IYTE GCRIS Database (Izmir Institute of Technology)
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Molecular Separation by Using Active and Passive Microfluidic Chip Designs: a Comprehensive Review
No full textSeparation and identification of molecules and biomolecules such as nucleic acids, proteins, and polysaccharides from complex fluids are known to be important due to unmet needs in various applications. Generally, many different separation techniques, including chromatography, electrophoresis, and magnetophoresis, have been developed to identify the target molecules precisely. However, these techniques are expensive and time consuming. “Lab-on-a-chip” systems with low cost per device, quick analysis capabilities, and minimal sample consumption seem to be ideal candidates for separating particles, cells, blood samples, and molecules. From this perspective, different microfluidic-based techniques have been extensively developed in the past two decades to separate samples with different origins. In this review, “lab-on-a-chip” methods by passive, active, and hybrid approaches for the separation of biomolecules developed in the past decade are comprehensively discussed. Due to the wide variety in the field, it will be impossible to cover every facet of the subject. Therefore, this review paper covers passive and active methods generally used for biomolecule separation. Then, an investigation of the combined sophisticated methods is highlighted. The spotlight also will be shined on the elegance of separation successes in recent years, and the remainder of the article explores how these permit the development of novel techniques. © 2023 The Authors. Advanced Materials Interfaces published by Wiley-VCH GmbH
Degraded Arid Soil Reclamation for Cotton Cultivation Using Organic Waste Amendments
No full textQatar is one of the most fertilizer-dependent countries due to challenging soil and climatic conditions. The country strives toward self-sufficiency in agricultural production in alignment with the Qatar National Vision 2030. Hence, this work investigates the potential of utilizing nutrient-rich resources that are currently wasted for the reclamation of degraded arid soils to support the cultivation of industrial crops such as cotton (Gossypium spp.). Two abundant organic wastes, industrial biosludge and cow dung compost, were employed as soil amendments at a 3% application rate on a silty loam soil with relatively high salinity (electrical conductivity = 5.60 dS/m) and compared with conventional chemical fertilization. Cotton (May 344 variety) was then grown on the biowaste-amended soils in lysimeters for ten months (March through January) spanning through the hot season in Qatar, with the average temperature ranging from 19 to 37 °C. Soil properties and plant growth characteristics, including soil metal concentrations, days to germination and flowering, plant height, and cotton yield, were determined at set periods. The results indicated that different from the chemical fertilizer treatment, the organic amendments led to a significant release of potassium eight months after planting, roughly twice the concentration available at the initial sampling period. In all treatments, soil magnesium and iron concentrations generally increased, while phosphorus and zinc decreased over time. There was generally no significant difference in the concentrations of metals analyzed such as chromium, copper, nickel, and zinc between soils amended with the organic wastes and chemical fertilizer. The concentrations of metals were below the regulatory limits for sewage sludge applied to soils. The days to germination were 2, 9, and 11, while the days to flowering were 61, 92, and 77 for the cow dung compost, biosludge, and fertilizer treatments, respectively. The average cumulative plant heights were 74, 65, and 63 cm, while the average cumulative cotton boll yield was 7.3, 5.4, and 2.6 tons/ha, respectively, in the cow dung compost, biosludge, and fertilizer treatments. The results demonstrate that the organic amendments, especially cow dung compost, can help reclamation of degraded/saline arid soils under the described pedo-climatic conditions. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024
Effect of Irradiation on Total Biophenol and Antioxidant Activity During Storage of Natural Black Table Olives Obtained Using Starter Culture
