cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11668700
title: A Patent Survey on the Biotechnological Production of 2,5-Furandicarboxylic acid (FDCA): Current Trends and Challenges

description: The production of 2,5-furandicarboxylic acid (FDCA) as a biobased commodity chemical has gained great importance over the last years. The possibility of replacing conventional polyethylene terephthalate (PET)-based plastics by polyethylene furanoate (PEF) is accelerating applied research in the direction of novel and highly productive synthesis routes to FDCA. This paper explores the patent activities related to FDCA production, with particular emphasis on the potential role that enzymatic catalytic methods may have. An increasing number of patent applications (and granted ones) have been disclosed over the last decade. The innovation is set on the development of multi-step catalytic processes, involving multi-enzymatic and chemoenzymatic cascades, or using whole-cells, either as resting (non-growing) biocatalysts or as living organisms in fermentative processes. Moreover, other innovative paths use substrates different from fructose and 5-hydroxymethylfurfural (HMF), such as gluconic acid, or furfural. Overall, opportunities for innovation exist, albeit current production metrics in biotechnological methods remain mostly at the proof-of-concept level. Large development efforts to reach industrial targets are needed, which may be stimulated by the less severe processing conditions expected for biotechnology, leading to energy savings, less by-product formation, and to the valorization of crude effluents.
DOI: 10.5281/zenodo.10545171
title: Integrated Preservation of Water Activity as Key to Intensified Chemoenzymatic Synthesis of Bio-Based Styrene Derivatives

description: The valorization of lignin-derived feedstocks by catalytic means enables their defunctionalization and upgrading to valuable products. However, the development of productive, safe, and low-waste processes remains challenging. This paper explores the industrial potential of a chemoenzymatic reaction performing the decarboxylation of bio-based phenolic acids in wet cyclopentyl methyl ether (CPME) by immobilized phenolic acid decarboxylase from Bacillus subtilis, followed by a base-catalyzed acylation. Key-to-success is the continuous control of water activity, which fluctuates along the reaction progress, particularly at high substrate loadings (triggered by different hydrophilicities of substrate and product). A combination of experimentation, thermodynamic equilibrium calculations, and MD simulations revealed the change in water activity which guided the integration of water reservoirs and allowed process intensification of the previously limiting enzymatic step. With this, the highly concentrated sequential two-step cascade (400 g·L–1) achieves full conversions and affords products in less than 3 h. The chemical step is versatile, accepting different acyl donors, leading to a range of industrially sound products. Importantly, the finding that water activity changes in intensified processes is an academic insight that might explain other deactivations of enzymes when used in non-conventional media.
DOI: 10.5281/zenodo.10545172
title: Integrated Preservation of Water Activity as Key to Intensified Chemoenzymatic Synthesis of Bio-Based Styrene Derivatives

description: The valorization of lignin-derived feedstocks by catalytic means enables their defunctionalization and upgrading to valuable products. However, the development of productive, safe, and low-waste processes remains challenging. This paper explores the industrial potential of a chemoenzymatic reaction performing the decarboxylation of bio-based phenolic acids in wet cyclopentyl methyl ether (CPME) by immobilized phenolic acid decarboxylase from Bacillus subtilis, followed by a base-catalyzed acylation. Key-to-success is the continuous control of water activity, which fluctuates along the reaction progress, particularly at high substrate loadings (triggered by different hydrophilicities of substrate and product). A combination of experimentation, thermodynamic equilibrium calculations, and MD simulations revealed the change in water activity which guided the integration of water reservoirs and allowed process intensification of the previously limiting enzymatic step. With this, the highly concentrated sequential two-step cascade (400 g·L–1) achieves full conversions and affords products in less than 3 h. The chemical step is versatile, accepting different acyl donors, leading to a range of industrially sound products. Importantly, the finding that water activity changes in intensified processes is an academic insight that might explain other deactivations of enzymes when used in non-conventional media.
DOI: 10.15468/dl.wa36dr
title: Occurrence Download

description: A dataset containing 23840 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is Mustela Linnaeus, 1758"
 ]
}

 The dataset includes 23840 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020733-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aab5gd
title: Occurrence Download

description: A dataset containing 3846 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Melaleuca leucadendra (L.) L.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3846 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087001-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.7808088
title: Diversely evolved xibalbin variants from remipede venom inhibit 3 potassium channels and activate PKA-II and Erk1/2 signalling

description: Background: The identification of novel toxins from overlooked and taxonomically exceptional species bears potential for various pharmacological applications. The remipede Xibalbanus tulumensis, an underwater cave-dwelling crustacean, is the only crustacean for which a venom system has been described. Its venom contains several xibalbin peptides that have an inhibitor cysteine knot (ICK) scaffold.

