Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
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Article Citation - WoS: 3Citation - Scopus: 41,2-Diboranes With Strong Donor Substitutes: Synthesis, Ovicidal and Larvicidal Effect on Important Vector Species(Elsevier, 2024) Bursali, Fatma; Sahin, Yueksel; Aygun, Muhittin; Sevincek, Resul; Biyik, H. Halil; Özgener, Hüseyin; Gurbuz, BurcinNovel control products are needed in the control of important insects like mosquitoes which are developing resistance to insecticides and larvicides currently in the market. Boron compounds have been demonstrated to exhibit antibacterial and anticancer effects. 1,2-diboranes with a long history and importance in boron chemistry have been described. These compounds are synthesized from reactions of 1,2-dichlordiborane derivatives with lidium amides (ArNHLi/Et2NLi, etc.). In addition to the three previously synthesized diborane compounds, five novel 1,2-diborane compounds were synthesized in good yield using the same method for the first time. The structures of the novel derivatives were characterized by nuclear magnetic resonance spectroscopy, and the molecular structure of one of them (2a) was also demonstrated using single crystal X-ray diffraction. In this preliminary study, the ovicidal and larvicidal effects of new 1,2-diamino-1,2-diborane derivatives against Aedes aegypti and Aedes albopictus eggs and larvae were investigated for the first time. Of these, 2a and 2e showed the highest ovicidal activity against both species, while 7, 4 and 2d showed particularly high larvicidal activity. Some 1,2-diborane derivatives were found to be significantly toxic, with LC50 values ranging from 14,930 to 27,975 mu g/mL. Some derivatives (6, 2a, 2c) were less effective against mosquito larvae. 1,2-Diborane derivatives have high ovicidal and larvicidal effects on mosquitoes and are therefore potential candidates for the development of new larvicides. Further studies are needed to evaluate its mode of action and safety. Understanding their mode of action against mosquito development is crucial to optimizing their use and reducing the potential development of resistance. Their potential effects on other mosquito species and non -target organisms need to be investigated.Article Citation - WoS: 6Citation - Scopus: 71,2-Diborolanes With Strong Donor Substituents: Synthesis and High Antimicrobial Activity(Academic Press, 2021) Şahin, Yüksel; Poyrazoğlu Çoban, Esin; Sevinçek, Resul; Bıyık, Halil H.; Özgener, Hüseyin; Aygün, Muhittin1,2-diborolanes with strong and without strong donor substituents have been described, and are also referred to as 1,2-diboracyclopentane. The 1,2-diaryl/alkyl-amino-1,2-diboracyclopentanes 2, 3, and 4 were obtained in good yield after the reaction of 1,2-dichloro-1,2-diboracyclopentane 1 with ArNHLi and Me3Si-NR2. The structures of these new derivatives were characterized by nuclear magnetic resonance spectroscopy. The molecular structures of 2b, 2c, 2e, 4, and 5f were also determined by single-crystal X-ray diffraction. The newly synthesized 1,2-borolanes are stable in air and showed particularly high activity against some Gram-positive bacteria. © 2020 Elsevier Inc.Article Citation - WoS: 2Citation - Scopus: 31-Octanol Is a Functional Impurity Modifying Particle Size and Photophysical Properties of Colloidal Zncdsse/Zns Nanocrystals(American Chemical Society, 2021) Sevim Ünlütürk, Seçil; Çağır, Ali; Varlıklı, Canan; Özçelik, SerdarImpurities in trioctylphophine (TOP) strongly affect nanocrystal synthesis. 1-Octanol among other contaminants in TOP is identified for the first time as a functional impurity by H-1 NMR. The deliberate addition of 1-octanol into trioctylphosphine reduced particle size and modified photophysical properties of ZnCdSSe/ZnS colloidal nanocrystals. NMR analysis furthermore revealed that 1-octanol is bonded to the nanocrystal surfaces. The ratio of integrals for the O-CH2 protons of 1-octanol, which is the lowest compared to the other ligands, suggests that 1-octanol plays a critical role to tune the particle size of nanocrystals. The increased amount of 1-octanol added into TOP reduces the particle size from 9.8 to 7.2 nm, causing a progressive blue shift in the UV-vis and PL spectra but leaving the alloy composition unaffected. The rate of nonradiative processes is enhanced with the amount of 1-octanol added into TOP, correlating with higher dislocation density observed in the