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Expert Opinion on the Utility of Telemedicine in Obesity Care: Recommendations on a Hybrid Multidisciplinary Integrated Care Follow-Up Algorithm
(Springer, 2024) Bayram, Fahri; Sonmez, Alper; Kiyici, Sinem; Akbas, Feray; Yetgin, Meral Kucuk; Yazici, Dilek; Cingi, Asim
Purpose of Review: The proposed expert opinion was prepared by a panel of obesity and law specialists from Turkey to review the utility of telemedicine in obesity care and to provide a guidance document with recommendations on a hybrid multidisciplinary integrated care follow-up algorithm and the legislation governing telemedicine practice to assist obesity specialists in practicing the telemedicine. Recent Findings: The efficacy and feasibility of telemedicine interventions in supporting obesity management programs even during pandemics confirm that obesity is a particularly well-suited field for telemedicine, emphasizing the strong likelihood of continued utilization of telemedicine in obesity management, beyond the pandemic period. Summary: Telemedicine has great potential to address several barriers to ongoing weight-management care, such as challenges of access to specialized care, cost, and time limitations as well as patient adherence to treatment. However, telemedicine practice should complement rather than replace the in-person visits which are unique in building rapport and offering social support. Accordingly, the participating experts recommend the use of a hybrid integrated care model in the management of obesity, with the use of telemedicine, as an adjunct to in-person visits, to enable the provision of suggested intensive obesity management via frequent visits by a multidisciplinary team of obesity specialists. Further research addressing the utility of telemedicine in terms of optimal modality and duration for successful long-term obesity management outcomes is necessary to develop specific guidelines on telemedicine practice. In addition, the legislation governing the norms and protocols on confidentiality, privacy, access, and liability needs to be improved. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2023.
Sodium-Selenium Batteries with Outstanding Rate Capability by Introducing Cubic Mn2O3 Electrocatalyst
(Wiley-V C H Verlag Gmbh, 2024) Erdol, Zeynep; Ata, Ali; Demir-Cakan, Rezan
With their high volumetric capacity and electronic conductivity, sodium-selenium (Na-Se) batteries have attracted attention for advanced battery systems. However, the irreversible deposition of sodium selenide (Na2Se) results in rapid capacity degradation and poor Coulombic efficiency. To address these issues, cubic alpha-Mn2O3 is introduced herein as an electrocatalyst to effectively catalyze Na2Se conversion and improve the utilization of active materials. The results show that the addition of 10 wt% Mn2O3 in the selenium/Ketjen black (Se/KB) composite enhances the conversion from Na2Se to Se by lowering activation energy barrier and leads to fast sodium-ion kinetics and low internal resistance. Consequently, the Mn2O3-based composite delivers a high specific capacity of 635 mAh & sdot; g(-1) at 675 mA & sdot; g(-1) after 250 cycles as well as excellent cycling stability for 800 cycles with a high specific capacity of 317 mAh & sdot; g(-1) even at the high current density of 3375 mA & sdot; g(-1). Due to the cubic Mn2O3 electrocatalyst, the performance of the composites is superior to existing state-of-the-art Na-Se batteries reported in the literature.
Genomic Surveillance and Molecular Characterization of SARS-CoV-2 Variants During the Peak of the Pandemic in Türkiye
(Springer/Plenum Publishers, 2024) Akcesme, Faruk Berat; Koprulu, Tugba Kul; Cam, Burcin Erkal; Is, Seyma; Keskin, Birsen Cevher; Akcesme, Betul; Baydili, Kursad Nuri
SARS-CoV-2 is a highly transmissible coronavirus and has caused a pandemic of acute respiratory disease. Genomic characterization of SARS-CoV-2 is important for monitoring and assessing its evolution. A total of 1.346 nasopharyngeal swab samples were collected but only 879 SARS-CoV-2 high-quality genomes were isolated, subjected to Next Generation Sequencing and analyzed both statistically and regarding mutations comprehensively. The distribution of clades and lineages in different cities of T & uuml;rkiye and the association of SARS-CoV-2 variants with age groups and clinical characteristics of COVID-19 were also examined. Furthermore, the frequency of the clades and lineages was observed in 10 months. Finally, non-synonymous mutations not defined in specific SARS-CoV-2 variants (during that period) were identified by performing mutation analysis. B.1.1.7 (Alpha) and B.1.617.2 (Delta) SARS-CoV-2 variants which have also been identified in our study from March to December 2021. We observed a significant association of SARS-CoV-2 variants with age groups and cities. Also, E:T9I, S:A27S, S:A67V, S:D796Y, S:K417N, S:N440K, S:R158X, S:S477N (below 1%-frequency) were determined as specific mutations belonging and shared with the Omicron variant that appeared later. Our study has highlighted the importance of constant monitoring of the genetic diversity of SARS-CoV-2 to provide better prevention strategies and it contributes to the understanding of SARS-CoV-2 from the past to the present.