No full textIn this study, it was aimed to determine the effects of different production and preservation methods on the shelf life and quality of the Gemlik variety of natural black table olives produced with low salt (2%). For this purpose, olives were processed by the traditional Turkish style dry salted black olive by using a starter culture. The MAP (Modified atmosphere packaging, 60% N2 and 40% CO2), vacuum and for the first time gamma irradiation methods (1, 3 and 5 kGy) were applied in the preservation of table olives. The 5 kGy irradiation treatment reduced the total phenolic amount and DPPH antioxidant activity of olives more than other irradiation doses. The pH (4.3–4.83) and titratable acidity (0.68–1.02%) of the samples changed in accordance with the legal regulations during the storage period (pH max. 5 and acidity min 0.3%). At the end of the fermentation and storage, total phenolic content and antioxidant activity decreased significantly (p-value 0.05). During the storage period, the total phenolic content in natural fermented olives (without starter culture) decreased from 232 to 144 mgCAE/100 g and in starter culture added table olives from 200 to 138 mgCAE/100 g. In addition, the antioxidant activity was changed between 60.94 and 47.14 μmolTE/100 g oil. As a result of the study, it was ensured that black table olives produced with less salt (2%) could be stored on the shelves for 6 months without using any preservatives. In addition, radiation effect on quality was relatively similar to other treatments (vacuum and MAP). © 2024 AOCS
Investigation of Aminoethyl Methacrylate Polymers for in Vivo Delivery of Mrna
No full textGüvenli ve etkili gen tedavileri için viral olmayan vektörlere büyük bir ihtiyaç vardır. Özellikle mRNA (mesajcı RNA) temelli gen tedavileri için polimerik vektörlerin kullanımı çok sınırlıdır. Bu tez kapsamında, zebra balığı embriyoları kullanılarak yeni geliştirilen bir polimerik vektörün in vivo transfeksiyon etkinliğinin, bilinen lipidik ve polimerik vektörlerle karşılaştırmalı olarak ön araştırmasının yapılması amaçlanmıştır. Bu amaç doğrultusunda, blok kopolimer, poli(oligo(etilen glikol) metakrilat)-b-poli(2-(amino)etil)amino)etil metakrilat, P(OEGMA)42-b-P(AEAEMA)48 ile Lipofectamine 3000 ve dallanmış polietilen iminin (PEI) (25 kDa) mRNA transfeksiyon etkinliği zebra balığı embriyoları modeli üzerinde in vivo olarak incelenmiştir. Çalışılan aralıkta en iyi uygulama bölgesi ve yöntemi, mRNA dozu, türü ve gelişim aşamasını belirlemek için önce çıplak mRNA veya Lipofectamine-mRNA kompleksleri kullanılarak birçok optimizasyon deneyi gerçekleştirildi. Optimizasyon deneylerinden elde edilen sonuçlar göz önünde bulundurularak, GFP-mRNA (2000 ng) ve N/P oranı 3.6 veya 7.3 olan P(OEGMA)42-b-P(AEAEMA)48 ile oluşturulan polipleksler, GFP ifadesini gözlemlemek için döllenmeden 48 saat sonraki gelişim aşamasında olan zebra balığı embriyolarının perikardiyal boşluğuna enjekte edildi. Karşılaştırma için çıplak mRNA, çıplak embriyolar, Lipofektamine-mRNA kompleksi ve PEI-mRNA polipleksleri kullanıldı. Örnekler enjeksiyondan 24 saat sonra konfokal mikroskobu kullanılarak görselleştirildi ve Image J ile analiz edildi. Blok kopolimer, altın standart polimerik vektör PEI ile karşılaştırılabilir transfeksiyon etkinliği gösterdi. Bu çalışmada elde edilen ön sonuçlar, mRNA tabanlı gen tedavileri için potansiyel bir polimerik vektör olarak P(OEGMA)42-b-P(AEAEMA)48'in in vivo uygulamaları üzerine daha fazla araştırma yapılmasının önünü açmaktadır.There is a tremendous need for non-viral vectors for safe and efficient gene therapies. Especially the use of polymeric vectors for messenger RNA (mRNA) based gene therapies is limited. Within the scope of this thesis, it is aimed to perform a preliminary investigation on the in vivo transfection ability of a newly developed polymeric vector using zebrafish embryos in comparison with well-known lipidic and polymeric vectors. In line with this goal, the mRNA transfection ability of the block copolymer, poly(oligo(ethylene glycol) methacrylate)-b-poly(2-(amino)ethyl)amino)ethyl methacrylate, P(OEGMA)42-b-P(AEAEMA)48 along with Lipofectamine 3000 and branched polyethylene imine (PEI) (25 kDa) was examined in vivo on zebrafish embryos. A number of optimization experiments were first performed using naked mRNA or Lipofectamine-mRNA complexes to determine the best administration site and method, mRNA dose, type and development stage of embryos within the studied range. Considering the results obtained from optimization experiments, polyplexes formed with GFP-mRNA (2000 ng) and P(OEGMA)42-b-P(AEAEMA)48 at an N/P ratio of 3.6 or 7.3 were injected into the pericardial cavity of developing zebrafish embryos at 48 hours post fertilization to observe GFP expression. Naked mRNA, naked embryos, Lipofectamine-mRNA complex, and PEI-mRNA polyplexes were used for comparison. Samples were visualized 24 hours after injection using confocal microscopy and analyzed with Image J. The block copolymer showed transfection efficiency comparable with the golden standard polymeric vector PEI. The preliminary results obtained in this study pave the way for further investigations on the in vivo applications of P(OEGMA)42-b-P(AEAEMA)48 as a potential polymeric vector for mRNA-based gene therapies