nanocrystals. As a conclusion, 1-octanol is proposed as a functional impurity that varies particle size and nonradiative photophysical processes in the ZnCdSSe/ZnS colloidal nanocrystals.Article Citation - WoS: 52Citation - Scopus: 581.55 Å-Resolution Structure of Ent-Copalyl Diphosphate Synthase and Exploration of General Acid Function by Site-Directed Mutagenesis(Elsevier, 2014) Köksal, Mustafa; Christianson, David W.; Peters, Reuben John; Potter, KevinBackground The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25 Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained. Method Use of crystallization additives yielded CPS crystals diffracting to 1.55 Å resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis. Results This work clarifies structure-function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed. Conclusions Two channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded "proton wires" that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg2 + required for optimal catalytic activity. General significance This work establishes structure-function relationships for class II terpenoid cyclases.Conference Object Citation - WoS: 3Citation - Scopus: 31/F Noise in Amorphous Silicon and Silicon-Germanium Alloys(SPIE, 2003) Johanson, Robert E.; Güneş, Mehmet; Kasap, Safa O.We report measurements of conductance noise of a-Si1-XGeX:H in two different geometries; one where the current flow is transverse to the surface and the other longitudinal to it. Because of the large increase in sample resistance in going from transverse to longitudinal conduction, it was not possible to measure both geometries at the same temperature. However, the temperature trends are compatible with a common noise source. For both geometries, alloying with up to 40% Ge reduces the noise magnitude by a factor of 50 over that found in a-Si:HArticle Citation - WoS: 10Citation - Scopus: 71/F Noise in Doped and Undoped Amorphous Silicon(Elsevier Ltd., 2000-05) Johanson, Robert E.; Güneş, Mehmet; Kasap, Safa O.We measured the spectrum of conductance fluctuations in n-type, p-type, and undoped hydrogenated amorphous silicon (a-Si:H) as a function of temperature. In general, the spectra can be fit to a power law, 1/fα, although in the p-type and undoped samples deviations from a strict power law occur. For n-type and p-type samples, the noise magnitude increases with temperature by approximately a factor of 5 from 295 to 450 K. The slope parameter, α, also increases with temperature in the p-type samples from near unity to 1.4 but not in the n-type sample where it remains near 1.05 independent of temperature. The undoped sample could be measured only over a limited range of elevated temperatures, but α does trend larger. The undoped and lightly doped material have similar noise levels but larger p-type doping reduces the noise by two orders of magnitude. Correlation measurements indicate the 1/f noise is Gaussian for all samples. However, intermittent random-telegraph noise is observed in n-type material.Conference Object Citation - WoS: 6Citation - Scopus: 101/F Noise in Hydrogenated Amorphous Silicon-Germanium Alloys(Institute of Electrical and Electronics Engineers, 2003-08) Johanson, Robert E.; Güneş, Mehmet; Kasap, Safa O.Measurements were made of conductance noise of a-Si:H and a-Si 1-xGex:H in two different geometries: one where the current flow is transverse to the surface and the other where it is longitudinal to the surface. Because of the large change in sample resistance between the two geometries, it was not possible to measure both geometries at the same temperature. For both geometries, alloyinzg with up to 40% Ge reduces the noise magnitude by several orders of magnitude over that found in a-Si:H. The decrease is incompatible with several popular noise models. Extrapolating the temperature trends for each geometry shows that it is possible that the noise observed in the transverse samples has the same origin as the higher frequency part of the double power law spectra observed in the longitudinal samples.Article Citation - WoS: 15Citation - Scopus: 141/F-noise Study of Undoped Intrinsic Hydrogenated Amorphous Silicon Thin Films(American Physical Society, 1999) Güneş, Mehmet; Johanson, Robert E.; Kasap, Safa O.Conductance fluctuations in four samples of undoped intrinsic hydrogenated amorphous silicon (a-Si:H) were measured in the temperature range of 450 K to 500 K and for frequencies from 2 Hz to 3 kHz. The