IYTE GCRIS Database (Izmir Institute of Technology)
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Plasma Proteomic Markers of Interleukin-1β Pathway Associated With Incident Age-Related Macular Degeneration in Persons With Aids
No full textObjective To evaluate the associations of plasma inflammatory proteins with age-related macular degeneration (AMD) in persons with the AIDS, using a discovery-based proteomics approach. Design A nested case-control study (analysis 1) and nested cohort study (analysis 2). Participants Persons with AIDS enrolled in the Longitudinal Study of the Ocular Complications with AIDS (LSOCA). Methods Cryopreserved plasma specimens obtained at baseline were assayed for inflammatory proteins using the Olink Inflammation Explore Panel 1. In analysis 1, baseline proteomic profiles for 26 persons with AIDS and incident intermediate-stage AMD 5 to 10 years after baseline and 49 matched controls (matched for age, biologic sex, race/ethnicity, and follow-up) without AMD were compared. In analysis 2, 475 persons from LSOCA with baseline plasma inflammatory proteomic profile measurements were followed for incident cataract and mortality. Main Outcome Measures Incident intermediate-stage AMD; incident cataract; and mortality. Results Of 365 measurable plasma inflammatory proteins, 118 (32%) were associated with incident intermediate-stage AMD at the false discovery rate-adjusted Q 0.05 level after adjustment for smoking, CD4+ T count, and plasma human immunodeficiency virus RNA level. Gene ontology pathway enrichment analysis identified the interleukin (IL)-1 beta pathway and wound healing pathways, including tissue inhibitor of metalloproteinase 3, as significantly associated with incident AMD. These associations were qualitatively different from those associated with incident cataracts, where elevated levels of inflammatory proteins were associated with a decreased risk of cataracts. A much broader number of inflammatory pathways, including those related to the adaptive immune system, were associated with mortality. Conclusions Upregulation of the IL-1 beta pathway appears to be associated with an increased risk of incident AMD in persons with AIDS. Given the availability of inhibitors of this pathway, inhibition of the IL-1 beta pathway may provide a therapeutic avenue for treatment of AMD. Financial Disclosure(s) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article. Ophthalmology Science 2025;5:100794 (c) 2025 by the American Academy of Ophthalmology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Macromolecular Changes in Cake Baking Process Studied by Fourier Transform Infrared Spectroscopy and Rheometry
No full textCake baking process was investigated using temperature increase profiles, FTIR spectroscopy, and rheological analysis. Three consecutive linear heating phases were identified, separated by two transition phases. The rheology results aligned well with the heating curve phases, showing two consecutive phases of viscosity decrease followed by a steady linear increase in viscosity during the phase. Each phase was analyzed at three temperature levels: 35 degrees C, 85 degrees C, and 112 degrees C. The FTIR spectroscopy studies did not detect significant changes in the cake batter between room temperature, 35 degrees C and 85 degrees C. However, at 112 degrees C, the samples showed significant increases in lipid peroxidation levels and compounds containing carbonyl bonds. Similarly, in the 112 degrees C cake samples, there was an increase in aggregated beta-sheet secondary structures of proteins and starch gelatinization, along with a concomitant decrease in starch crystallinity
Ti-Cu Dry Electrodes for Biomedical Sensing: Tribocorrosion Performance Under Simulated Skin Conditions
No full textMonitoring electromyographic (EMG) activity is crucial for diagnosing musculoskeletal disorders and understanding neuromuscular systems. Dry electrodes represent a significant advancement over traditional wet electrodes by eliminating the need for gels, thereby extending lifespan, simplifying skin preparation, and facilitating prolonged remote monitoring. However, challenges such as higher impedance and susceptibility to motion artifacts, along with issues of user discomfort and signal distortion, persist with existing metal-coated or entirely metal dry electrodes. This study explores an alternative approach using Ti-Cu thin films deposited on polymeric substrates to enhance electrical, electrochemical, and tribo-electrochemical