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2021

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Silk Fiber-Based Composite Nanofiber Tissue Scaffold Produced With Electrospinning Method, Meti̇n Yüksek, Mehmet Akalin, Erhan Sancak, Erkan İşgören, Onur Atak, Derya Saltik Çi̇rki̇n, Ali̇ Beyi̇t Jan 2021

Silk Fiber-Based Composite Nanofiber Tissue Scaffold Produced With Electrospinning Method, Meti̇n Yüksek, Mehmet Akalin, Erhan Sancak, Erkan İşgören, Onur Atak, Derya Saltik Çi̇rki̇n, Ali̇ Beyi̇t

Turkish Journal of Chemistry

Wound dressings are one of the most rapidly expanding areas in medical textiles. In recent years, a large number of functional wound dressing has been developed. The aims of these products are to speed up the wound healing process and to provide maximum comfort for patients. Today, the multidisciplinary studies are required to improve further existed wound dressings. The results of such research studies are also promised new hopes for the Turkish textile industry weakened by the global competition. For this purpose, three different polymers were selected as silk fibroin (SF) / polycaprolactone (PCL) / polyethylene oxide (PEO). The productions …

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Tunable Aryl Alkyl Pyrazolium Tetrafluoroborate Ionic Liquids/Salts: Synthesis,Characterization, And Applications For Removal Of Methyl Orange From Aqueous Solution, Melek Canbulat Özdemi̇r Jan 2021

Tunable Aryl Alkyl Pyrazolium Tetrafluoroborate Ionic Liquids/Salts: Synthesis,Characterization, And Applications For Removal Of Methyl Orange From Aqueous Solution, Melek Canbulat Özdemi̇r

Turkish Journal of Chemistry

In this work, new tunable aryl alkyl pyrazolium tetrafluoroborate ionic liquids/salts, 2-ethyl-1-(p-X-phenyl)-3,5- dimethylpyrazolium tetrafluoroborate [X: -Br (4a), -OCH3 (4b), -NO2 (4c)] and 2-butyl-1-(p-X-phenyl)-3,5-dimethylpyrazolium tetrafluoroborate [X: -Br (5a), -OCH3 (5b), -NO2 (5c)], were synthesized by following halide-free synthetic route. Their chemical structures were identified through NMR (1H, 13C, 19F), IR, elemental analysis, and HRMS data. The synthesized 4a-4c and 5a-5c salts were used for the removal studies of methyl orange dye from aqueous solutions. The effects of specific parameters such as nature of the solvent, pH, contact time, amount and structure of the salts, and concentration of potassium chloride on the …

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Rees/Aaee Special Focus On Ethics: Introduction By Guest Editor, Shannon Chance, Shannon Chance Jan 2021

Rees/Aaee Special Focus On Ethics: Introduction By Guest Editor, Shannon Chance, Shannon Chance

Articles

Today, more than ever, we see the significance of ethics in developing and sustaining the built, social, and natural environments around us. We also recognise the need to develop engineering students’ knowledge, skills, and values regarding engineering, innovation, design, production, and the like. Engineers’ actions can have intended as well as unintended consequences, and we as a community need to become more aware of the outcomes and implications of our work. In response to the many topics presented at the REES 2019, the REEN Board selected ethics as the focus for this special issue and joined with AAEE to publish …

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Here You Have To Be Mixing: Collaborative Learning On An Engineering Program In Ireland As Experienced By A Group Of Young Middle Eastern Women, Shannon Chance, Bill Williams Jan 2021

Here You Have To Be Mixing: Collaborative Learning On An Engineering Program In Ireland As Experienced By A Group Of Young Middle Eastern Women, Shannon Chance, Bill Williams

Articles

This research project uses grounded theory to analyze interviews conducted with eight women from Oman and Kuwait. Members of the sample group were studying together at an institute of technology in Dublin, Ireland. The paper reports patterns in 15 interviews collected in the years 2014, 2015, 2016, and 2017 to provide a longitudinal overview of the experience of the learners. During the coding process, three major themes emerged having to do with the experience of learning with others and/or learning in groups. The first theme involved communication within the group and the group's approaches to working together. The second identified …

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Virfim: An Ai And Internet Of Medical Things-Driven Framework For Healthcare Using Smart Sensors, Sunder Ali Khowaja Jan 2021

Virfim: An Ai And Internet Of Medical Things-Driven Framework For Healthcare Using Smart Sensors, Sunder Ali Khowaja

Articles

No abstract provided.