noise spectra divide into two regions that each fit a 1/fα power law but with different slope parameters α and different temperature dependences. At low frequencies, α is greater than unity and increases with temperature. At high frequencies, α is near 0.6 and temperature independent, but the noise magnitude decreases rapidly with temperature. We infer from the different dependences on temperature that the noise is generated by two independent mechanisms operating simultaneously in a-Si:H. We also observe that the 1/f noise exhibits a quadratic dependence on bias current and Gaussian statistics.Article 1/Nc Expansion and Anomaly Cancellation in the Presence of Electroweak Interactions(IOP Publishing Ltd., 1998-03) Erdem, RecaiWe study the question of a consistent formulation of the 1/Nc expansion in the presence of electroweak interactions. We show that in some cases the previous formulation leads to an unrealistic picture. We improve the scheme. We derive the corresponding hypercharge and electric charge values of fermions under the requirement that the standard model in the large-Nc limit should be free of chiral gauge anomalies. We find that the resulting hypercharge and the electric charge values for quarks are the same as for the standard model.Book Part 1960s Tax Law and Non-Muslim Exodus From Istanbul: Turkification of the City(Taylor & Francis, 2023) Akpınar, İpekThis chapter discusses the urban consequences of the expulsion of Istanbul Greeks in 1964. It demonstrates the urban impact of the 16 March 1964 decree that terminated the residence of 12, 000 Greek passport holders in Istanbul (a population of 40, 000 with their relatives), who were given 24 hours to leave the city and allowed to carry only 20 kilograms of belongings or US$22 with them. The event also alarmed many other non-Muslim families to emigrate from Istanbul, while the city was receiving a large influx of immigrants from rural lands due to the growing industrialization and urbanization. Akpinar discusses the urban planning interventions in Istanbul under the Menderes and subsequent governments throughout the 1950s and 1960s as ad-hoc or intentional steps toward Turkification, in which discrimination and the resulting emigration of Istanbul Greeks played a significant part. © 2024 selection and editorial matter, Esra Akcan and Iftikhar Dadi; individual chapters, the contributors.Conference Object Citation - WoS: 5Citation - Scopus: 6The 1st Workshop on Model-Based Verification & Validation: Directed Acyclic Graph Modeling of Security Policies for Firewall Testing(Institute of Electrical and Electronics Engineers Inc., 2009) Tuğlular, Tuğkan; Kaya, Özgür; Müftüoğlu, Can Arda; Belli, FevziCurrently network security of institutions highly depend on firewalls, which are used to separate untrusted network from trusted one by enforcing security policies. Security policies used in firewalls are ordered set of rules where each rule is represented as a predicate and an action. This paper proposes modeling of firewall rules via directed acyclic graphs (DAG), from which test cases can be automatically generated for firewall testing. The approach proposed follows test case generation algorithm developed for event sequence graphs. Under a local area network setup with the aid of a specifically developed software for this purpose, generated test cases are converted to network test packets, test packets are sent to the firewall under test (FUT), and sent packets are compared with passed packets to determine test result.Article 2’-Methylklavuzon Causes Lipid-Lowering Effects on A549 Non-Small Cell Lung Cancer Cells and Significant Changes on Dna Structure Evidenced by Fourier Transform Infrared Spectroscopy(Elsevier, 2020) Ceylan, Çağatay; Aksoy, Hatice Nurdan; Çağır, Ali; Çetinkaya, HakkıVarious chemical agents are used in the treatment of Non-Small Cell Lung Cancer (NSCLC). 2?-methylklavuzon was proposed as a potential chemotherapeutic agent in cancer treatment based on its topoisomerase inhibition activity. In this study the cellular effects of 2?-methylklavuzon was evaluated on A549 cancer cells using FTIR spectroscopy. 2?-methylklavuzon induced significant changes on both the whole cell lyophilizates and the lipid extracts of the A549 lung cancer cells. 2?-methylklavuzon caused significant structural changes in A549 cell DNA structure: T, A and G DNA breathing modes are lost after the drug application indicating the loss of topoisomerase activity. The level of transcription and RNA synthesis was enhanced. 