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van Maris, Antonius J. A., ProfessorORCID iD iconorcid.org/0000-0001-5319-7511
Publications (10 of 50) Show all publications
Daga-Quisbert, J., Rajarao, G. K., van Maris, A. J. A., Romero-Jaldin, A. M., Mercado-Guzman, A., Fernandez, C. E. & Quillaguaman, J. (2024). Assessing water quality of a hypereutrophic alkaline urban lake and its coagulation-treated water using metagenomic analysis. Water, Air and Soil Pollution, 235(6), Article ID 350.
Open this publication in new window or tab >>Assessing water quality of a hypereutrophic alkaline urban lake and its coagulation-treated water using metagenomic analysis
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2024 (English)In: Water, Air and Soil Pollution, ISSN 0049-6979, E-ISSN 1573-2932, Vol. 235, no 6, article id 350Article in journal (Refereed) Published
Abstract [en]

The study on Lake Alalay, an urban alkaline lake facing increasing pollution, focused on the impact of coagulation treatment on its water quality and microbiome. The findings revealed higher nutrient concentrations, specifically phosphate and ammonium, compared to the 2019 benchmark. The lake was found to be dominated by Proteobacteria, followed by Cyanobacteria, with Desulfobacterota thriving in areas with low dissolved oxygen. Arthrospira and Roseobacter, halo-alkali-tolerant photosynthetic bacterial genera, were detected at all sampling points. Local phosphate and oxygen concentration variations led to distinct microbial communities on the lake's surface. Despite these differences, long-term ex-situ studies on water treatment with iron chloride and poly-aluminum chloride reduced the relative abundance of Cyanobacteria, promoting the presence of Proteobacteria and Bacteroidota. However, the coagulants required higher quantities than those typically used in small shallow lakes to precipitate phosphate and improve water quality effectively. Furthermore, the large-scale assay of lake water treatment with coagulants failed to eliminate Vibrio and Acinetobacter multidrug-resistant bacteria. In conclusion, the study underscores the need to prevent the inflow of polluted water into Lake Alalay and implement effective measures to deal with the existing chemical and biological contamination.

Place, publisher, year, edition, pages
Springer Nature, 2024
Keywords
Alkaline hypereutrophic lake, Lake Alalay, Urban lake
National Category
Water Engineering
Identifiers
urn:nbn:se:kth:diva-347197 (URN)10.1007/s11270-024-07177-3 (DOI)001228901900006 ()2-s2.0-85193952628 (Scopus ID)
Note

QC 20240604

Available from: 2024-06-04 Created: 2024-06-04 Last updated: 2024-06-04Bibliographically approved
Sjöberg, G., Reķēna, A., Fornstad, M., Lahtvee, P. J. & van Maris, A. J. A. (2024). Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by Saccharomyces cerevisiae. Metabolic engineering, 82, 49-59
Open this publication in new window or tab >>Evaluation of enzyme-constrained genome-scale model through metabolic engineering of anaerobic co-production of 2,3-butanediol and glycerol by Saccharomyces cerevisiae
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2024 (English)In: Metabolic engineering, ISSN 1096-7176, E-ISSN 1096-7184, Vol. 82, p. 49-59Article in journal (Refereed) Published
Abstract [en]