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Triage Of Potential Covid-19 Patients From Chest X-Ray Images Using Hierarchical Convolutional Networks, Sunder Ali Khowaja Jan 2021

Triage Of Potential Covid-19 Patients From Chest X-Ray Images Using Hierarchical Convolutional Networks, Sunder Ali Khowaja

Articles

No abstract provided.

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Cascaded And Recursive Convnets (Crcnn): An Effective And Flexible Approach For Image Denoising, Sunder Ali Khowaja Jan 2021

Cascaded And Recursive Convnets (Crcnn): An Effective And Flexible Approach For Image Denoising, Sunder Ali Khowaja

Articles

No abstract provided.

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Stratifying Ischaemic Stroke Patients Across 3 Treatment Windows Using T2 Relaxation Times, Ordinal Regression And Cumulative Probabilities, Bryony Mcgarry, Elizabeth Hunter, Robin Damian, Michael Knight, Philip Clatworthy, George Harston, Keith Muir, Risto Kauppinen, John Kelleher Jan 2021

Stratifying Ischaemic Stroke Patients Across 3 Treatment Windows Using T2 Relaxation Times, Ordinal Regression And Cumulative Probabilities, Bryony Mcgarry, Elizabeth Hunter, Robin Damian, Michael Knight, Philip Clatworthy, George Harston, Keith Muir, Risto Kauppinen, John Kelleher

Conference papers

Unknown onset time is a common contraindication for anti-thrombolytic treatment of ischaemic stroke. T2 relaxation-based signal changes within the lesion can identify patients within or beyond the 4.5-hour intravenous thrombolysis treatment-window. However, now that intra-arterial thrombolysis is recommended between 4.5 and 6 hours from symptom onset and mechanical thrombectomy is considered safe between 6 and 24 hours, there are three treatment-windows to consider. Here we show a cumulative ordinal regression model, incorporating the T2 relaxation time, predicts the probabilities of a patient being within one of the three treatment-windows and is more accurate than signal intensity changes from T2 weighted …

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Zero-Shot Action Recognition With Knowledge Enhanced Generative Adversarial Networks, Kaiqiang Huang, Luis Miralles-Pechuán, Susan Mckeever Jan 2021

Zero-Shot Action Recognition With Knowledge Enhanced Generative Adversarial Networks, Kaiqiang Huang, Luis Miralles-Pechuán, Susan Mckeever

Conference papers

Zero-Shot Action Recognition (ZSAR) aims to recognise action classes in videos that have never been seen during model training. In some approaches, ZSAR has been achieved by generating visual features for unseen classes based on the semantic information of the unseen class labels using generative adversarial networks (GANs). Therefore, the problem is converted to standard supervised learning since the unseen visual features are accessible. This approach alleviates the lack of labelled samples of unseen classes. In addition, objects appearing in the action instances could be used to create enriched semantics of action classes and therefore, increase the accuracy of ZSAR. …

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Just-In-Time Biomass Yield Estimation With Multi-Modal Data And Variable Patch Training Size, Patricia O'Byrne, Patrick Jackman Dr., Damon Dr. Berry Dr., Thomas Lee, Michael French, Robert J. Ross Jan 2021

Just-In-Time Biomass Yield Estimation With Multi-Modal Data And Variable Patch Training Size, Patricia O'Byrne, Patrick Jackman Dr., Damon Dr. Berry Dr., Thomas Lee, Michael French, Robert J. Ross

Conference papers

The just-in-time estimation of farmland traits such as biomass yield can aid considerably in the optimisation of agricultural processes. Data in domains such as precision farming is however notoriously expensive to collect and deep learning driven modelling approaches need to maximise performance but also acknowledge this reality. In this paper we present a study in which a platform was deployed to collect data from a heterogeneous collection of sensor types including visual, NIR, and LiDAR sources to estimate key pastureland traits. In addition to introducing the study itself we address two key research questions. The first of these was the …

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Interactive Learning Approach For Arabic Target-Based Sentiment Analysis, Husamelddin Balla, Marisa Llorens, Sarah Jane Delany Jan 2021

Interactive Learning Approach For Arabic Target-Based Sentiment Analysis, Husamelddin Balla, Marisa Llorens, Sarah Jane Delany