Comparison of Linear and Nonlinear Twist Extrusion Processes With Crystal Plasticity Finite Element Analysis
No full textThe mechanical characteristics of polycrystalline metallic materials are influenced significantly by various microstructural parameters, one of which is the grain size. Specifically, the strength and the toughness of polycrystalline metals exhibit enhancement as the grain size is reduced. Applying severe plastic deformations (SPDs) has a noticeable result in obtaining metallic materials with ultrafine-grained (UFG) microstructure. SPD, executed through conventional shaping methods like extrusion, plays a pivotal role in the evolution of the texture, which is closely related to the plastic behavior and ductility. A number of SPD processes have been developed to generate ultrafine-grained materials, each having a different shear deformation mechanism. Among these methods, linear twist extrusion (LTE) presents a non-uniform and non-monotonic form of severe plastic deformation, leading to significant shifts in the microstructure. Prior research demonstrates the capability of the LTE process to yield consistent, weak textures in pre-textured copper. However, limitations in production efficiency and the uneven distribution of grain refinement have curbed the widespread use of LTE in industrial settings. This has facilitated the development of an improved novel method, that surpasses the traditional approach, known as the nonlinear twist extrusion procedure (NLTE). The NLTE method innovatively adjusts the channel design of the mold within the twist section to mitigate strain reversal and the rotational movement of the workpiece, both of which have been identified as shortcomings of twist extrusion. Accurate anticipation of texture changes in SPD processes is essential for mold design and process parameter optimization. The performance of the proposed extrusion technique should still be studied. In this context, here, a single crystal (SC) of copper in billet form, passing through both LTE and NLTE, is analyzed, employing a rate-dependent crystal plasticity finite element (CPFE) framework. CPFE simulations were performed for both LTE and NLTE of SC copper specimens having 100> or 111> directions parallel to the extrusion direction initially. The texture evolution as well as the cross-sectional distribution of the stress and strain is studied in detail, and the performance of both processes is compared
Entanglement and Invariance of Qubit-Qubit, Qubit-Qutrit and Qutrit-Qutrit Quantum States
No full textMevcut tez, saf iki kübit, kübit-kütrit ve iki kütrit durumlarının dolanıklık özelliklerinin incelenmesine ayrılmıştır. Dolanıklık, esasen bileşik kuantum durumlarının klasik olmayan bir özelliğidir ve kuantum hesaplamasında ve kuantum bilgi teorisinde önemli bir rol oynar. Durumların dolanıklığını karakterize etmek için, saf bileşik durumun dolanıklığını karışık azaltılmış yoğunluklu matrisle ilişkilendiren azaltılmış yoğunluk matrisi yaklaşımını kullanırız. Azaltılmış yoğunluk matrisinin Von Neumann entropisi ve karesel eşzamanlılık olarak doğrusal entropi, dolanıklığı ölçmek için kullanılır. Üniter bir kübit ve bir kütrit kapılarını kullanarak, dönüşümler altında dolanıklığın değişmezliğini gösteririz. Bu, aynı seviyedeki dolanık durumların sürekli olarak parametrelendirilmiş kümesini oluşturmamızı sağlar. Sonuçları, verilen karışık durum için arıtmanın hesaplanması ve manyetik alanda iki kübit spin XYZ modeli için ortalama enerjinin maksimum dolaşık minimumunu bulmak için uyguluyoruz.The present thesis is devoted to studies of entanglement properties of pure twoqubit, qubit-qutrit and two-qutrit states. Entanglement is essentially non-classical characteristics of composite quantum states and it plays a key point in quantum computation and quantum information theory. To characterize entanglement of the states we use the reduced density matrix approach, which relates entanglement of pure composite state with mixed reduced density matrix. Von Neumann entropy of the reduced density matrix and the linear entropy, as squared concurrence are used to quantify entanglement. By using the unitary one qubit and one qutrit gates we show invariance of entanglement under the transformations. This allows us to construct continuously parametrized set of the same level entangled states. We apply the results for calculation of purification for given mixed state and for finding maximally entangled minimum of average energy for two-qubit spin XYZ model in magnetic field
