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Öğe Construction of protein sequence databases for metaproteomics: a review of the current tools and databases(2024) Arıkan, Muzaffer; Atabay, BaşakIn metaproteomics studies, constructing a reference protein sequence database that is both comprehensive and not overly large is critical for the peptide identification step. Therefore, the availability of well-curated reference databases and tools for custom database construction is essential to enhance the performance of metaproteomics analyses. In this review, we first provide an overview of metaproteomics by presenting a concise historical background, outlining a typical experimental and bioinformatics workflow, emphasizing the crucial step of constructing a protein sequence database for metaproteomics. We then delve into the current tools available for building such databases, highlighting their individual approaches, utility, and advantages and limitations. Next, we examine existing protein sequence databases, detailing their scope and relevance in metaproteomics research. Then, we provide practical recommendations for constructing protein sequence databases for metaproteomics, along with an overview of the current challenges in this area. We conclude with a discussion of anticipated advancements, emerging trends, and future directions in the construction of protein sequence databases for metaproteomics.Öğe A review on machine learning applications: CVI risk assessment(2024) Birlik, Ayşe Banu; Tozan, Hakan; Köse, Kevser BanuComprehensive literature has been published on the development of digital health applications using machine learning methods in cardiovascular surgery. Many machine learning methods have been applied in clinical decision-making processes, particularly for risk estimation models. This review of the literature shares an update on machine learning applications for cardiovascular intervention (CVI) risk assessment. This study selected peer-reviewed scientific publications providing sufficient detail about machine learning methods and outcomes predicting short-term CVI risk in cardiac surgery. Thirteen articles fulfilling pre-set criteria were reviewed and tables were created presenting the relevant characteristics of the studies. The review demonstrates the usefulness of machine learning methods in high-risk CVI applications, identifies the need for improvement, and provides efficient support for future prediction models for the healthcare system.Öğe Centralized healthcare database for ensuring better healthcare: Are we lagging behind?(Professional Medical Publications, 2024) Tariq, Sundus; Tariq, Saba; Shoukat, Ahmad AdnanDatabase is an organized set of large information gathered and stored electronically to be retrieved whenever required. The systematically stored information can be accessed, analyzed, updated or moved to other databases as per the requirement. A centralized healthcare database (CHD) is a memory house of health data from a wider population, where information such as health records, financial data, billing and claims information and inventory use is not only stored systematically but can also be retrieved, analyzed, and integrated. The data can be assessed by the health care providers, researchers, policy makers, institutions and by the patients themselves.Öğe Functionalized graphitic carbon nitrides for environmental and sensing applications(Wiley, 2021) Fidan, Tuçe; Torabfam, Milad; Saleem, Qandeel; Wang, Chao; Kurt, Hasan; Yüce, Meral; Tang, Junwang; Bayazıt, Mustafa KemalGraphitic carbon nitride (g-C3N4) is a metal-free semiconductor that has been widely regarded as a promising candidate for sustainable energy production or storage. In recent years, g-C3N4 has become the center of attention by virtue of its impressive properties, such as being inexpensive, easily fabricable, nontoxic, highly stable, and environment friendly. Herein, the recent research developments related to g-C3N4 are outlined, which sheds light on its future prospective. Various synthetic methods and their impact on the properties of g-C3N4 are detailed, along with discussion on frequently used characterization methods. Different approaches for g-C3N4 surface functionalization, mainly categorized under covalent and noncovalent strategies, are outlined. Moreover, the processing methods of g-C3N4, such as g-C3N4-based thin films, hierarchical, and hybrid structures, are explored. Next, compared with the extensively studied energy-related applications of the modified g-C(3)N(4)s, relatively less-examined areas, such as environmental and sensing, are presented. By highlighting the strong potential of these materials and the existing research gaps, new researchers are encouraged to produce functional g-C3N4-based materials using diverse surface modification and processing routes.Öğe Nanoplasmonic biosensors: Theory, structure, design, and review of recent applications(Elsevier, 2021) Kurt, Hasan; Pishva, Parsa; Pehlivan, Zeki Semih; Arsoy, Elif Gül; Saleem, Qandeel; Bayaz, Mustafa Kemal; Yüce, MeralNanoplasmonic biosensing shows an immense potential to satisfy the needs of the global health industry -low-cost, fast, and portable automated systems; highly sensitive and real-time detection; multiplexing and miniaturization. In this review, we presented the theory of nanoplasmonic biosensing for popular detection schemes -SPR, LSPR, and EOT -and underline the consideration for nanostructure design, material selection, and their effects on refractometric sensing performance. Later, we covered the bottom-up and top-down nanofabrication methods for nanoplasmonic biosensors. Subsequently, we reviewed the recent examples of nanoplasmonic biosensors over a wide range of clinically relevant analytes in the diagnosis and prognosis of a wide range of diseases and conditions such as biomarker proteins, infectious bacteria, viral agents. Finally, we discussed the challenges of nanoplasmonic biosensing toward clinical translation and proposed strategic avenues to be competitive against current clinical detection methods. Hopefully, nanoplasmonic biosensing can realize its potential through successful demonstrations of clinical translation in the upcoming years.