Enrichment, characterization, and sand consolidation application of urease active calcite-producing bacteria
(Springer Heidelberg, 2024) Kosma, Elvan Burcu; Manav-Demir, Neslihan; Civelek-Yoruklu, Hulya; Ozkaya, Bestami
Minerals such as calcium carbonate, which is prevalent in marble and limestone, are present naturally in rocks. Both physicochemical processes and microbial processes can result in the creation of calcium carbonate in nature, as is well documented. In this study, microbiologically induced calcite precipitation potential of three different Travertine-type water sources (Pamukkale Travertine Spring (PTS), Pamukkale Travertine Terraces (PTT), and Red Travertine of Karahayit (RTK)) using three different incubation media (NB, NB3, and ATCC1832) were investigated. After enrichment with ATCC1832 media, urease assays were positive for all of the microbial sources. The PTS and PTT were cultured with ATCC1832 medium for 48 h, which showed the best results for urease activity and microbial growth among other samples. Metagenome analyses indicated that PTT enriched with ATCC1832 media contains > 99% Firmicutes, while PTS enriched with ATCC1832 contains > 99% Proteobacteria at the Phylum level. Results from SEM-EDX and XRD analysis revealed that calcite and/or vaterite were the minerals that emerged from the mineralization of the PTS and PTT during incubation. The type of calcium carbonate crystals tended to change from one form to another when the incubation period extends from 72 to 120 h. Both the PTS and the PTT were able to precipitate calcite within the sand column. However, the bacteria from the PTT (26% CaCO3) outperformed those from the PTS (18% CaCO3) in terms of calcium carbonate deposition on the 21st day of incubation.
Key genes and pathways in the molecular landscape of pancreatic ductal adenocarcinoma: A bioinformatics and machine learning study
(Elsevier Sci Ltd, 2024) Eyuboglu, Sinan; Alpsoy, Semih; Uversky, Vladimir N.; Coskuner-Weber, Orkid
Pancreatic ductal adenocarcinoma (PDAC) is recognized for its aggressive nature, dismal prognosis, and a notably low five-year survival rate, underscoring the critical need for early detection methods and more effective therapeutic approaches. This research rigorously investigates the molecular mechanisms underlying PDAC, with a focus on the identification of pivotal genes and pathways that may hold therapeutic relevance and prognostic value. Through the construction of a protein-protein interaction (PPI) network and the examination of differentially expressed genes (DEGs), the study uncovers key hub genes such as CDK1, KIF11, and BUB1, demonstrating their substantial role in the pathogenesis of PDAC. Notably, the dysregulation of these genes is consistent across a spectrum of cancers, positing them as potential targets for wide-ranging cancer therapeutics. This study also brings to the fore significant genes encoding intrinsically disordered proteins, in particular GPRC5A and KRT7, unveiling promising new pathways for therapeutic intervention. Advanced machine learning techniques were harnessed to classify PDAC patients with high accuracy, utilizing the key genetic markers as a dataset. The Support Vector Machine (SVM) model leveraged the hub genes to achieve a sensitivity of 91 % and a specificity of 85 %, while the RandomForest model notched a sensitivity of 91 % and specificity of 92.5 %. Crucially, when the identified genes were cross-referenced with TCGA-PAAD clinical datasets, a tangible correlation with patient survival rates was discovered, reinforcing the potential of these genes as prognostic biomarkers and their viability as targets for therapeutic intervention. This study's findings serve as a potent testament to the value of molecular analysis in enhancing the understanding of PDAC and in advancing the pursuit for more effective diagnostic and treatment strategies.