Yapay zeka
No full text2 Temmuz 2024 tarihinde İYTE’de düzenlenen Girişimcilik ve İnovasyon temalı Lise Bilim Kampında farklı liselerden seçilen 35 öğrenciye “Yapay Zeka Destekli Araştırma Teknikleri” dersi kapsamında yapılmış sunumdur
A Note on Variants of Euler's Φ-Function
No full textIt is well-known that the sum of the firstnconsecutive integers alwaysdivides thek-th power sum of the firstnconsecutive integers whenkis odd. Motivatedby this result, in this note, we study the divisibility properties of the power sum ofpositive integers that are coprime tonand not surpassingn. First, we prove a finitenessresult for our divisibility sets using smooth numbers in short intervals. Then, we findthe exact structure of a certain divisibility set that contains the orders of these powersums and our result is of computational flavour
Biomolecular Fingerprints of the Effect of Zoledronic Acid on Prostate Cancer Stem Cells: Comparison of 2d and 3d Cell Culture Models
No full textRevealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research. © 2024 Elsevier Inc
Is She a Feminist Icon Now? Barbie 2023 Movie and a Critique of Postfeminism
No full textThis study seeks to analyse Greta Gerwig’s Barbie 2023 movie, exploring how it playfully interacts with academic criticisms by incorporating them into its narrative in a humorous way. This article intends to investigate how the movie serves as a critique of postfeminist media texts by highlighting how it affects women's psychological well-being, illustrating the ways in which it can be debilitating. The movie also highlights the unfulfilled psychological aspects of feminism, rendering it a feminist text in that regard. A thematic analysis of the movie prompts a discussion on how a character who has been a postfeminist icon transforms into a feminist narrative identity. In the beginning of the film, Barbie resides within a paradisiacal realm characterized by unwavering agency and authority. She lives in Barbieland where “every day is a great day”. This mirrors the way in which both girls and boys immerse themselves in their imaginative play, constructing their microcosms replete with agency and the role of the protagonist (Yakali Camoglu, 2020). However, as individuals mature into adulthood, the shift is palpable and the world they encounter demands a relinquishment of some of that power, leading them to transition from active agents to potentially objectified subjects in certain contexts. This is symbolised in Barbie’s own transition from Barbieland (imaginations of childhood) to the Real World (adulthood) in the end of the movie. The movie engages in the critique that Barbie encounters, as her portrayal symbolizes the unrealistic standards imposed on women, portraying them as unattainable ideals. Although her initial intent -supposedly- is to empower girls by rescuing them from the confines of stereotypical maternal roles and introducing them to diverse occupations, her portrayal inadvertently immerses them in a realm where not only physical perfection but also success in careers and relationships is expected—a realm where limitless possibilities coexist with a profound burden. This postfeminist portrayal offers a vision of boundless potential achievable through belief in self, but concurrently fosters a burdensome mental strain and self-objectification among women, entangling them in a constant cycle of self-critique. This predicament forms the crux of Barbie's critical error, leading her to relinquish her paradisiacal abode, Barbieland, and embrace the realm of real-world womanhood. By assuming the complex roles women navigate, Barbie forfeits her idyllic sanctuary and immerses herself in a world where the concept of "perfection" is inherently absent, as authenticity takes precedence over plastic constructs. After identifying the existing literature on Barbie, the article proceeds to present the theoretical framework, which is postfeminism, and outlines the research methodology. The results of the thematic analysis reveal Barbie's active engagement in critiquing the postfeminist media culture in which she was a prominent figure. This pivotal process underscores Barbie's latest contribution to the realm of media studies, transforming from a text entrenched in postfeminist ideals to embodying a feminist narrative. © The Author(s) 2024