2?-methylklavuzon induced single stranded DNA formation evidenced by the increase in the ratio of asymmetric/symmetric phosphate stretching modes. 2?-methylklavuzon induced band shifts only in the asymmetric mode of phosphate bonds not in the symmetrical phosphate bond stretching. 2?-methylklavuzon induced A form of DNA topography. In addition to the changes in the DNA structure and transcription 2?-methylklavuzon also caused lipid-lowering effect in A549 cancer cells. 2?-methylklavuzon suppressed lipid unsaturation, however, it induced formation of lipids with ring structures. 2?-methylklavuzon suppressed phosphate-containing lipids significantly and decreased carbonyl containing lipids and cholesterol slightly. 2?-methylklavuzon caused increases in the hydrocarbon chain length. Overall, 2?-methylklavuzon can be used as a lipid-lowering compound in the treatment of NSCLC and other cancer therapies. © 2020 Elsevier B.V.Article Citation - WoS: 17Citation - Scopus: 162-D Analysis of Ge Implanted Sio2 Surfaces by Laser-Induced Breakdown Spectroscopy(Elsevier Ltd., 2008-10) Yalçın, Şerife; Örer, Sabiha; Turan, Raşit2-D elemental distribution of Ge in silicon oxide substrates with differing implantation doses of between 3 × 1016 cm- 2 and 1.5 × 1017 cm- 2 has been investigated by Laser-Induced Breakdown Spectroscopy (LIBS). Spectral emission intensity has been optimized with respect to time, crater size, ablation depth and laser energy. Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM) coupled with Energy-Dispersive X-Ray Spectroscopy (EDX) have been utilized to obtain crater depth, morphology and elemental composition of the sample material, respectively. LIBS spectral data revealed the possibility of performing 2-D distribution analysis of Ge atoms in silicon oxide substrate. EDX analysis results confirmed that LIBS is capable to detect Ge atoms at concentrations lower than 0.2% (atomic). LIBS as a fast semi-quantitative analysis method with 50 μm lateral and 800 nm depth resolution has been evaluated. Results illustrate the potential use of LIBS for rapid, on-line assessment of the quality of advanced technology materials during the manufacturing process. © 2008 Elsevier B.V. All rights reserved.Conference Object 2-D Thresholding of the Connectivity Map Following the Multiple Sequence Alignments of Diverse Datasets(ACTA Press, 2013) Doğan, Tunca; Karaçalı, BilgeMultiple sequence alignment (MSA) is a widely used method to uncover the relationships between the biomolecular sequences. One essential prerequisite to apply this procedure is to have a considerable amount of similarity between the test sequences. It's usually not possible to obtain reliable results from the multiple alignments of large and diverse datasets. Here we propose a method to obtain sequence clusters of significant intragroup similarities and make sense out of the multiple alignments containing remote sequences. This is achieved by thresholding the pairwise connectivity map over 2 parameters. The first one is the inferred pairwise evolutionary distances and the second parameter is the number of gapless positions on the pairwise comparisons of the alignment. Threshold curves are generated regarding the statistical parameter values obtained from a shuffled dataset and probability distribution techniques are employed to select an optimum threshold curve that eliminate as much of the unreliable connectivities while keeping the reliable ones. We applied the method on a large and diverse dataset composed of nearly 18000 human proteins and measured the biological relevance of the recovered connectivities. Our precision measure (0.981) was nearly 20% higher than the one for the connectivities left after a classical thresholding procedure displaying a significant improvement. Finally we employed the method for the functional clustering of protein sequences in a gold standard dataset. We have also measured the performance, obtaining a higher F-measure (0.882) compared to a conventional clustering operation (0.827).Article 21st Century Urban Aesthetics in the Post Critical Age: Sanart Publication(Istanbul Teknik Universitesi, Faculty of Architecture, 2025) Kök, S.; Akpinar, İ.This research problematized the relationship between human and the built environment in the 21st century, which it describes as post-critical, and examined the relationship between them in a theoretical framework through