Conference papers

Recently, the majority of sentiment analysis researchers focus on target-based sentiment analysis because it delivers in-depth analysis with more accurate results as compared to traditional sentiment analysis. In this paper, we propose an interactive learning approach to tackle a target-based sentiment analysis task for the Arabic language. The proposed IALSTM model uses an interactive attentionbased mechanism to force the model to focus on different parts (targets) of a sentence. We investigate the ability to use targets, right and left contexts, and model them separately to learn their own representations via interactive modeling. We evaluated our model on two different datasets: …

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K-Nearest Neighbour Classifiers - A Tutorial, Padraig Cunningham, Sarah Jane Delany Jan 2021

K-Nearest Neighbour Classifiers - A Tutorial, Padraig Cunningham, Sarah Jane Delany

Conference papers

Perhaps the most straightforward classifier in the arsenal or Machine Learning techniques is the Nearest Neighbour Classifier – classification is achieved by identifying the nearest neighbours to a query example and using those neighbours to determine the class of the query. This approach to classification is of particular importance because issues of poor run-time performance is not such a problem these days with the computational power that is available. This paper presents an overview of techniques for Nearest Neighbour classification focusing on; mechanisms for assessing similarity (distance), computational issues in identifying nearest neighbours and mechanisms for reducing the dimension of …

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Cellular Iron Storage And Trafficking Are Affected By Gtn Stimulation In Primary Glial And Meningeal Cell Culture, Lati̇fe Arzu Aral, Mehmet Ali̇ Ergün, Hayrunni̇sa Bolay Belen Jan 2021

Cellular Iron Storage And Trafficking Are Affected By Gtn Stimulation In Primary Glial And Meningeal Cell Culture, Lati̇fe Arzu Aral, Mehmet Ali̇ Ergün, Hayrunni̇sa Bolay Belen

Turkish Journal of Biology

A well-balanced intracellular iron trafficking in glial cells plays a role in homeostatic processes. Elevated intracellular iron triggers oxidative stress and cell damage in many neurological disorders, including migraine. This study aimed to investigate the effects of glyceryl trinitrate (GTN), on cellular iron homeostasis, matrixmetalloproteinase (MMP)-9, and calcitonin gene related peptide (CGRP) receptor (CRLR/CGRPR1) production in microglia, astrocyte, and meningeal cell cultures. Primary glial and meningeal cells in culture were exposed to GTN for 24 h. Messenger RNA expression was assessed using qPCR. Iron accumulation was visualized via modified Perl?s histochemistry. MMP-9 levels in cell culture supernatants were measured using …

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Expression Profiles Of Interferon-Related Genes In Cells Infected With Influenza A Viruses Or Transiently Transfected With Plasmids Encoding Viral Rna Polymerase, Eli̇f Çağlayan, Kadi̇r Turan Jan 2021

Expression Profiles Of Interferon-Related Genes In Cells Infected With Influenza A Viruses Or Transiently Transfected With Plasmids Encoding Viral Rna Polymerase, Eli̇f Çağlayan, Kadi̇r Turan

Turkish Journal of Biology

Influenza A viruses frequently change their genetic characteristics, which leads to the emergence of new viruses. Consequently, elucidation of the relationship between influenza A virus and host cells has a great importance to cope with viral infections. In this study, it was aimed to determine expression profiles of interferon response genes in human embryonic kidney 293 (HEK293) cells infected with human (A/WSN-H1N1) and avian influenza A viruses (duck/Pennsylvania/10218/84/H5N2) or transfected with plasmids encoding viral RdRP subunits and, to obtain clues about the genes that may be important for the viral pathogenesis. The HEK293 cells cultured in a 12-well plate were …

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Current Mutatome Of Sars-Cov-2 In Turkey Reveals Mutations Of Interest, Doğa Eski̇er, Evren Akalp, Özlem Dalan, Gökhan Karakülah, Yavuz Oktay Jan 2021

Current Mutatome Of Sars-Cov-2 In Turkey Reveals Mutations Of Interest, Doğa Eski̇er, Evren Akalp, Özlem Dalan, Gökhan Karakülah, Yavuz Oktay

Turkish Journal of Biology

As the underlying pathogen for the COVID-19 pandemic that has affected tens of millions of lives worldwide, SARS-CoV-2 and its mutations are among the most urgent research topics worldwide. Mutations in the virus genome can complicate attempts at accurate testing or developing a working treatment for the disease. Furthermore, because the virus uses its own proteins to replicate its genome, rather than host proteins, mutations in the replication proteins can have cascading effects on the mutation load of the virus genome. Due to the global, rapidly developing nature of the COVID-19 pandemic, local demographics of the virus can be difficult …

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Cover And Contents Jan 2021

Cover And Contents

Turkish Journal of Biology

No abstract provided.