Electromagnetic radiation and biophoton emission in neuronal communication and neurodegenerative diseases
(Pergamon-Elsevier Science Ltd, 2025) Erboz, Aysin; Kesekler, Elif; Gentili, Pier Luigi; Uversky, Vladimir N.; Coskuner-Weber, Orkid
The intersection of electromagnetic radiation and neuronal communication, focusing on the potential role of biophoton emission in brain function and neurodegenerative diseases is an emerging research area. Traditionally, it is believed that neurons encode and communicate information via electrochemical impulses, generating electromagnetic fields detectable by EEG and MEG. Recent discoveries indicate that neurons may also emit biophotons, suggesting an additional communication channel alongside the regular synaptic interactions. This dual signaling system is analyzed for its potential in synchronizing neuronal activity and improving information transfer, with implications for brain-like computing systems. The clinical relevance is explored through the lens of neurodegenerative diseases and intrinsically disordered proteins, where oxidative stress may alter biophoton emission, offering clues for pathological conditions, such as Alzheimer's and Parkinson's diseases. The potential therapeutic use of Low-Level Laser Therapy (LLLT) is also examined for its ability to modulate biophoton activity and mitigate oxidative stress, presenting new opportunities for treatment. Here, we invite further exploration into the intricate roles the electromagnetic phenomena play in brain function, potentially leading to breakthroughs in computational neuroscience and medical therapies for neurodegenerative diseases.
Recycling of NdFeB magnets employing oxidation, selective leaching, and iron precipitation in an autoclave
(Royal Soc Chemistry, 2023) Emil-Kaya, Elif; Polat, Buse; Stopic, Srecko; Guermen, Sebahattin; Friedrich, Bernd
The increasing production of neodymium-iron-boron (NdFeB) magnets for technological applications results in disposal problems. NdFeB magnets contain a significant quantity of rare earth elements (REEs). China is the largest REEs producer, but it applies quotas and increases the export prices of REEs. To address this issue, this study aims at investigating the recovery process of REEs from scrap NdFeB magnets. After oxidation of NdFeB magnet powders, selective leaching with nitric acid was carried out to achieve high-purity REE-rich leaching liquor. First, the oxidation kinetics of NdFeB powders was studied in detail to determine the oxidation temperature and duration. Afterwards, the effects of selective leaching parameters, including acid concentration, leaching temperature, stirring speed and solid/liquid ratio, were examined by analysis of variance (ANOVA) analysis based on Taguchi method. The most substantial parameters were assigned to be the temperature and solid/liquid ratio. Eventually, the dissolution kinetics were studied to propose a model for REEs. Several universal equations for dissolution kinetics were tested, and (1 - (1 - x) = k x tn) gives the best results for REEs. The findings show that the leaching process follows the shrinking core model. Activation energy was calculated to be 40.375 kJ mol(-1) for REEs. As the last step, the iron dissolved during leaching was precipitated as hematite in the autoclave. The hematite precipitation experiments were performed based on the Box-Behnken design. The effect of precipitation parameters was investigated by ANOVA analysis, and the precipitation process was optimized using response surface methodology (RSM), which resulted in the minimum iron and maximum REEs content in the leach liquor.
Oil-in-Water Emulsions Probed Using Fluorescence Multivariate-Curve-Resolution Spectroscopy
(Amer Chemical Soc, 2024) Gundogdu, Gulsum; Topuzlu, Ezgi Yilmaz; Mutlu, Ferhat; Ertekin, Umay E.; Okur, Halil I.
Hydrophobic surfaces in contact with aqueous media are omnipresent in nature. A plethora of key biological and physiological processes occur at the interface of immiscible fluids. Besides its fundamental importance, probing such interfaces is rather challenging, especially when one medium is bathed in the other. Herein, we demonstrate a fluorescence-based method that probes the oil-water interface and interfacial processes through surface dielectric perturbations. The fluorescence response of Nile Red is measured in hexadecane in water nanoemulsions. Three major spectral components appear: two from the bulk liquid media (hexadecane and water) and a distinct band at around 640 nm due to the interfacial component. Such spectra are deconvoluted using the multivariate-curve-resolution algorithm, and interface-correlated fluorescence spectra are attained. The influence of anionic sodium dodecylbenzenesulfonate (SDBS) and cationic cetyltrimethylammonium bromide (CTAB) surfactants on the oil-water interface is elucidated with concentration-dependent measurements. A charge-dependent spectral shift is observed. The interface correlated band at 641 nm for bare hexadecane nanoemulsions red shifts in the presence of anionic surfactants, indicating an apparent dielectric increase. In contrast, the same band gradually blue shifts with increasing cationic surfactant concentration, indicating an apparent interface dielectric decrease. Such a method can be utilized to probe alterations at interfaces beyond the oil/water interface.