properties. The research specifically investigates the corrosion and tribocorrosion behaviour of these Ti-Cu thin films in an artificial sweat environment, comparing them to pure Ti and Cu films. Chemical, microstructural, topographical, and electrical characterizations were conducted, alongside evaluations of electrochemical and tribo-electrochemical behaviour. The results indicate that while all films showed rupture under sliding, TiCu0.34 thin films exhibited superior corrosion resistance due to their unique microstructure. This study suggests that TiCu0.34 electrodes may offer a promising balance between corrosion resistance and electrical performance for wearable applications, although improvements in adhesion are necessary to withstand mechanical loads
Bioremediation of Marine Sediments Contaminated by a Mixture of Persistent Organic Pollutants
No full textPoliklorlu bifeniller (PCBs) ve polibromlu difenil eterler (PBDEs) gibi kalıcı organik kirleticiler, çevrede karışım halinde bulunarak ekosistem ve insan sağlığı için önemli riskler oluşturur. Bu küresel sorunun çözümü bu kirleticilerin çevresel ortamlardan uzaklaştırılması, yani iyileştirilmesidir. Bu çalışma, endüstriyel faaliyetlerin yoğun olduğu Aliağa, İzmir, Türkiye'deki gemi söküm sahalarından alınan kirlenmiş sedimanlar kullanılarak, biyoogmentasyon (BO) ve biyostimulasyon (BS) gibi biyoiyileştirme stratejilerinin etkinliğini sediman mikrokozmları ile incelemiştir. Mikrobiyal analizler, sedimanlarda Chloroflexi filumu ile ilişkili mikroorganizmaların çokluğunu (%37,6) ortaya koymuştur ve bu mikroorganizmalar zenginleştirilerek BO uygulaması için kullanılmıştır, BS uygulamasında ise doğal mikrobiyal aktiviteyi teşvik etmek amacıyla ortama mikrobesinler sağlanmıştır. BO ve BS, toplam PCB'ler için sırasıyla %14 ve %19, PBDE'ler için ise %33 ve %24 olarak giderim verimlilikleri sağlamış; bu değerler, doğal giderim (PCB'ler için %12 ve PBDE'ler için %8) setine kıyasla daha iyi performans gösterdiği için harici katkıların önemini kanıtlamıştır. PCB'ler için bozunma hızları BO'da (0,00124 klor/bifenil/gün-Cl/bp/gün) BS'den (0,00085 Cl/bp/gün) daha yüksek iken, PBDE'lerin bozunma hızı BS'de (0,00945 brom/difenil eter/gün-Br/dp/gün) BO'ya (0,00741 Br/dp/gün) kıyasla daha hızlı olmuştur. BO ve BS stratejileri toplam PCB ve PBDE konsantrasyonlarını azaltmış olsa da, zamanla daha düşük halojenli bileşiklerin oluşumu ekotoksikolojik riski işaret etmiştir. PCB-52 sürekli olarak yüksek risk sergilerken, BDE-28 BS'de yüksek risk kategorisine çıkmış ve BDE-153 tüm uygulamalarda yüksek ve orta risk seviyeleri arasında değişiklik göstermiştir. Bu bulgular, in situ biyoiyileştirme uygulamalarından önce laboratuvar ölçekli çalışmaların yapılmasının, giderim verimliliği ve potansiyel riskleri değerlendirme açısından önemini ve gerekliliğini vurgulamaktadır.Persistent organic pollutants, such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), existing as mixtures in the environment, pose significant risks to ecosystems and human health. Removing these pollutants from contaminated environments, i.e. remediation, offers a solution to this global issue. This study investigated the effectiveness of bioremediation strategies, specifically bioaugmentation (BA) and biostimulation (BS), in sediment microcosms using historically contaminated sediments from shipbreaking yards in the heavily industrialized area of Aliağa, İzmir. Microbial analyses revealed 37.6% abundance of Chloroflexi-related microorganisms in the sediments, which were subsequently enriched for BA treatment. BS treatment involved adding micronutrients to stimulate native microbial activity. BA and BS achieved higher removal efficiencies for total PCBs (14% and 19%, respectively) and PBDEs (33% and 24%) compared to natural attenuation (12% for PCBs and 8% for PBDEs) set, proving the importance of external amendments for better removal. Degradation rates for PCBs were higher in BA (0.00124 chlorine per biphenyl per day-Cl/bp/day) than in BS (0.00085 Cl/bp/day) whereas PBDE degradation was faster in BS (0.00945 bromine per diphenyl ether per day-Br/dp/day) compared to BA (0.00741 Br/dp/day). Although BA and BS strategies reduced total PCB and PBDE concentrations, the formation of lower halogenated congeners indicated an ecotoxicological risk. PCB-52 exhibited consistently high risks while BDE-28 escalated to high risk in BS, and BDE-153 fluctuated between high and moderate risks across all treatments. These findings emphasized the importance and necessity of conducting laboratory-scale studies prior to in situ bioremediation applications to evaluate removal efficiencies and potential risks