Enzyme-constrained genome-scale models (ecGEMs) have potential to predict phenotypes in a variety of conditions, such as growth rates or carbon sources. This study investigated if ecGEMs can guide metabolic engineering efforts to swap anaerobic redox-neutral ATP-providing pathways in yeast from alcoholic fermentation to equimolar co-production of 2,3-butanediol and glycerol. With proven pathways and low product toxicity, the ecGEM solution space aligned well with observed phenotypes. Since this catabolic pathway provides only one-third of the ATP of alcoholic fermentation (2/3 versus 2 ATP per glucose), the ecGEM predicted a growth decrease from 0.36 h−1 in the reference to 0.175 h−1 in the engineered strain. However, this <3-fold decrease would require the specific glucose consumption rate to increase. Surprisingly, after the pathway swap the engineered strain immediately grew at 0.15 h−1 with a glucose consumption rate of 29 mmol (g CDW)−1 h−1, which was indeed higher than reference (23 mmol (g CDW)−1 h−1) and one of the highest reported for S. cerevisiae. The accompanying 2,3-butanediol- (15.8 mmol (g CDW)−1 h−1) and glycerol (19.6 mmol (g CDW)−1 h−1) production rates were close to predicted values. Proteomics confirmed that this increased consumption rate was facilitated by enzyme reallocation from especially ribosomes (from 25.5 to 18.5 %) towards glycolysis (from 28.7 to 43.5 %). Subsequently, 200 generations of sequential transfer did not improve growth of the engineered strain, showing the use of ecGEMs in predicting opportunity space for laboratory evolution. The observations in this study illustrate both the current potential, as well as future improvements, of ecGEMs as a tool for both metabolic engineering and laboratory evolution.

Place, publisher, year, edition, pages
Elsevier BV, 2024
Keywords
2, 3-Butanediol, Anaerobic, Enzyme-constrained genome-scale model, Metabolic engineering, Proteomics
National Category
Microbiology
Identifiers
urn:nbn:se:kth:diva-343485 (URN)10.1016/j.ymben.2024.01.007 (DOI)001181818000001 ()38309619 (PubMedID)2-s2.0-85183971243 (Scopus ID)
Note

QC 20240215

Available from: 2024-02-15 Created: 2024-02-15 Last updated: 2024-04-05Bibliographically approved
Ljungqvist, E. E., Daga-Quisbert, J., van Maris, A. J. A. & Gustavsson, M. (2024). Insights into the rapid metabolism of Geobacillus sp. LC300: unraveling metabolic requirements and optimal growth conditions. Extremophiles, 28(1), Article ID 6.
Open this publication in new window or tab >>Insights into the rapid metabolism of Geobacillus sp. LC300: unraveling metabolic requirements and optimal growth conditions
2024 (English)In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 28, no 1, article id 6Article in journal (Refereed) Published
Abstract [en]

This study investigated the metabolism of Geobacillus sp. LC300, a promising biorefinery host organism with high substrate utilization rates. A new defined medium was designed and tested that allows for exponential growth to elevated cell densities suitable for quantitative physiological studies. Screening of the metabolic requirements of G. sp. LC300 revealed prototrophy for all essential amino acids and most vitamins and only showed auxotrophy for vitamin B12 and biotin. The effect of temperature and pH on growth rate was investigated, adjusting the optimal growth temperature to several degrees lower than previously reported. Lastly, studies on carbon source utilization revealed a capability for fast growth on several common carbon sources, including monosaccharides, oligosaccharides, and polysaccharides, and the highest ever reported growth rate in defined medium on glucose (2.20 h(-1)) or glycerol (1.95 h(-1)). These findings provide a foundation for further exploration of G. sp. LC300's physiology and metabolic regulation, and its potential use in bioproduction processes.

Place, publisher, year, edition, pages
Springer Nature, 2024
Keywords
Geobacillus, Thermophile, Defined medium, Quantitative physiology, Metabolism, Bioprocess
National Category
Microbiology
Identifiers
urn:nbn:se:kth:diva-340664 (URN)10.1007/s00792-023-01319-x (DOI)001111169100001 ()38036917 (PubMedID)2-s2.0-85178398025 (Scopus ID)
Note