Reactive capture and electrochemical conversion of CO2 with ionic liquids and deep eutectic solvents
(Royal Soc Chemistry, 2024) Dongare, Saudagar; Zeeshan, Muhammad; Aydogdu, Ahmet Safa; Dikki, Ruth; Kurtoglu-Oztulum, Samira F.; Coskun, Oguz Kagan; Munoz, Miguel
Ionic liquids (ILs) and deep eutectic solvents (DESs) have tremendous potential for reactive capture and conversion (RCC) of CO2 due to their wide electrochemical stability window, low volatility, and high CO2 solubility. There is environmental and economic interest in the direct utilization of the captured CO2 using electrified and modular processes that forgo the thermal- or pressure-swing regeneration steps to concentrate CO2, eliminating the need to compress, transport, or store the gas. The conventional electrochemical conversion of CO2 with aqueous electrolytes presents limited CO2 solubility and high energy requirement to achieve industrially relevant products. Additionally, aqueous systems have competitive hydrogen evolution. In the past decade, there has been significant progress toward the design of ILs and DESs, and their composites to separate CO2 from dilute streams. In parallel, but not necessarily in synergy, there have been studies focused on a few select ILs and DESs for electrochemical reduction of CO2, often diluting them with aqueous or non-aqueous solvents. The resulting electrode-electrolyte interfaces present a complex speciation for RCC. In this review, we describe how the ILs and DESs are tuned for RCC and specifically address the CO2 chemisorption and electroreduction mechanisms. Critical bulk and interfacial properties of ILs and DESs are discussed in the context of RCC, and the potential of these electrolytes are presented through a techno-economic evaluation.
Slx5/Slx8 SUMO-targeted ubiquitin ligase deficiency shortens lifespan due to increased mutation accumulation in yeast
(Oxford Univ Press, 2025) Thomas, Pinar B.; Kaluc, Nur; Cavli, Irmak N.; Tuna, Bilge G.
Chronological lifespan (CLS) in budding yeast Saccharomyces cerevisiae, which is defined as the time nondividing cells in saturation remain viable, has been utilized as a model to study post-mitotic aging in mammalian cells. CLS is closely related to entry into and maintenance of a quiescent state. Many rearrangements that direct the quiescent state enhance the ability of cells to endure several types of stress. Small ubiquitin-like modifier (SUMO)-targeted ubiquitin ligases (STUbLs) play a critical role in mediating an adaptive response to various stresses. In this study, we investigated the effect of a STUbL, Slx5/Slx8, on CLS in budding yeast. We showed that both SLX5 and SLX8 deletions accelerate chronological aging, resulting in a decreased maximum and mean lifespan. slx5 Delta cells were capable of entering or maintaining a quiescent state during aging. On the other hand, aging slx5 Delta and slx8 Delta cells had both increased spontaneous mutation accumulation. Our data together indicate that Slx5/Slx8 STUbL is required for normal rate of aging by preventing increased spontaneous mutation accumulation during aging. Slx5/Slx8 STUbL deficiency accelerates aging in yeast.
Non-cognitive skills and labour market performance of immigrants
(Public Library Science, 2023) Akay, Alpaslan; Yilmaz, Levent
This paper investigates how non-cognitive skills relate to the relative labour market performance of immigrants. Using the German Socio-Economic Panel (SOEP) and the Five-Factor Model of personality as a proxy for the non-cognitive skills, we show that these skills matter for the labour market integration of immigrants in the host country. We use two comparison benchmarks. Compared to an average native, immigrants' non-cognitive skills, e.g., extroversion or emotional stability, can lead to 5-15 percentage points lower lifetime employment probability disadvantage implying a better overall integration. Comparing immigrants and natives with the same type and level of non-cognitive skills suggests that returns of extroversion and openness to experience are higher among immigrants, leading to 3-5 percentage points lower lifetime employment probability disadvantage. These results are robust with respect to self-selection, non-random returns to the home country, stability of personality, and estimators. Our detailed analysis suggests that non-cognitive skills (especially extroversion) are substitutes for the standard human capital measures (e.g., formal education and training) among low educated immigrants, while there is no significant relative return of non-cognitive skills among highly educated immigrants.
