatma algoritmamızın formülleri (Zhou, 2008)'deki çalışmasına dayanmaktadır. Biz bu çalışmadaki anlamsal zenginleştirmeyi Vikipedi kullanarak genişlettik . Ayrıca, Vikipedi kategorilerin ve yönlendirmelerini anlamsal bilgi geliştirme yönünde ekledik. Daha açık konuşmak gerekirse, bu çalışma anlamsal yumuşatma yaklaşımını görülen Vikipedi başlıklarını, bu başlıkların kategorileri ve yönlendirmelerini kullanılarak Twitter veri kümesini zenginleştirmek amaçlı kullanılmıştır. Yaklaşımımızı anlamsal sınıflandırma amacıyla tweet' ler üzerinde uyguladık. Yapılan birçok testin sonucunda görülmüştür ki Twitter Sentiment 140 veri kümesi üzerinde, yaklaşımımız Naive Bayes algoritmasının başarısını arttırmakta ve Karar Destek Makinelerini geçmektedir.This work was supported in part by The Scientific and Technological Research Council of Turkey (TÜBİTAK) grant number 111E239.PREFACE, IV -- ABSTRACT, V -- ÖZET, VI -- ACKNOWLEDGMENT, VII -- LIST OF FIGURES, VIII -- LIST OF TABLES, IX -- LIST OF SYMBOLS, X -- ABBREVIATIONS, XI -- 1. INTRODUCTION, 1 -- 2. RELATED WORK, 4 -- 3. APPROACH, 28 -- 3.1. Naive Bayes Algorithm, 28 -- 3.2. Smoothing Methods, 29 -- 3.2.1. Laplace Smoothing, 29 -- 3.2.2. Jelinek-Mercer Smoothing, 30 -- 3.2.3. Semantic Smoothing, 31 -- 3.3. Wikipedia Based Semantic Smoothing Model, 33 -- 3.3.1. Freebase Wikipedia Extractor, 34 -- 3.3.2. Term Extractor, 35 -- 3.3.3. Wiki Concept Extractor, 35 -- 3.3.4. Topic Signatures, 36 -- 3.3.5. Wikipedia Articles, Categories and Redirects, 37 -- 4. EXPERIMENTAL SETUP, 41 -- 4.1. Twitter Data Set, 41 -- 4.2. Twitter Enriched with Wikipedia Articles, Categories & Redirects Data Sets, 46 -- 5. EXPERIMENTAL RESULTS, 48 -- 6. CONCLUSION, 56 -- REFERENCES, 59 -- BIOGRAPHY, 6
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