QC 20231211

Available from: 2023-12-11 Created: 2023-12-11 Last updated: 2024-08-20Bibliographically approved
Daga-Quisbert, J., Mendieta, D., Rajarao, G. K., van Maris, A. J. A. & Quillaguamán, J. (2024). Production of ectoine by Vreelandella boliviensis using non-aseptic repeated-batch and continuous cultivations in an air-lift bioreactor. International Microbiology, 1-10
Open this publication in new window or tab >>Production of ectoine by Vreelandella boliviensis using non-aseptic repeated-batch and continuous cultivations in an air-lift bioreactor
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2024 (English)In: International Microbiology, p. 1-10Article in journal (Refereed) Published
Place, publisher, year, edition, pages
Springer, 2024
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-365056 (URN)
Available from: 2025-06-17 Created: 2025-06-17 Last updated: 2025-06-17
Koendjbiharie, J. G., Kuil, T., Nurminen, C. M. .. & van Maris, A. J. A. (2024). The 6-phosphofructokinase reaction in Acetivibrio thermocellus is both ATP- and pyrophosphate-dependent. Metabolic engineering, 86, 41-54
Open this publication in new window or tab >>The 6-phosphofructokinase reaction in Acetivibrio thermocellus is both ATP- and pyrophosphate-dependent
2024 (English)In: Metabolic engineering, ISSN 1096-7176, E-ISSN 1096-7184, Vol. 86, p. 41-54Article in journal (Refereed) Published
Abstract [en]

Acetivibrio thermocellus (formerly Clostridium thermocellum) is a potential platform for lignocellulosic ethanol production. Its industrial application is hampered by low product titres, resulting from a low thermodynamic driving force of its central metabolism. It possesses both a functional ATP- and a functional PPi-dependent 6-phosphofructokinase (PPi-Pfk), of which only the latter is held responsible for the low driving force. Here we show that, following the replacement of PPi-Pfk by cytosolic pyrophosphatase and transaldolase, the native ATP-Pfk is able to carry the full glycolytic flux. Interestingly, the barely-detectable in vitro ATP-Pfk activities are only a fraction of what would be required, indicating its contribution to glycolysis has consistently been underestimated. A kinetic model demonstrated that the strong inhibition of ATP-Pfk by PPi can prevent futile cycling that would arise when both enzymes are active simultaneously. As such, there seems to be no need for a long-sought-after PPi-generating mechanism to drive glycolysis, as PPi-Pfk can simply use whatever PPi is available, and ATP-Pfk complements the rest of the PFK-flux. Laboratory evolution of the ΔPPi-Pfk strain, unable to valorize PPi, resulted in a mutation in the GreA transcription elongation factor. This mutation likely results in reduced RNA-turnover, hinting at transcription as a significant (and underestimated) source of anabolic PPi. Together with other mutations, this resulted in an A. thermocellus strain with the hitherto highest biomass-specific cellobiose uptake rate of 2.2 g/gx/h. These findings are both relevant for fundamental insight into dual ATP/PPi Pfk-nodes, which are not uncommon in other microorganisms, as well as for further engineering of A. thermocellus for consolidated bioprocessing.

Place, publisher, year, edition, pages
Elsevier BV, 2024
Keywords
6-Phosphofructokinase, Acetivibrio thermocellus, Clostridium thermocellum, Futile cycle, Kinetic model, Pyrophosphatase, Pyrophosphate, Transaldolase
National Category
Biochemistry Molecular Biology
Identifiers
urn:nbn:se:kth:diva-353421 (URN)10.1016/j.ymben.2024.09.002 (DOI)001316861700001 ()39245400 (PubMedID)2-s2.0-85203514791 (Scopus ID)
Note

QC 20241011

Available from: 2024-09-19 Created: 2024-09-19 Last updated: 2025-02-20Bibliographically approved
Schroeder, W. L., Kuil, T., van Maris, A. J. A., Lynd, L. R. & Maranas, C. D. (2023). A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis. Metabolic engineering, 77, 306-322
Open this publication in new window or tab >>A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis
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2023 (English)In: Metabolic engineering, ISSN 1096-7176, E-ISSN 1096-7184, Vol. 77, p. 306-322Article in journal (Refereed) Published
Abstract [en]