Öğe Sağlık teknolojisi değerlendirmede çok kriterli karar verme yaklaşımları üzerine bir derleme çalışması(Düzce Üniversitesi, 2020) Almula Karadayı, Melis; Yılmaz, Beyza Özlem; Erol, Bilgehan Eren; Tozan, HakanSağlık sektöründe yer alan ilaçlar, tıbbi tedavi prosedürleri, tıbbı cihazlar, cerrahi teknikler ve sağlık sistemleri Sağlık Teknolojisi Değerlendirme (STD) kapsamında değerlendirilmektedir. Bu tip sağlık teknolojilerinin çeşitli yönlerden ele alınarak belirlenen kriterler ve istenen hedef doğrultusunda değerlendirilmesinde STD gittikçe popülerleşen bir yöntemdir. Sağlık sektöründe kaynakların kısıtlı olması ve maliyetlerin son yıllarda artış göstermesi, bu sektördeki karar vericileri etkili, güvenilir ve rasyonel adımlar atmaya itmiş ve STD’ye olan ilgiyi artırmıştır. STD’ye olan ilginin artmasıyla beraber kapsamı da çok kriterli ve paydaşlı olacak şekilde genişlemiştir. Çok Kriterli Karar Verme (ÇKKV) yöntemleri birden fazla kriter altında alternatifler arasından en iyi alternatifin seçilmesinde önemli rol oynar. Sağlık sektöründe yaşanan gelişmeler, sağlıkta eniyileme ve kanıta dayalı tıp uygulamalarının yaygınlaşması STD çalışmalarında ÇKKV yöntemlerine olan ilgiyi her geçen gün artırmaktadır. Bu derleme çalışmasında, literatürde son 10 yılda yapılanSTD çalışmaları ve ÇKKV yaklaşımlarıyla yapılan STD çalışmaları kapsamlı bir biçimde özetlenmiş ve sınıflandırılmıştır. Ayrıca derleme çalışmasının sonucunda, STD çalışmalarında ÇKKV yöntemlerinin kullanımının 2008 yılından sonra hızlı bir şekilde arttığı gözlemlenmiştir. En sık kullanılan ÇKKV yöntemlerinin ise AHP (Analitik Hiyerarşi Prosesi), EVIDEM (Evidence and Value: Impact on DecisionMaking) ve ağırlıklı çarpım olduğu sonucuna ulaşılmıştır.Öğe Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014–2019)(Springer, 2019) Pehlivan, Zeki Semih; Torabfam, Milad; Kurt, Hasan; Ow-Yang, Cleva; Hildebrandt, Niko; Yüce, MeralFluorescence resonance energy transfer, one of the most powerful phenomena for elucidating molecular interactions, has been extensively utilized as a biosensing tool to provide accurate information at the nanoscale. Numerous aptamer- and nanomaterial-based FRET bioassays has been developed for detection of a large variety of molecules. Affinity probes are widely used in biosensors, in which aptamers have emerged as advantageous biorecognition elements, due to their chemical and structural stability. Similarly, optically active nanomaterials offer significant advantages over conventional organic dyes, such as superior photophysical properties, large surface-to-volume ratios, photostability, and longer shelf life. In this report (with 175 references), the use of aptamer-modified nanomaterials as FRET couples is reviewed: quantum dots, upconverting nanoparticles, graphene, reduced graphene oxide, gold nanoparticles, molybdenum disulfide, graphene quantum dots, carbon dots, and metal-organic frameworks. Tabulated summaries provide the reader with useful information on the current state of research in the field.Öğe How to make nanobiosensors: Surface modification and characterisation of nanomaterials for biosensing applications(Royal Society of Chemistry, 2017) Yüce, Meral; Kurt, HasanThis report aims to provide the audience with a guideline for construction and characterisation of nanobiosensors that are based on widely used affinity probes including antibodies and aptamers and nanomaterials such as carbon-based nanomaterials, plasmonic nanomaterials and luminescent nanomaterials. The affinity probes and major methodologies that have been extensively used to make nanobiosensors, such as thiol-metal interactions, avidin-biotin interaction, p-interactions and EDC-NHS chemistry, were described with the most recent examples from the literature. Characterisation techniques that have been practised to validate nanoparticle surface modification with antibodies and aptamers, including gel electrophoresis, ultraviolet-visible spectrophotometry, dynamic light scattering and circular dichroism were described with examples. This report mainly covers the reports published between 2014 and 2017.Öğe Utilization of biased G protein-coupled receptor signaling towards development of safer and personalized therapeutics(MDPI, 2019) İlter, Metehan; Mansoor, Samman; Şensoy, ÖzgeG protein-coupled receptors (GPCRs) are involved in a wide variety of physiological processes. Therefore, approximately 40% of currently prescribed drugs have targeted this receptor family. Discovery of beta-arrestin mediated signaling and also separability of G protein and beta-arrestin signaling pathways have switched the research focus in the GPCR field towards development of biased ligands, which provide engagement of the receptor with a certain effector, thus enriching a specific signaling pathway. In this review, we summarize possible factors that impact signaling profiles of GPCRs such as oligomerization, drug treatment, disease conditions, genetic background, etc. along with relevant molecules that can be used to modulate signaling properties of GPCRs such as allosteric or bitopic ligands, ions, aptamers and pepducins. Moreover, we also discuss the importance of inclusion of pharmacogenomics and molecular dynamics simulations to achieve a holistic understanding of the relation between genetic background and structure and function of GPCRs and GPCR-related proteins. Consequently, specific downstream signaling pathways can be enriched while those that bring unwanted side effects can be prevented on a patient-specific basis. This will improve studies that centered on development of safer and personalized therapeutics, thus alleviating the burden on economy and public health.