aesthetics. Within this framework, it has analyzed selected articles from the proceedings book published by SANART (Association of Aesthetics and Visual Arts). This study has defined aesthetics as a way of relating human beings to their environment. It redefined holistic aesthetic thought through approaches that focus on uncertain, porous, relational boundaries and social processes. With new perspectives that reject the dualism of subject and object, the process associated with the concepts of movement and becoming have been conceptualized through the process of urban experience from the perspective of Manuel DeLanda. This study has analyzed the urban discourses presented in SANART publications with a focus on ’movement’. It has interpreted these movements as a feature of the built environment as it is shaped by the capacities of bodies and space. It has argued that a movementoriented evaluation of urban aesthetics would further the development of the critical field. © 2025, Istanbul Teknik Universitesi, Faculty of Architecture. All rights reserved.Article Citation - WoS: 37Citation - Scopus: 362d Vibrational Properties of Epitaxial Silicene on Ag(111)(IOP Publishing Ltd., 2017-03) Solonenko, Dmytro; Gordan, Ovidiu D.; Le Lay, Guy; Şahin, Hasan; Cahangirov, Seymur; Zahn, Dietrich R. T.; Vogt, PatrickThe two-dimensional silicon allotrope, silicene, could spur the development of new and original concepts in Si-based nanotechnology. Up to now silicene can only be epitaxially synthesized on a supporting substrate such as Ag(111). Even though the structural and electronic properties of these epitaxial silicene layers have been intensively studied, very little is known about its vibrational characteristics. Here, we present a detailed study of epitaxial silicene on Ag(111) using in situ Raman spectroscopy, which is one of the most extensively employed experimental techniques to characterize 2D materials, such as graphene, transition metal dichalcogenides, and black phosphorous. The vibrational fingerprint of epitaxial silicene, in contrast to all previous interpretations, is characterized by three distinct phonon modes with A and E symmetries. Both, energies and symmetries of theses modes are confirmed by ab initio theory calculations. The temperature dependent spectral evolution of these modes demonstrates unique thermal properties of epitaxial silicene and a significant electron-phonon coupling. These results unambiguously support the purely two-dimensional character of epitaxial silicene up to about 300°C, whereupon a 2D-to-3D phase transition takes place. The detailed fingerprint of epitaxial silicene will allow us to identify it in different environments or to study its modifications.Conference Object Citation - Scopus: 13-D Switching Fabric Node Design(ACTA Press, 2004) Dinleyici, Mehmet Salih; Akın, OsmanIn this work we investigate an all-optical switching node that can be controlled by means of a transient grating, which is formed by interference of two Gaussian beams. This design considers 3-D architecture of switching fabrics.. real profile of Gaussian beams and fast switching time requirements. Four Wave Mixing (FWM) technique is applied in the evanescent field region of waveguide, showing chi((3)) nonlinearity. The formed grating is analysed by standart methods to obtain reflection coefficient and then coupling coefficient for power exchange between waveguides.Article Citation - WoS: 11Citation - Scopus: 143D Bioprinting of mouse pre-osteoblasts and human MSCs using bioinks consisting of gelatin and decellularized bone particles(Iop Publishing Ltd, 2024) Kara, Aylin; Distler, Thomas; Akkineni, Ashwini Rahul; Tihminlioglu, Funda; Gelinsky, Michael; Boccaccini, Aldo R.One of the key challenges in biofabrication applications is to obtain bioinks that provide a balance between printability, shape fidelity, cell viability, and tissue maturation. Decellularization methods allow the extraction of natural extracellular matrix, preserving tissue-specific matrix proteins. However, the critical challenge in bone decellularization is to preserve both organic (collagen, proteoglycans) and inorganic components (hydroxyapatite) to maintain the natural composition and functionality of bone. Besides, there is a need to investigate the effects of decellularized bone (DB) particles as a tissue-based additive in bioink formulation to develop functional bioinks. Here we evaluated the effect of incorporating DB particles