Lignocellulosic biomass is an abundant and renewable source of carbon for chemical manufacturing, yet it is cumbersome in conventional processes. A promising, and increasingly studied, candidate for lignocellulose bioprocessing is the thermophilic anaerobe Clostridium thermocellum given its potential to produce ethanol, organic acids, and hydrogen gas from lignocellulosic biomass under high substrate loading. Possessing an atypical glycolytic pathway which substitutes GTP or pyrophosphate (PPi) for ATP in some steps, including in the energy-investment phase, identification, and manipulation of PPi sources are key to engineering its metabolism. Previous efforts to identify the primary pyrophosphate have been unsuccessful. Here, we explore pyrophosphate metabolism through reconstructing, updating, and analyzing a new genome-scale stoichiometric model for C. thermocellum, iCTH669. Hundreds of changes to the former GEM, iCBI655, including correcting cofactor usages, addressing charge and elemental balance, standardizing biomass composition, and incorporating the latest experimental evidence led to a MEMOTE score improvement to 94%. We found agreement of iCTH669 model predictions across all available fermentation and biomass yield datasets. The feasibility of hundreds of PPi synthesis routes, newly identified and previously proposed, were assessed through the lens of the iCTH669 model including biomass synthesis, tRNA synthesis, newly identified sources, and previously proposed PPi-generating cycles. In all cases, the metabolic cost of PPi synthesis is at best equivalent to investment of one ATP suggesting no direct energetic advantage for the cofactor substitution in C. thermocellum. Even though no unique source of PPi could be gleaned by the model, by combining with gene expression data two most likely scenarios emerge. First, previously investigated PPi sources likely account for most PPi production in wild-type strains. Second, alternate metabolic routes as encoded by iCTH669 can collectively maintain PPi levels even when previously investigated synthesis cycles are disrupted. Model iCTH669 is available at github.com/maranasgroup/iCTH669.

Place, publisher, year, edition, pages
Elsevier BV, 2023
Keywords
Clostridium thermocellum, Bioprocessing, Pyrophosphate, Modeling, Metabolism, Glycolysis
National Category
Other Medical Biotechnology
Identifiers
urn:nbn:se:kth:diva-330499 (URN)10.1016/j.ymben.2023.04.003 (DOI)001007426300001 ()37085141 (PubMedID)2-s2.0-85156276223 (Scopus ID)
Note

QC 20230630

Available from: 2023-06-30 Created: 2023-06-30 Last updated: 2023-06-30Bibliographically approved
Daga-Quisbert, J., Rajarao, G. K., Ugarte, F., van Maris, A. J. A. & Quillaguaman, J. (2023). Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes. FEMS Microbiology Ecology, 99(8), Article ID fiad073.
Open this publication in new window or tab >>Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes
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2023 (English)In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 99, no 8, article id fiad073Article in journal (Refereed) Published
Abstract [en]

Lake Pastos Grandes in Bolivia is mainly composed of salt flats, which are sporadically and only partially submerged during the wet season. In the present study, the chemical composition of water samples of the lake and some influent rivers was determined. We found that it is likely that the lake was influenced by the dilution of metals from ancient evaporites. We performed the first metagenomic studies of this lake. Analyses of shotgun metagenomics revealed that the relative abundances of Burkholderiales and Pseudomonadales were noteworthy in the water samples, whereas the archaea belonging to the Halobacteriales and Cyanobacteria from subsection III had high abundances in the salt flat. The eukaryotes Crustacea and Diatomea exhibited the highest abundances in the water samples. We investigated further the potential effect of human activities on the nitrogen cycle mobilization in the lake and the propagation of antimicrobial resistance genes. This is the first report about the cycle in the lake. Additionally, rifamycin resistance genes and genes related to efflux pumps, which are not considered a hazard when identified in metagenomes, had the uppermost relative abundances in all sampling points. We found that Lake Pastos Grandes hitherto does not show an appreciable influence by anthropogenic actions. The microbiome of Lake Pastos Grandes, including microbial distribution, the nitrogen cycle and antibiotic resistance genes, was analyzed.