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Prediction Of Host-Pathogen Protein Interactions By Extended Network Model, İrfan Kösesoy, Murat Gök, Tamer Kahveci̇ Jan 2021

Prediction Of Host-Pathogen Protein Interactions By Extended Network Model, İrfan Kösesoy, Murat Gök, Tamer Kahveci̇

Turkish Journal of Biology

Knowledge of the pathogen-host interactions between the species is essentialin order to develop a solution strategy against infectious diseases. In vitro methods take extended periods of time to detect interactions and provide very few of the possible interaction pairs. Hence, modelling interactions between proteins has necessitated the development of computational methods. The main scope of this paper is integrating the known protein interactions between thehost and pathogen organisms to improve the prediction success rate of unknown pathogen-host interactions. Thus, the truepositive rate of the predictions was expected to increase.In order to perform this study extensively, encoding methods and learning algorithms …

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Transcriptome Profiles Associated With Selenium-Deficiency-Dependent Oxidative Stress Identify Potential Diagnostic And Therapeutic Targets In Liver Cancer Cells, Damla Gözen, Deni̇z Cansen Kahraman, Kübra Narci, Huma Shehwana, Özlen Konu, Rengül Çeti̇n Atalay Jan 2021

Transcriptome Profiles Associated With Selenium-Deficiency-Dependent Oxidative Stress Identify Potential Diagnostic And Therapeutic Targets In Liver Cancer Cells, Damla Gözen, Deni̇z Cansen Kahraman, Kübra Narci, Huma Shehwana, Özlen Konu, Rengül Çeti̇n Atalay

Turkish Journal of Biology

Hepatocellular carcinoma (HCC) is one of the most common cancer types with high mortality rates and displays increased resistance to various stress conditions such as oxidative stress. Conventional therapies have low efficacies due to resistance and off-target effects in HCC. Here we aimed to analyze oxidative stress-related gene expression profiles of HCC cells and identify genes that could be crucial for novel diagnostic and therapeutic strategies. To identify important genes that cause resistance to reactive oxygen species (ROS), a model of oxidative stress upon selenium (Se) deficiency was utilized. The results of transcriptome-wide gene expression data were analyzed in which …

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Arid4b Physically Interacts With Tfap2c In Mouse Embryonic Stem Cells, Ezgi̇ Gül Keski̇n, Jialiang Huang, Ni̇hal Terzi̇ Çi̇zmeci̇oğlu Jan 2021

Arid4b Physically Interacts With Tfap2c In Mouse Embryonic Stem Cells, Ezgi̇ Gül Keski̇n, Jialiang Huang, Ni̇hal Terzi̇ Çi̇zmeci̇oğlu

Turkish Journal of Biology

Precise regulation of gene expression is required for embryonic stem cell (ESC) differentiation. Transcription factor (TF) networks coordinate the balance of pluripotency and differentiation in response to extracellular and intracellular signals. Chromatin factors work alongside TFs to achieve timely regulation of gene expression for differentiation process. Our previous studies showed that a member of the Sin3a corepressor complex, Arid4b, is critical for proper mouse ESC differentiation into mesoderm and endoderm. We found elevated histone 3 lysine 27 acetylation (H3K27Ac) in a subset of genomic loci in meso/endoderm directed arid4b? cells, coincident with their derepression. We reasoned that Sin3a complex may …

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Helicobacter-Stimulated Il-10-Producing B Cells Suppress Differentiation Of Lipopolysaccharide/Helicobacter Felis-Activated Stimulatory Dendritic Cells, Doğuş Altunöz, Ayça Sayi Yazgan Jan 2021

Helicobacter-Stimulated Il-10-Producing B Cells Suppress Differentiation Of Lipopolysaccharide/Helicobacter Felis-Activated Stimulatory Dendritic Cells, Doğuş Altunöz, Ayça Sayi Yazgan