Effects of the Amyotrophic Lateral Sclerosis-related Q108P Mutation on the Structural Ensemble Characteristics of CHCHD10
(Bentham Science Publ Ltd, 2024) Alici, Hakan; Uversky, Vladimir N.; Kang, David E.; Woo, Junga Alexa; Coskuner-Weber, Orkid
Introduction The Q108P pathological variant of the mitochondrial Coiled-Coil-Helix-Coiled-Coil-Helix Domain-Containing Protein 10 (CHCHD10) has been implicated in amyotrophic lateral sclerosis (ALS). Both the wild-type and CHCHD10Q108P proteins exhibit intrinsically disordered regions, posing challenges for structural studies with conventional experimental tools.Method This study presents the foundational characterization of the structural features of CHCHD10Q108P and compares them with those of the wild-type counterpart. We conducted multiple run molecular dynamics simulations and bioinformatics analyses.Result Our findings reveal distinct differences in structural properties, free energy surfaces, and the outputs of principal component analysis between these two proteins. These results contribute significantly to the comprehension of CHCHD10 and its Q108P variant in terms of pathology, biochemistry, and structural biology.Conclusion The reported structural properties hold promise for informing the development of more effective treatments for ALS.
Remineralization potential of a novel varnish: an in vitro evaluation
(Mre Press, 2024) Gokce, Ayse Nur Parlakyildiz; Kelesoglu, Ergun; Sagir, Kadir; Kargul, Betul
Despite fluoride's widespread use in preventing dental caries, it remains a significant oral disease with some drawbacks. Consequently, new preventative agents have emerged that can function independently of fluoride. Our aim is to demonstrate the efficacy of newly developed varnishes, 3% Rennou (theobromine calcium and phosphate) and 1% Rennou, in remineralizing initial caries. In our experiment, 40 human enamel samples were randomly allocated into four groups of 10 samples each as: Group 1 (G1): 5% NaF (Colgate PreviDent (R)), Group 2 (G2): 1% Rennou (R), Group 3 (G3): 3% Rennou (R) and Group 4 (G4): Casein Phosphopeptide-Amorphous Calcium Phosphate + Fluoride (MI Varnish (TM) GC). To produce an artificial carious lesion in the enamel, the samples were kept in a demineralizing solution for 72 hours. Samples underwent pH cycling for 6 days in order to induce remineralization. The means of the three measurements were compared, and the percentage of Surface Microhardness Recovery in (SMHR%) was calculated. Scanning Electron Microscopy (SEM) was used for qualitative assessment of surface changes. G1 had the highest SMHR% value, followed by G3, G2 and G4. The One-way ANOVA (Analysis of Variance) showed significant differences in the SMHR% values among the groups after six days of cycling (p < 0.001). In pairwise comparisons, groups did not show differences in means of SMHR% except for G1 and G4 (p = 0.006). In the SEM Images, after treatment within the NaF group, many flaky sediments were found on the enamel surface. Similarly, the maximum mineral gain was seen in the NaF and Rennou groups. SEM images of both varnish surfaces revealed a uniform layer interspersed with shapeless precipitates. All varnishes treated artificial enamel lesions to varying degrees. However, both concentrations of Rennou showed remineralization potential comparable to 5% NaF in acceptable statistical measurements. Thus, it could be used as a potentially effective preventive measure for pediatric patients.
Editorial: Responsible Research and Innovation as a toolkit: indicators, application, and context
(Frontiers Media Sa, 2023) Buchmann, Tobias; Dreyer, Marion; Mueller, Matthias; Pyka, Andreas
[No abstract available]
Responsibly shaping technology innovation for the energy transition: an RRI indicator system as a tool
(Frontiers Media Sa, 2023) Buchmann, Tobias; Wolf, Patrick; Mueller, Matthias; Dreyer, Marion; Dratsdrummer, Frank; Witzel, Bianca
Efforts to reduce global greenhouse gas emissions have had limited success. For many, the hopes rest on new energy innovations to advance the energy transition process. In this paper, we develop a Responsible Research and Innovation (RRI) base indicator system to steer the design of innovations in the field of energy transition innovations and, thus, improve social acceptance of these innovations. We propose a guideline for its application to assist R&D performing organizations and funding organizations in the design, selection, and communication of research proposals. The indicator system is intended to promote early integration of environmental and social aspects, support the formation of teams aware of the different responsibility aspects of innovation, and monitor progress in regard to relevant RRI dimensions.