of different sizes (<= 45 and <= 100 mu m) and concentrations (1%, 5%, 10% (wt %)) into bioink formulations containing gelatin (GEL) and pre-osteoblasts (MC3T3-E1) or human mesenchymal stem cells (hTERT-MSCs). In addition, we propose a minimalistic bioink formulation using GEL, DB particles and cells with an easy preparation process resulting in a high cell viability. The printability properties of the inks were evaluated. Additionally, rheological properties were determined with shear thinning and thixotropy tests. The bioprinted constructs were cultured for 28 days. The viability, proliferation, and osteogenic differentiation capacity of cells were evaluated using biochemical assays and fluorescence microscopy. The incorporation of DB particles enhanced cell proliferation and osteogenic differentiation capacity which might be due to the natural collagen and hydroxyapatite content of DB particles. Alkaline phosphatase activity is increased significantly by using DB particles, notably, without an osteogenic induction of the cells. Moreover, fluorescence images display pronounced cell-material interaction and cell attachment inside the constructs. With these promising results, the present minimalistic bioink formulation is envisioned as a potential candidate for bone tissue engineering as a clinically translatable material with straightforward preparation and high cell activity.Article Citation - WoS: 6Citation - Scopus: 83d Electrode Use in Mdc for Enhanced Removal of Boron From Geothermal Water(Elsevier, 2022-05) Gören, Ayşegül Yağmur; Ökten, Hatice EserMicrobial desalination cell (MDC) is a significantly promising technology due to its simultaneous features of electricity production, wastewater treatment and desalination. In this paper, the three-dimensional (3D) sponge with activated carbon-chitosan (AC-CS) was synthesized to enhance the efficiency of the MDC system. Effects of operating parameters (boron concentration, electrode surface area, catholyte solution, and activated sludge volume) on MDC performance were also investigated. The MDC with 3D AC-CS anode provided a higher power density of 970 mW/m2, boron removal efficiency of 75.9%, and COD removal efficiency of >90% under optimized conditions. The maximum boron and COD removal efficiencies were 65.6 and 81.4% with the power density of 866.9 mW/m2 for geothermal brine. Moreover, BET analysis showed that the 3D AC-CS anode presented high surface area (230 m2/g) and pore volume (0.202 cm3/g). As an overall result, not only the production of 3D sponge anode electrodes with AC-CS composite was achieved but also desalination and power generation results that were comparable with the literature were presented.Conference Object 3d Modeling of a Historical Mine Waste Site Using Uav Images: Estimation of Stockpile Volumes(Springer, 2023) Önal, Okan; Gündüz, OrhanIn recent decades, the use of Unmanned Aerial Vehicles (UAV) for land surveying became very popular because of their simplicity and low cost. Aerial images of the site can be used for the reconstruction of the site’s 3D digital model. Once proper calibrations are made, these digital models can be used for several purposes including stockpile volume estimation, stability analyses, forensic engineering and archiving, etc. In this study, the 3D model of an abandoned historical mine waste disposal site located in Balıkesir-Turkey was reconstructed for the estimation of the waste stockpile volumes. The historical mine site is a facility that was abandoned more than 80 years ago. Mine wastes of different quality were disposed of in and around the site along the hydrologically intermittent creek that passes through the site. No engineered precautions were taken at the site to reduce the environmental impacts and all waste piles were exposed to the natural eroding effect of precipitation and wind. The total amount of the waste volume is not known accurately, which prevents researchers to quantify the potential impacts associated with different waste stockpiles. Thus, a 3D digital model of the site was created by using UAV data obtained from a quadcopter and later processed to obtain a digital topography of the site with an improved accuracy value of ± 2 cm. The stockpiles were later analyzed with geographic information systems to characterize the magnitude of mine wastes and to propose alternative engineering solutions for environmental mitigation. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd 2023.