Turkish Journal of Biology

Regulatory B cells (Bregs) produce antiinflammatory cytokines and inhibits proinflammatory response. Recently, immunosuppressive roles of Bregs in the effector functions of dendritic cells (DCs) were demonstrated. However, cross talk between Bregs and DCs in Helicobacter infection remains unknown. Here, we showed that direct stimulation of bone marrow-derived DCs (BMDCs) with Helicobacter felis (H. felis) antigen upregulates their CD86 surface expression and causes the production of interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), interleukin-12 (IL-12), and interleukin-10 (IL-10). Furthermore, prestimulation of DCs with supernatants derived from both Helicobacter-stimulated IL-10- B (Hfstim-IL-10- B) or IL-10+ B (Hfstim-IL-10+) cells suppresses the secretion of …

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Crosstalk Between Autophagy And Dna Repair Systems, Si̇nem Sarikaya, Hati̇ce Çakir, Devri̇m Gözüaçik, Yunus Akkoç Jan 2021

Crosstalk Between Autophagy And Dna Repair Systems, Si̇nem Sarikaya, Hati̇ce Çakir, Devri̇m Gözüaçik, Yunus Akkoç

Turkish Journal of Biology

Autophagy and DNA repair are two essential biological mechanisms that maintain cellular homeostasis. Impairment of these mechanisms was associated with several pathologies such as premature aging, neurodegenerative diseases, and cancer. Intrinsic or extrinsic stress stimuli (e.g., reactive oxygen species or ionizing radiation) cause DNA damage. As a biological stress response, autophagy is activated following insults that threaten DNA integrity. Hence, in collaboration with DNA damage repair and response mechanisms, autophagy contributes to the maintenance of genomic stability and integrity. Yet, connections and interactions between these two systems are not fully understood. In this review article, current status of the associations …

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Identification Of Differentially Expressed Micrornas In Primary Esophageal Achalasia By Next-Generation Sequencing, Mahin Gholipour, Javad Mikaeli, Seyed Javad Mowla, Mohammad Reza Bakhtiarzadeh, Marie Saghaeian Jazi, Naeme Javid, Narges Fazlollahi, Masoud Khoshnia, Naser Behnampour, Abdolvahab Moradi Jan 2021

Identification Of Differentially Expressed Micrornas In Primary Esophageal Achalasia By Next-Generation Sequencing, Mahin Gholipour, Javad Mikaeli, Seyed Javad Mowla, Mohammad Reza Bakhtiarzadeh, Marie Saghaeian Jazi, Naeme Javid, Narges Fazlollahi, Masoud Khoshnia, Naser Behnampour, Abdolvahab Moradi

Turkish Journal of Biology

Molecular knowledge regarding the primary esophageal achalasia is essential for the early diagnosis and treatment of this neurodegenerative motility disorder. Therefore, there is a need to find the main microRNAs (miRNAs) contributing to the mechanisms of achalasia. This study was conducted to determine some patterns of deregulated miRNAs in achalasia. This case-control study was performed on 52 patients with achalasia and 50 nonachalasia controls. The miRNA expression profiling was conducted on the esophageal tissue samples using the next-generation sequencing (NGS). Differential expression of miRNAs was analyzed by the edgeR software. The selected dysregulated miRNAs were additionally confirmed using the quantitative …

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The Promising Effects Of Bmp2 Transfected Mesenchymal Stem Cells On Humanosteosarcoma, Ahmet Si̇nan Sari, Emre Demi̇rçay, Ahmet Öztürk, Ayşen Terzi̇, Erdal Karaöz Jan 2021

The Promising Effects Of Bmp2 Transfected Mesenchymal Stem Cells On Humanosteosarcoma, Ahmet Si̇nan Sari, Emre Demi̇rçay, Ahmet Öztürk, Ayşen Terzi̇, Erdal Karaöz

Turkish Journal of Biology

Selective targeting of transfected mesenchymal stem cells (MSCs) carrying specific antioncogenes to the tumor was suggested as a treatment option. Bone morphogenetic protein-2 (BMP2) was shown to inhibit the proliferation and aggressiveness of osteosarcoma (OS) cells. Here, we aimed to assess the homing efficiency of intraperitoneally administered hMSCs transfected with BMP2 to the tumoral site and their effects on OS using an orthotopic xenograft murine model. Orthotopic xenograft murine model of OS in sixweek- old female NOD/SCID mice using 143B cells was established. hMSCs transfected with BMP2 (BMP2+hMSC) were used. In vivo experiments performed on four groups of mice that …