Place, publisher, year, edition, pages
Oxford University Press (OUP), 2023
Keywords
Bolivian Andean region, environmental metagenomics, high-altitude lake, Lake Pastos Grandes, salt flat
National Category
Microbiology Oceanography, Hydrology and Water Resources
Identifiers
urn:nbn:se:kth:diva-333814 (URN)10.1093/femsec/fiad073 (DOI)001035142900002 ()37401151 (PubMedID)2-s2.0-85165521472 (Scopus ID)
Note

QC 20230810

Available from: 2023-08-10 Created: 2023-08-10 Last updated: 2024-06-10Bibliographically approved
Pöschel, L., Guevara-Martínez, M., Hörnström, D., van Maris, A. J. A. & Buchhaupt, M. (2023). Engineering of thioesterase YciA from Haemophilus influenzae for production of carboxylic acids. Applied Microbiology and Biotechnology, 107(20), 6219-6236
Open this publication in new window or tab >>Engineering of thioesterase YciA from Haemophilus influenzae for production of carboxylic acids
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2023 (English)In: Applied Microbiology and Biotechnology, ISSN 0175-7598, E-ISSN 1432-0614, Vol. 107, no 20, p. 6219-6236Article in journal (Refereed) Published
Abstract [en]

Abstract: Acyl-CoA-thioesterases, which hydrolyze acyl-CoA-esters and thereby release the respective acid, have essential functions in cellular metabolism and have also been used to produce valuable compounds in biotechnological processes. Thioesterase YciA originating from Haemophilus influenzae has been previously used to produce specific dicarboxylic acids from CoA-bound intermediates of the ethylmalonyl CoA pathway (EMCP) in Methylorubrum extorquens. In order to identify variants of the YciA enzyme with the capability to hydrolyze so far inaccessible CoA-esters of the EMCP or with improved productivity, we engineered the substrate-binding region of the enzyme. Screening a small semi-rational mutant library directly in M. extorquens yielded the F35L variant which showed a drastic product level increase for mesaconic acid (6.4-fold) and 2-methylsuccinic acid (4.4-fold) compared to the unaltered YciA enzyme. Unexpectedly, in vitro enzyme assays using respective M. extorquens cell extracts or recombinantly produced thioesterases could not deliver congruent data, as the F35L variant showed strongly reduced activity in these experiments. However, applied in an Escherichia coli production strain, the protein variant again outperformed the wild-type enzyme by allowing threefold increased 3-hydroxybutyric acid product titers. Saturation mutagenesis of the codon for position 35 led to the identification of another highly efficient YciA variant and enabled structure-function interpretations. Our work describes an important module for dicarboxylic acid production with M. extorquens and can guide future thioesterase improvement approaches. Key points:

• Substitutions at position F35 of YciAHI changed the productivity of YciA-based release of carboxylic acid products in M. extorquens AM1 and E. coli.

• YciAHI F35N and F35L are improved variants for dicarboxylic production of 2-methylsuccinic acid and mesaconic acid with M. extorquens AM1.

• In vitro enzyme assays did not reveal superior properties of the optimized protein variants.

Place, publisher, year, edition, pages
Springer Nature, 2023
Keywords
3-Hydroxybutyric acid, Dicarboxylic acids, Enzyme engineering, Methylorubrum extorquens, Thioesterase
National Category
Biochemistry Molecular Biology
Identifiers
urn:nbn:se:kth:diva-338509 (URN)10.1007/s00253-023-12691-1 (DOI)001046949500002 ()37572123 (PubMedID)2-s2.0-85167810181 (Scopus ID)
Note

QC 20231114

Available from: 2023-11-14 Created: 2023-11-14 Last updated: 2025-02-20Bibliographically approved
Suits, K., Annus, I., Kandler, N., Karlsson, T., van Maris, A. J. A., Kaseva, A., . . . Rajarao, G. K. (2023). Overview of the (Smart) Stormwater Management around the Baltic Sea. Water, 15(8), 1623, Article ID 1623.
Open this publication in new window or tab >>Overview of the (Smart) Stormwater Management around the Baltic Sea
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2023 (English)In: Water, E-ISSN 2073-4441, Vol. 15, no 8, p. 1623-, article id 1623Article, review/survey (Refereed) Published
Abstract [en]

In this review paper, we investigate the management of the quality of stormwater in the Baltic Sea region. Current stormwater management practices, standards, and legislation do not accurately depict stormwater quality, resulting in an underestimation of its environmental impact. The digitalization and harmonization of stormwater management through the implementation of e-monitoring (online or continuous monitoring) allow for the collection of data. This data can be used to improve stormwater quality and quantity management, thereby reducing the environmental harm induced by anthropogenic activities. Based on the literature review, supporting tables and matrices are proposed to assist decision-makers and other interested parties in developing and implementing "smart" stormwater management solutions. In this article, we demonstrate that such systems can enhance stormwater management and system performance by leveraging data-driven operation and maintenance. Another advantage of the approach is that it contributes to a healthier urban environment and ecosystem well-being.