Observable-Enriched Entanglement
No full textWe introduce methods of characterizing entanglement on the example of the quantum skyrmion Hall effect, in which entanglement measures are enriched by the matrix representations of operators for observables. These observable operator matrix representations can enrich the partial trace over subsets of a system's degrees of freedom, yielding reduced density matrices useful in computing various measures of entanglement, which also preserve the observable expectation value. We focus here on applying these methods to compute observableenriched entanglement spectra, unveiling bulk-boundary correspondences of canonical four-band models for topological skyrmion phases and their connection to simpler forms of bulk-boundary correspondence. Given the fundamental roles entanglement signatures and observables play in the study of quantum systems and the fundamental generalization of the interpretation and treatment of spin within the framework of the quantum skyrmion Hall effect, concepts of observable-enriched entanglement introduced here are broadly applicable to myriad problems of quantum systems
Understanding the Role of a Specific Microenvironment in Personal Exposure To Semi-Volatile Organic Compounds Using Silicone Wristbands
No full textAssessment of personal exposure to semi-volatile organic compounds was facilitated using silicone wristbands (SWBs), an easy-to-use sampler that reflects total inhalation and dermal exposure from all the microenvironments and the activities in which the user was involved. Hence, SWBs help understand exposure from various routes, activities, and microenvironments. Offices are critical microenvironments where workers spend one-third of their daily time on weekdays; hence exposure from offices should be more extensively studied. This study aimed to investigate the personal exposure of university personnel and elaborate on the contribution of the exposure due to the office air to their overall exposure using SWBs. One SWB was worn by the participant, and another was hung in their office. After seven days of sampling on the wrist, exposure to polycyclic aromatic hydrocarbons (PAHs) was found to be related to combustion activities at home or from open fire, whereas exposure to organophosphate esters and phthalates was suggested to originate from building materials, such as flooring materials and paints, and consumer products, e.g. mattresses and furniture. PAHs in the participants' offices were influenced by the transport of outdoor air and phthalates from the ceiling material. Then, we estimated the equivalent air concentrations using the SWBs sampled from the offices and previously developed sampling rates and partition coefficients. The estimated office air exposure contributions to total inhalation and dermal exposure were 83%, 51%, and 39% for fluorene, tri(n-butyl) phosphate, and tris(2-chloro isopropyl) phosphate, respectively. These findings were consistent with the statistical analysis of personal data. To conclude, this study highlighted the importance of specific microenvironments in our exposure to particular SVOCs, offering strategies for indoor air quality management and human health risk assessment
Differential Susceptibility and Role for Senescence in Cart Cells Based on Costimulatory Domains
No full textDespite the success of chimeric antigen receptor T (CART) cell therapy in hematological malignancies, durable remissions remain low. Here, we report CART senescence as a potential resistance mechanism in 41BB-costimulated CART cell therapy. To mimic cancer relapse, we utilized an in vitro model with repeated CART cell activation cycles followed by rest periods. Using CD19-targeted CART cells with costimulation via 4-1BB-CD3 zeta (BB zeta) or CD28-CD3 zeta (28 zeta), we showed that CART cells undergo functional, phenotypical, and transcriptomic changes of senescence, which is more prominent in BB zeta. We then utilized two additional independent strategies to induce senescence through MYC activation and irradiation. Induction of senescence impaired BB zeta activity but improved 28 zeta activity in preclinical studies. These findings were supported by analyses of independent patient data sets; senescence signatures in CART cell products were associated with non-response to BB zeta but with improved clinical outcomes in 28 zeta treatment. In summary, our study identifies senescence as a potential mechanism of failure predominantly in 41BB-costimulated CART cells