An in silico study of how histone tail conformation affects the binding affinity of ING family proteins
(Peerj Inc, 2022) Gül, Nadir; Yildiz, Ahmet
Background. Due to its intrinsically disordered nature, the histone tail is conformationally heterogenic. Therefore, it provides specific binding sites for different binding proteins or factors through reversible post-translational modifications (PTMs). For instance, experimental studies stated that the ING family binds with the histone tail that has methylation on the lysine in position 4. However, numerous complexes featuring a methylated fourth lysine residue of the histone tail can be found in the UniProt database. So the question arose if other factors like the conformation of the histone tail affect the binding affinity. Methods. The crystal structure of the PHD finger domain from the proteins ING1, ING2, ING4, and ING5 are docked to four histone H3 tails with two different conformations using Haddock 2.4 and ClusPro. The best four models for each combination are selected and a two-sample t-test is performed to compare the binding affinities of helical conformations vs. linear conformations using Prodigy. The proteinprotein interactions are examined using LigPlot. Results. The linear histone conformations in predicted INGs-histone H3 complexes exhibit statistically significant higher binding affinity than their helical counterparts (confidence level of 99%). The outputs of predicted models generated by the molecular docking programs Haddock 2.4 and ClusPro are comparable, and the obtained proteinprotein interaction patterns are consistent with experimentally confirmed binding patterns. Conclusion. The results show that the conformation of the histone tail is significantly affecting the binding affinity of the docking protein. Herewith, this in silico study demonstrated in detail the binding preference of the ING protein family to histone H3 tail. Further research on the effect of certain PTMs on the final tail conformation and the interaction between those factors seem to be promising for a better understanding of epigenetics.
The prolonged effect of Kinesio Taping on joint torque and muscle activity
(Taylor & Francis Ltd, 2022) Kulli, Hilal Denizoglu; Karabulut, Derya; Arslan, Yunus Ziya
PurposeAlthough Kinesio Taping has been extensively used, evidence about the effect of Kinesio Taping is still insufficient. The aim is to determine the effect of Kinesio Taping on elbow joint torque and muscle activity in time and frequency domains.Materials and MethodsThirty-eight healthy subjects were (27 females and 11 males) randomly divided into control and Kinesio Taping groups. Kinesio Taping was applied over biceps brachii muscle in Kinesio Taping group, whereas no taping was applied to control group. Maximum elbow joint torque and electromyography activity in time and frequency domains were assessed during maximum isometric contraction of biceps brachii muscle at baseline, after 10 min, 30 min, and 24 h. Repeated measure ANOVA and mixed ANOVA tests were used for in-group and between-group comparisons, respectively.ResultsElbow joint torques among four assessment sessions were statistically altered in Kinesio Taping group and greater in Kinesio Taping group than in control group (F(3,57)= 3.317, p = 0.026, eta p2 = 0.149; F(3,108)=3.325, p = 0.022, eta p2 = 0.085; respectively). No difference was found in time domain muscle activity among assessment sessions in each group and comparison of groups (p > 0.05). Low-gamma band activity was changed among assessment sessions in Kinesio Taping group (F(3,57)= 6.946, p < 0.001, eta p2 = 0.268) while group x time interaction was not determined.ConclusionsKinesio Taping may influence joint torque of elbow more than without Kinesio Taping condition in 24th hour but the interpretation of this effect as a muscle strength enhancement compared with baseline can be arguable. Even if Kinesio Taping could not affect muscle activity in time domain, low-gamma band activity which is closely related to somatosensorial input may reach highest magnitude 24 h after Kinesio Taping.
How an ACE2 mimicking epitope-MIP nanofilm recognizes template-related peptides and the receptor binding domain of SARS-CoV-2
(Royal Society of Chemistry, 2022) Zhang, Xiaorong; Waffo, Armel T.; Yarman, Aysu; Kovacs, Norbert; Bognar, Zsofia; Wollenberger, Ulla; El-Sherbiny, Ibrahim M.; Hassan, Rabeay Y. A.; Bier, Frank F.; Gyurcsanyi, Robert E; Zebger, Ingo; Scheller, Frieder W.
