IYTE GCRIS Database (Izmir Institute of Technology)
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Tcgex: a Powerful Visual Interface for Exploring and Analyzing Cancer Gene Expression Data
No full textAnalyzing gene expression data from the Cancer Genome Atlas (TCGA) and similar repositories often requires advanced coding skills, creating a barrier for many researchers. To address this challenge, we developed The Cancer Genome Explorer (TCGEx), a user-friendly, web-based platform for conducting sophisticated analyses such as survival modeling, gene set enrichment analysis, unsupervised clustering, and linear regression-based machine learning. TCGEx provides access to preprocessed TCGA data and immune checkpoint inhibition studies while allowing integration of user-uploaded data sets. Using TCGEx, we explore molecular subsets of human melanoma and identify microRNAs associated with intratumoral immunity. These findings are validated with independent clinical trial data on immune checkpoint inhibitors for melanoma and other cancers. In addition, we identify cytokine genes that can be used to predict treatment responses to various immune checkpoint inhibitors prior to treatment. Built on the R/Shiny framework, TCGEx offers customizable features to adapt analyses for diverse research contexts and generate publication-ready visualizations. TCGEx is freely available at https://tcgex.iyte.edu.tr, providing an accessible tool to extract insights from cancer transcriptomics data
Exploring User Nature Experience in Urban Green Spaces Through Biophilic Design
No full textIncreasing urbanisation limits human interaction with natural environments, underscoring the critical importance of urban green spaces for daily nature engagement. Biophilic design, which focuses on enhancing human interactions with nature in the built environment, provides an opportunity to fosterthis engagement. This study investigates how the characteristics of urban green spaces impact the users' nature experiences within the experience-based framework of biophilic design. Focusing on three neighbourhood parks in the Bostanl ; imath; neighbourhood of Kar ; scedilimath;yaka district, Izmir (T ; uuml;rkiye), the research evaluates nature experiences at both environmental and individual levels. The environmental level analysis assessed the nature experience potential of each park, while a nature experience workshop gathered insights into individual nature experiences. The findings indicate that nature experiences in urban green spaces are influenced by a combination of individual and environmental factors, challenging the effectiveness of a uniform approach in the design of these spaces. The study also provides empirical evidence that specific park characteristics- such as quietness, vegetation, size, accessibility, and sense of place-influence the users' nature experiences. This research highlights the value of the experience-based framework of biophilic design for understanding and enhancing user-nature interactions and it underscores its importance in guiding future urban green space planning and design strategies
Assessment of Cytotoxic Potentials of Isoindole-Derived Compounds With Epoxy Alcohol Functionalities on Different Cancer Cell Lines and Molecular Docking Analysis
No full textObjective: Isoindoline and epoxycyclohexane derivatives are known to exert beneficial effects on various inflammatory pathologies, including cancer. This study uniquely evaluates the cytotoxic potential of four synthesized isoindoline derivatives against five different cancer cell lines. Methods: Cancer cell lines were treated with varying concentrations of each derivative and incubated for 24, 48, and 72 h. Cytotoxicity was assessed via cell growth inhibition assays and cell membrane damage tests. Additionally, molecular docking studies were conducted to examine the interaction of the compounds with key cancer-related proteins: human tankyrase 1, c-MET, estrogen receptor alpha, androgen receptor, and EGFR. Results and Discussion: The epoxy alcohol derivatives demonstrated a dose-dependent cytotoxic effect, inhibited cell proliferation, and induced membrane damage in adenocarcinoma cell lines. Apoptosis rates and in vitro wound healing assays further supported their antiproliferative potential. Conclusions: These findings suggest that epoxy isoindole derivatives may serve as promising anticancer agents for the treatment of cervical, lung, prostate, and breast cancers due to their cytotoxic and antiproliferative activities. Molecular docking results corroborated their potential mechanism of action
Antimicrobial Edible Films of Emerging Hydrocolloids Extracted From Food Processing Waste
No full textThis chapter aims to review recent major developments related to antimicrobial edible packaging based on emerging hydrocolloids extracted from food processing wastes. The chapter consists of antimicrobial packaging examples of the most promising emerging hydrocolloids extracted from processing wastes. The major hydrocolloids discussed include fish and poultry gelatins, mushroom, insect, and snail chitosans, oilseed meal proteins (e.g., proteins from meals of quinoa, flaxseed, hazelnut, cottonseed, sunflower, rapeseed, etc.), citrus alternative pectins (e.g., apple, watermelon, mango, passion fruit, and fig pectins), and nonconventional starches (e.g., banana and taro peel starches, pineapple stem starches, avocado, jackfruit, sugar palm, loquat, and mango seed starches, etc.). A particular emphasis has been put on packaging incorporating natural phenolic antimicrobials that are also mostly extracted from waste. Therefore, a rich content was prepared for those who are interested in developing novel sustainable antimicrobial packaging that contributes to the circular economy and global problems such as climate change and food security. © 2025 Elsevier Inc. All rights reserved