Functional Manipulation of Nonspherical Nanoparticles With Cascaded Reconfigurable Modules
No full textSelective nanoparticle sorting is essential for applications requiring monodisperse distributions, yet conventional methods lack adaptability for shape-based separation. This study introduces a reconfigurable optical manipulation technique that dynamically sorts spherical and non-spherical nanoparticles using cascaded modules based on evanescent fields. Optical forces were calculated using the Discrete Dipole Approximation (DDA) method, enabling the modeling of various particle shapes and accurately capturing rotational and translational movements. Two cascaded strategies are proposed: the first approach enables fluid-assisted filtration by selectively trapping spherical particles while allowing non-spherical ones to be carried away by the flow. The second strategy first induces the rotational alignment of particles and then employs a trapping mechanism that selectively retains specific geometries, enabling the separation of spherical and non-spherical nanoparticles. Unlike traditional approaches, this method enables high-precision, shape-selective separation without external flow modifications. The results demonstrate unprecedented control and efficiency in nanoparticle sorting, offering a scalable, high-throughput solution for microfluidic and optofluidic applications
Decision-Support Approaches for Sustainable Water Resource Management in Northwest Algeria
No full textThis study investigates water resource management in the Wilaya of Mostaganem, northwest Algeria, using the water evaluation and planning (WEAP) decision support tool in combination with the analytic hierarchy process (AHP). As water scarcity becomes increasingly critical due to population growth, agricultural demands, and climate variability, effective management strategies are essential. This research employs WEAP to simulate various water demand and supply scenarios, assessing the impacts of irrigation efficiency, industrial development, and climate conditions on water availability. Under the ASI scenario, unsatisfied water demand may reach 4.3 hm3 per year by 2027. However, improving irrigation efficiency could reduce this by up to 50% compared to the reference scenario. Seasonal variations reveal deficits reaching 3.2 hm3 per month during the summer months of July through October. Additionally, the study highlights that a significant increase in water demand, exceeding 80 hm3 by 2060, can be mitigated through improved water supply initiatives, such as constructing new dams. The integration of AHP enables the prioritization of management strategies based on stakeholder preferences, demonstrating that adapting to climate change can stabilize demand below 50 million cubic meters. This integrated approach provides valuable insights for policymakers and stakeholders in developing sustainable water resource strategies that address the challenges faced by the Mostaganem region. © (2025), (Polskie Towarzystwo Inzynierii Ekologicznej (PTIE)). All rights reserved
Dynamic Recognition of the Nucleosome Core Particle by Select Chromatin Factors
No full textThe intricate interactions between the nucleosome core particle and chromatin-binding proteins control essential biological functions templated by DNA. The nucleosome is a symmetrical and disc-shaped nucleoprotein which binds several chromatin factors in a 2:1 stoichiometry. We report computational evidence for a DNA-sequence-driven emergence of asymmetry whereby the nucleosome binding affinities of the chromatin factors are altered on each side even though the protein factors bind chemically equivalent proteinous interfaces of the nucleosome. Furthermore, none of these proteins interact directly with the nucleosomal DNA. Using atomistic molecular dynamics simulations, we surveyed five chromatin factors that are known to bind the nucleosome in a 2:1 stoichiometry. In four factors, we found that the nucleosomal gyre that binds DNA strongly is also more preferred. These factors are Sir3, PRC1, RCC1, and SAGA-DUB. However, a fifth chromatin factor, 53BP1, prefers the gyre with the weaker DNA binding with higher affinity. We argue that this tunability in nucleosome affinity could be related to the function of the chromatin interactors as 53BP1 could prefer loose DNA gyres to execute its DNA repair function. © 2025 The Authors. Published by Elsevier B.V