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Identification Of Serum Predictors Of N-Acetyl-L-Cysteine And Isoproterenol Induced Remodelling In Cardiac Hypertrophy, Dharaniyambigai Kuberapandian, Victor Arokia Doss Jan 2021

Identification Of Serum Predictors Of N-Acetyl-L-Cysteine And Isoproterenol Induced Remodelling In Cardiac Hypertrophy, Dharaniyambigai Kuberapandian, Victor Arokia Doss

Turkish Journal of Biology

Cardiac hypertrophy (CH), leading to cardiac failure is due to chronic metabolic alterations occurring during cellular stress. Besides the already known relationship between oxidative stress and CH, there are implications of reductive stress leading to CH. This study attempted to develop reductive stress-based CH rat model using n-acetyl-L-cysteine (NAC), a glutathione agonist that was compared with typical isoproterenol (ISO) induced CH model. The main objective was to identify serum metabolites that can serve as potent predictors for seven routine clinical and diagnostic parameters in CH: 3-hydroxybutyrate (3-HB), lactic acid (LA), urea, and ECG-CH parameters (QRS complex, R-amplitude, R-R interval, heart …

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Analyzing Differentially Expressed Genes And Pathways Of Bex2-Deficient Mouse Lung Via Rna-Seq, Noor Bahadar, Hanif Ullah, Salah Adlat, Rajiv Kumar Sah, May Zun Zaw Myint, Zin Mar Oo, Fatoumata Binta Bah, Farooq Hayel Nagi, Hsu Htoo, Ahmad Ud Din, Xuechao Feng, Yaowu Zheng Jan 2021

Analyzing Differentially Expressed Genes And Pathways Of Bex2-Deficient Mouse Lung Via Rna-Seq, Noor Bahadar, Hanif Ullah, Salah Adlat, Rajiv Kumar Sah, May Zun Zaw Myint, Zin Mar Oo, Fatoumata Binta Bah, Farooq Hayel Nagi, Hsu Htoo, Ahmad Ud Din, Xuechao Feng, Yaowu Zheng

Turkish Journal of Biology

Bex2 is well known for its role in the nervous system, and is associated with neurological disorders, but its role in the lung's physiology is still not reported. To elucidate the functional role of Bex2 in the lung, we generated a Bex2 knock-out (KO) mouse model using the CRISPR-Cas9 technology and performed transcriptomic analysis. A total of 652 genes were identified as differentially expressed between Bex2-/- and Bex2+/+ mice, out of which 500 were downregulated, while 152 were upregulated genes. Among these DEGs, Ucp1, Myh6, Coxa7a1, Myl3, Ryr2, RNaset2b, Npy, Enob1, Krt5, Myl2, Hba-a2, and Nrob2 are the most prominent …

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Identification Of Differentially Expressed Genomic Repeats In Primary Hepatocellular Carcinoma And Their Potential Links To Biological Processes And Survival, Gökhan Karakülah, Ci̇hangi̇r Yandim Jan 2021

Identification Of Differentially Expressed Genomic Repeats In Primary Hepatocellular Carcinoma And Their Potential Links To Biological Processes And Survival, Gökhan Karakülah, Ci̇hangi̇r Yandim

Turkish Journal of Biology

Hepatocellular carcinoma (HCC) is one of the deadliest cancers. Research on HCC so far primarily focused on genes and provided limited information on genomic repeats, which constitute more than half of the human genome and contribute to genomic stability. In line with this, repeat dysregulation was significantly shown to be pathological in various cancers and other diseases. In this study, we aimed to determine the full repeat expression profile of HCC for the first time. We utilised two independent RNA-seq datasets obtained from primary HCC tumours with matched normal tissues of 20 and 17 HCC patients, respectively. We quantified repeat …

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Investigation Of The Efficacy Of Paclitaxel On Some Mirnas Profiles In Breast Cancer Stem Cells, Eli̇f Ertürk, Ferda Ari, Oğuzhan Akgün, Engi̇n Ulukaya, Cem İsmai̇l Küçükali̇, Şaki̇r Ümi̇t Zeybek Jan 2021