The Spheroidization Behavior of Low Alloy White Cast Iron and Its Effect on Impact Toughness and Wear Resistance
No full textThe effect of spheroidization on impact toughness and wear resistance, together with the spheroidization kinetics of a low alloy white cast iron (LAWCI) have been studied. Spheroidization process was carried out using two different routes; intercritical annealing and subcritical annealing both of which were followed by furnace cooling to room temperature. Both routes involve a process window, which is determined by holding time and temperature. For the intercritical annealing the spheroidization window is significantly shorter (0.5-3 h) than the conventional subcritical spheroidization (6 - 12 h); and that process window narrows with increasing intercritical annealing temperature. The intercritical spheroidization involves 3 distinct stages; (i) partial, followed by (ii) fully spheroidization of lamellar pearlitic matrix by divorced eutectoid transformation (DET); and (iii) partially spheroidization by pearlitic structure formation in previous fully spheroidized region. The end of third stage produces almost fully pearlitic matrix, which is coarser than the as-cast condition. In case of subcritical spheroidization, the process window opens after about 6 hours and the size of spherical carbides gets larger with time. The as-cast LAWCI having a microstructure composed of eutectic carbide network and pearlite matrix exhibits and impact toughness of 4.6 J. Spheroidization process not only changes the lamellar pearlitic structure into spheroidized carbides but also slightly reduces the amount of eutectic carbides. Those microstructural changes greatly improve the impact toughness of LAWCI up to 11.8 J; whereas some decrease in the wear resistance. For spheroidized LAWCI, mean diameter of carbides (D), interparticle spacing of carbides (s), and number of carbides per area (n) seems to be important microstructural variations to determine the impact toughness and wear properties. Taking properties of the current material into consideration, spheroidized white cast irons may be a viable alternative material for industrial applications, offering a trade-off between wear resistance and toughness
Investigating the Effects of Functionalized Single Wall Carbon Nanotubes on the Cure Behavior of a Carbon/Epoxy Prepreg System by an Optimized Parameter Approach
No full textCarbon/Epoxy composite materials are used in a wide range of applications due to their superior performance. However, their properties are strongly related to cross-linking reactions occurring during the curing process, and a prior estimation of curing parameters is the key to manufacturing the desired material. This study builds a mathematical model to solve the inverse kinetic problem based on differential scanning calorimetry data and later presents its use in curing experiments. The method derived (Gamze-Murat-Neslisah (GMN) approach) determines the pre-exponential and activation energy of the curing process. Later, an extended experimental study was performed. Functionalized single-wall carbon nanotubes (F-SWCNTs) were prepared by oxidizing their surface with carboxyl to enhance the dispersion of the nanoparticulates. The epoxy resin systems were modified with 0.05%, 0.1%, and 0.2% wt. F-SWCNTs, which were impregnated on carbon fibers (CFs). The curing behavior was studied, cure kinetic parameters were determined, and the thermal behavior was characterized. Differential scanning calorimetry (DSC) data sets for CF/epoxy prepregs containing F-SWCNTs were used for the verification of the proposed method. It was found that the GMN approach is in good agreement with the experimentally measured data for all kinetic parameters. The addition of F-SWCNTs increased the material's curing efficiency as the CNTs enhanced heat transport in composites, reducing the activation energy. The results obtained from the GMN algorithm were also found in good agreement with the well-known Kissinger-Akahira-Sunose (KAS) and Kissinger methods, while the current GMN method revealed itself as an accurate algorithm to obtain the activation energy
Pupillometric and Perceptual Approaches Provide Independent Estimates of Melanopsin Activity in Humans
No full textStudy Objectives: Melanopsin-expressing retinal ganglion cells, which provide light information to time sleep and entrain circadian clocks, also influence perceived brightness raising the possibility that psychophysical paradigms could be used to explore the origins and implications of variability in melanopic sensitivity. We aimed to develop accessible psychophysical tests of melanopic vision and relate outcomes with a pupillometric measure of melanopsin function (post-illumination pupil response) and prior light exposure. Methods: Individually calibrated pairs of isoluminant stimuli differing in melanopic radiance from a four primary source were presented sequentially with superimposed random color offsets in a two alternative forced choice brightness preference paradigm to 41 naïve adult participants with personal light exposure data for the prior 7 days and post-illumination pupil response measures defined by comparing maintained pupil constriction for luminance matched “red” vs “blue” pulses. Results: Across participants we observed the expected tendency to report positive melanopsin contrast stimuli as “brighter” (one-tailed t-test p 0.001), but