Here we aim to gain a mechanistic understanding of the formation of epitope-imprinted polymer nanofilms using a non-terminal peptide sequence, i.e. the peptide GFNCYFP (G485 to P491) of the SARS-CoV-2 receptor binding domain (RBD). This epitope is chemisorbed on the gold surface through the central cysteine 488 followed by the electrosynthesis of a similar to 5 nm thick polyscopoletin film around the surface confined templates. The interaction of peptides and the parent RBD and spike protein with the imprinted polyscopoletin nanofilm was followed by electrochemical redox marker gating, surface enhanced infrared absorption spectroscopy and conductive AFM. Because the use of non-terminal epitopes is especially intricate, here we characterize the binding pockets through their interaction with 5 peptides rationally derived from the template sequence, i.e. implementing central single amino acid mismatch as well as elongations and truncations at its C- and N- termini. Already a single amino acid mismatch, i.e. the central Cys488 substituted by a serine, results in ca. 15-fold lower affinity. Further truncation of the peptides to tetrapeptide (EGFN) and hexapeptide (YFPLQS) results also in a significantly lower affinity. We concluded that the affinity towards the different peptides is mainly determined by the four amino acid motif CYFP present in the sequence of the template peptide. A higher affinity than that for the peptides is found for the parent proteins RBD and spike protein, which seems to be due to out of cavity effects caused by their larger footprint on the nanofilm surface.
Classification of breast cancer histopathological images using DenseNet and transfer learning
(Hindawi Publishing Corporation, 2022) Wakili, Musa Adamu; Shehu, Harisu Abdullahi; Sharif, Md. Haidar; Sharif, Md. Haris Uddin; Umar, Abubakar; Kusetoğulları, Hüseyin; İnce, İbrahim Furkan; Uyaver, Şahin
Breast cancer is one of the most common invading cancers in women. Analyzing breast cancer is nontrivial and may lead to disagreements among experts. Although deep learning methods achieved an excellent performance in classification tasks including breast cancer histopathological images, the existing state-of-the-art methods are computationally expensive and may overfit due to extracting features from in-distribution images. In this paper, our contribution is mainly twofold. First, we perform a short survey on deep-learning-based models for classifying histopathological images to investigate the most popular and optimized training-testing ratios. Our findings reveal that the most popular training-testing ratio for histopathological image classification is 70%: 30%, whereas the best performance (e.g., accuracy) is achieved by using the training-testing ratio of 80%: 20% on an identical dataset. Second, we propose a method named DenTnet to classify breast cancer histopathological images chiefly. DenTnet utilizes the principle of transfer learning to solve the problem of extracting features from the same distribution using DenseNet as a backbone model. The proposed DenTnet method is shown to be superior in comparison to a number of leading deep learning methods in terms of detection accuracy (up to 99.28% on BreaKHis dataset deeming training-testing ratio of 80%: 20%) with good generalization ability and computational speed. The limitation of existing methods including the requirement of high computation and utilization of the same feature distribution is mitigated by dint of the DenTnet.
Production of rare earth element oxide powders by solution combustion: a new approach for recycling of NdFeB magnets
(Royal Society of Chemistry, 2022) Kaya, Elif Emil; Stopic, Srecko; Gürmen, Sebahattin; Friedrich, Bernd
NdFeB magnets are employed in various technological applications due to their outstanding magnetic properties, such as high maximum energy product, high remanence and high coercivity. Production of NdFeB has gathered more interest, therefore the demand for rare earth elements (REEs) has continuously increased. The recovery of REEs has become essential to satisfy this demand in recent years. In the present study, a promising flowsheet is proposed for REEs recovery from NdFeB magnets, as follows: (1) acid baking, (2) employment of ultrasound-assisted water leaching, (3) the production of rare earth oxides (RE oxides) by a solution combustion method, and (4) a calcination process. There are several problems in conventional precipitation such as loss of a high amount of metal during precipitation and use of a high amount of precipitation agents. It is worth mentioning that the consumed precipitation agents in the solution are not easily recyclable. This study aims especially to investigate the production of RE oxides from recycled NdFeB magnets by solution combustion as an alternative to conventional precipitation methods. In this way, impurities that may have come to the system from the precipitation agents were prevented. Moreover, in the production of RE oxides via the above-mentioned method, precipitation agents and filtration steps were not necessary.

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