Investigation Of The Efficacy Of Paclitaxel On Some Mirnas Profiles In Breast Cancer Stem Cells, Eli̇f Ertürk, Ferda Ari, Oğuzhan Akgün, Engi̇n Ulukaya, Cem İsmai̇l Küçükali̇, Şaki̇r Ümi̇t Zeybek

Turkish Journal of Biology

Understanding of the functions of microRNAs in breast cancer and breast cancer stem cells have been a hope for the development of new molecular targeted therapies. Here, it is aimed to investigate the differences in the expression levels of let-7a, miR-10b, miR-21, miR-125b, miR-145, miR-155, miR-200c, miR-221, miR-222 and miR-335, which associated with gene and proteins in MCF-7 (parental) and MCF-7s (Mammosphere/stem cell-enriched population/CD44+/CD24-cells) cells treated with paclitaxel. MCF-7s were obtained from parental MCF-7 cells. Cytotoxic activity of paclitaxel was determined by ATP assay. Total RNA isolation and cDNA conversion were performed from the samples. Changes in expression levels of …

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Phylostat: A Web-Based Tool To Analyze Paralogous Clade Divergencein Phylogenetic Trees, Eli̇f Özçeli̇k, Nurdan Kuru, Ogün Adebali̇ Jan 2021

Phylostat: A Web-Based Tool To Analyze Paralogous Clade Divergencein Phylogenetic Trees, Eli̇f Özçeli̇k, Nurdan Kuru, Ogün Adebali̇

Turkish Journal of Biology

Phylogenetic trees are useful tools to infer evolutionary relationships between genetic entities. Phylogenetics enables not only evolution-based gene clustering but also the assignment of gene duplication and deletion events to the nodes when coupled with statistical approaches such as bootstrapping. However, extensive gene duplication and deletion events bring along a challenge in interpreting phylogenetic trees and require manual inference. In particular, there has been no robust method of determining whether one of the paralog clades systematically shows higher divergence following the gene duplication event as a sign of functional divergence. Here, we provide Phylostat, a graphical user interface that enables …

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Identifying Specific Matrix Metalloproteinase-2-Inhibiting Peptides Through Phage Display-Based Subtractive Screening, Ayli̇n Özdemi̇r Bahadir, Bertan Koray Balcioğlu, Müge Serhatli, Şeyma Işik, Berri̇n Erdağ Jan 2021

Identifying Specific Matrix Metalloproteinase-2-Inhibiting Peptides Through Phage Display-Based Subtractive Screening, Ayli̇n Özdemi̇r Bahadir, Bertan Koray Balcioğlu, Müge Serhatli, Şeyma Işik, Berri̇n Erdağ

Turkish Journal of Biology

Gelatinases A and B, which are members of the matrix metalloproteinase (MMP) family, play essential roles in cancer development and metastasis, as they can break down basal membranes. Therefore, the determination and inhibition of gelatinases is essential for cancer treatment. Peptides that can specifically block each gelatinase may, therefore, be useful for cancer treatment. In this study, subtractive panning was carried out using a 12-mer peptide library to identify peptides that block gelatinase A activity (MMP-2), which is a key pharmacological target. Using this method, 17 unique peptide sequences were determined. MMP-2 inhibition by these peptides was evaluated through zymogram …

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Combination Of Classical And Statistical Approaches To Enhance The Fermentation Conditions And Increase The Yield Of Lipopeptide(S) By Pseudomonas Sp. Oxdc12: Its Partial Purification And Determining Antifungal Property, Vivek Chauhan, Vivek Dhiman, Shamsher S. Kanwar Jan 2021

Combination Of Classical And Statistical Approaches To Enhance The Fermentation Conditions And Increase The Yield Of Lipopeptide(S) By Pseudomonas Sp. Oxdc12: Its Partial Purification And Determining Antifungal Property, Vivek Chauhan, Vivek Dhiman, Shamsher S. Kanwar

Turkish Journal of Biology

Around 200 different lipopeptides (LPs) have been identified to date, most of which are produced via Bacillus and Pseudomonas species. The clinical nature of the lipopeptide (LP) has led to a big surge in its research. They show antimicrobial and antitumor activities due to which mass-scale production and purification of LPs are beneficial. Response surface methodology (RSM) approach has emerged as an alternative in the field of computational biology for optimizing the reaction parameters using statistical models. In the present study, Pseudomonas sp. strain OXDC12 was used for production and partial purification of LPs using Thin Layer Chromatography (TLC). The …

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