Place, publisher, year, edition, pages
MDPI AG, 2023
Keywords
urban stormwater management, water quality, smart cities, green infrastructure, e-monitoring, surrogate parameters
National Category
Water Engineering Environmental Sciences Human Geography
Identifiers
urn:nbn:se:kth:diva-327395 (URN)10.3390/w15081623 (DOI)000977998000001 ()2-s2.0-85156265183 (Scopus ID)
Note

QC 20230526

Available from: 2023-05-26 Created: 2023-05-26 Last updated: 2024-06-10Bibliographically approved
Kuil, T., Nurminen, C. M. .. & van Maris, A. J. A. (2023). Pyrophosphate as allosteric regulator of ATP-phosphofructokinase in Clostridium thermocellum and other bacteria with ATP- and PPi-phosphofructokinases. Archives of Biochemistry and Biophysics, 743, Article ID 109676.
Open this publication in new window or tab >>Pyrophosphate as allosteric regulator of ATP-phosphofructokinase in Clostridium thermocellum and other bacteria with ATP- and PPi-phosphofructokinases
2023 (English)In: Archives of Biochemistry and Biophysics, ISSN 0003-9861, E-ISSN 1096-0384, Vol. 743, article id 109676Article in journal (Refereed) Published
Abstract [en]

The phosphofructokinase (Pfk) reaction represents one of the key regulatory points in glycolysis. While most organisms encode for Pfks that use ATP as phosphoryl donor, some organisms also encode for PPi-dependent Pfks. Despite this central role, the biochemical characteristics as well as the physiological role of both Pfks is often not known. Clostridium thermocellum is an example of a microorganism that encodes for both Pfks, however, only PPi-Pfk activity has been detected in cell-free extracts and little is known about the regulation and function of both enzymes. In this study, the ATP- and PPi-Pfk of C. thermocellum were purified and biochemically characterized. No allosteric regulators were found for PPi-Pfk amongst common effectors. With fructose-6-P, PPi, fructose-1,6-bisP, and Pi PPi-Pfk showed high specificity (KM < 0.62 mM) and maximum activity (Vmax > 156 U mg-1). In contrast, ATP-Pfk showed much lower affinity (K0.5 of 9.26 mM) and maximum activity (14.5 U mg-1) with fructose-6-P. In addition to ATP, also GTP, UTP and ITP could be used as phosphoryl donors. The catalytic efficiency with GTP was 7-fold higher than with ATP, suggesting that GTP is the preferred substrate. The enzyme was activated by NH4+, and pronounced inhibition was observed with GDP, FBP, PEP, and especially with PPi (Ki of 0.007 mM). Characterization of purified ATP-Pfks originating from eleven different bacteria, encoding for only ATP-Pfk or for both ATP- and PPi-Pfk, identified that PPi inhibition of ATP-Pfks could be a common phenomenon for organisms with a PPi-dependent glycolysis.

Place, publisher, year, edition, pages
Elsevier BV, 2023
Keywords
Clostridium thermocellum, Acetivibrio thermocellus, Phosphofructokinase, Pyrophosphate, PPi, Allosteric regulation, Glycolysis
National Category
Biochemistry Molecular Biology
Identifiers
urn:nbn:se:kth:diva-333542 (URN)10.1016/j.abb.2023.109676 (DOI)001026883500001 ()37380119 (PubMedID)2-s2.0-85163509822 (Scopus ID)
Note

QC 20230803

Available from: 2023-08-03 Created: 2023-08-03 Last updated: 2025-02-20Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-5319-7511

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