with substantial inter-individual variability in both sensitivity (melanopsin contrast at criterion preference p = 0.75) and amplitude (preference at maximum melanopic contrast). There was little correlation between these psychophysical outcomes and post-illumination pupil response magnitude, or between either psychophysical or post-illumination pupil response measures and light history metrics (pairwise Pearson correlation coefficients -0.5> 0.5). Random forest machine learning failed to satisfactorily predict outcome for either psychophysical or post-illumination pupil response measures based upon these inputs. Conclusions: Our findings reveal that estimates of melanopic function provided by perceptual and pupillometric paradigms can be largely independent of one another and of recent history of light exposure. © The Author(s) 2024. Published by Oxford University Press on behalf of Sleep Research Society
Towards Renewable Energy Islands in Türkiye: Potential and Challenges
No full textThe necessity of renewables is increasing day by day due to increasing energy demand. Therefore, novel approaches and methods for producing electricity in an environmentally friendly manner are valuable and critical. The seas have enormous potential in terms of wind, waves, solar, and hydrogen systems. The study presents the investigation of the potential dynamics for energy island formation on T ; uuml;rkiye borders. Also, targets, legislation, and environmental and social concerns are discussed comprehensively. Results show that offshore wind and hydrogen are promising systems shortly while solar and wave energy needs more research for T ; uuml;rkiye. The Marmara and Aegean Seas are considered technically feasible for offshore wind installations, while the Mediterranean and Aegean Seas have the highest technical solar potential. In addition, the highest wave power is detected along the line from I(center dot)zmir to Antalya Coast while hydrogen energy systems receive great interest with academic and industrial projects in the Marmara Coastline. Profiting from marine energy, marine spatial planning, and grid availability are detected as the shortcoming issues in T ; uuml;rkiye. The study could give critical information to energy planners, and decision makers for potential projects
Microporous Carbon Spheres for the Enrichment of Lead From Water Samples With Determination by Microsample Injection System - Flame Atomic Absorption Spectrometry (MIS-FAAS)
No full textMicroporous carbon spheres (MCSs) are advanced materials known for their high surface area, well-developed pore structure, low density, and rapid molecular diffusion, making them highly effective in solid-phase extraction (SPE) and other applications. In this study, MCSs synthesized from previously reported resorcinol-formaldehyde resin were employed as an adsorbent for the extraction and preconcentration of Pb(II) ions. The material was comprehensively characterized to confirm its suitability for adsorption applications. The adsorption and desorption behavior of MCSs toward lead ions was systematically examined under optimized conditions, including pH, eluent volume, eluent type, eluent concentration, and sample volume. Microinjection microsample injection system-flame atomic absorption spectrometry (MIS-FAAS) was used for the determination of lead ions. Experimental results from batch experiments showed that the MCSs exhibited a maximum adsorption capacity of 37.31 mg g-1. Under optimal conditions (pH 8.0, 1.0 mL of 0.1 M HNO3 eluent, and 10 mg of adsorbent), a preconcentration factor of 100 was achieved, with recovery values exceeding 90%. The method exhibited a limit of detection (LOD) of 0.73 mu g L-1. The developed method was successfully applied to real water samples, including tap water, entering industrial wastewater, and exiting industrial wastewater, confirming its potential for use in environmental monitoring and contamination control
Radially Aligned Carbon Nanotube Glass Fiber Composites as Ion-Selective Microelectrodes
No full textDetection of ions is challenging due to their small size, rapid diffusion, and high mobility, especially for assaying in samples of low volumes. Among the traditional analytical methods, potentiometric ion-selective electrodes (ISE) have become a popular choice for detecting ions as they are cost-effective, user-friendly and can be miniaturized, making them useful for on-site analysis. In this context, radially aligned carbon nanotubes (RACNT) directly grown on glass fibers (GF) via the chemical vapor deposition method is investigated as a solid contact material for the fabrication of ion-selective microelectrodes (mu ISE) upon incorporating specific ionophores within a polymeric encapsulation membrane. As an illustration, sensitive detection of ammonium ions is accomplished by the fabricated mu ISE (plasticized PVC membrane containing nonactin ionophores), which yielded a LOD and a linear response range between 7.5 x 10-6 and 1.0 x 10-5 to 1.0 x 10-1 M, respectively. The mu ISE fabricated with RACNT-GF as an interface material exhibited improvements in LOD and enhanced the detection selectivity as compared to a conventional ISE fabricated using planar solid contact materials such as graphite. We hypothesize that the fabricated mu ISE with a high surface area and mechanical durability maximize the accommodation of ionophores in the barrier membrane for yielding improved potentiometric responses. Experimental results illustrate that the mu ISE possesses the potential to be utilized for the fabrication of selective and sensitive ISE upon incorporation of specific ionophores with RACNT-GF composites