Result: Our screenings revealed that all tested xibalbin variants particularly inhibit potassium channels. Xib1 and xib13, with their eight-cysteine domain similar to spider knottins also inhibit voltage-gated sodium channels. No activity was noted on calcium channels. Expanding the functional testing we demonstrate that xib1 and xib13 increase PKA-II and Erk1/2 sensitization signaling in nociceptive neurons, which may initiate pain sensitization. Our phylogenetic analysis suggests that xib13 either originates from the common ancestor of pancrustaceans or earlier while xib1 is more restricted to remipedes. The ten-cysteine scaffolded xib2 emerged from xib1, a result that is supported by our phylogenetic and machine learning-based analyses.

Conclusions: Our functional characterization of synthesized variants of xib1, xib2, and xib13 elucidates their potential as inhibitors of potassium channels in mammalian systems. The specific interaction of xib2 with Kv1.6 channels, which are relevant to treating variants of epilepsy, shows potential for further studies. At higher concentrations, xib1 and xib13 activate the kinases PKA-II and ERK1/2 in mammalian sensory neurons, suggesting pain sensitization and potential applications related to pain research and therapy. While tested insect channels suggest that all probably act as neurotoxins, the biological function of xib1, xib2, and xib13 requires further elucidation. A novel finding on their evolutionary origin is the apparent emergence of X. tulumensis-specific xib2 from xib1. Our study is an important cornerstone for future studies to untangle the origin and function of these enigmatic proteins as important components of remipede but also other pancrustacean and arthropod venoms.
DOI: 10.5281/zenodo.7808089
title: Diversely evolved xibalbin variants from remipede venom inhibit 3 potassium channels and activate PKA-II and Erk1/2 signalling

description: Background: The identification of novel toxins from overlooked and taxonomically exceptional species bears potential for various pharmacological applications. The remipede Xibalbanus tulumensis, an underwater cave-dwelling crustacean, is the only crustacean for which a venom system has been described. Its venom contains several xibalbin peptides that have an inhibitor cysteine knot (ICK) scaffold.

Result: Our screenings revealed that all tested xibalbin variants particularly inhibit potassium channels. Xib1 and xib13, with their eight-cysteine domain similar to spider knottins also inhibit voltage-gated sodium channels. No activity was noted on calcium channels. Expanding the functional testing we demonstrate that xib1 and xib13 increase PKA-II and Erk1/2 sensitization signaling in nociceptive neurons, which may initiate pain sensitization. Our phylogenetic analysis suggests that xib13 either originates from the common ancestor of pancrustaceans or earlier while xib1 is more restricted to remipedes. The ten-cysteine scaffolded xib2 emerged from xib1, a result that is supported by our phylogenetic and machine learning-based analyses.

Conclusions: Our functional characterization of synthesized variants of xib1, xib2, and xib13 elucidates their potential as inhibitors of potassium channels in mammalian systems. The specific interaction of xib2 with Kv1.6 channels, which are relevant to treating variants of epilepsy, shows potential for further studies. At higher concentrations, xib1 and xib13 activate the kinases PKA-II and ERK1/2 in mammalian sensory neurons, suggesting pain sensitization and potential applications related to pain research and therapy. While tested insect channels suggest that all probably act as neurotoxins, the biological function of xib1, xib2, and xib13 requires further elucidation. A novel finding on their evolutionary origin is the apparent emergence of X. tulumensis-specific xib2 from xib1. Our study is an important cornerstone for future studies to untangle the origin and function of these enigmatic proteins as important components of remipede but also other pancrustacean and arthropod venoms.
DOI: 10.57745/75tpwc
title: Questionnaire.pdf

description: Retranscription au format .PDF du questionnaire diffusé sur le WEB aux enquêtés
DOI: 10.5281/zenodo.12162836
title: GRIPP-2 checklist for 'Patient and public involvement in the design and protocol development for a platform randomised trial to evaluate diagnostic tests to optimise antimicrobial therapy (PROTECT)'
DOI: 10.5281/zenodo.12162837
title: GRIPP-2 checklist for 'Patient and public involvement in the design and protocol development for a platform randomised trial to evaluate diagnostic tests to optimise antimicrobial therapy (PROTECT)'
DOI: 10.15468/es0n3l
title: Coleoptera
DOI: 10.15468/dl.jkzvxy
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Abrotanella rostrata Swenson)"
 ]
}

 The dataset includes 24 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087002-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10528903
title: Cobalt-Mediated Photochemical C−H Arylation of Pyrroles

description: Optimized geometries in xyz-format, supplement to the journal article published in Angew. Chem. Int. Ed. 2024, e202405780 (https://doi.org/10.1002/anie.202405780).
DOI: 10.5281/zenodo.10528904
title: Cobalt-Mediated Photochemical C−H Arylation of Pyrroles

description: Optimized geometries in xyz-format, supplement to the journal article published in Angew. Chem. Int. Ed. 2024, e202405780 (https://doi.org/10.1002/anie.202405780).
DOI: 10.15468/dl.eqqdpe
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Macaca arctoides (I.Geoffroy Saint-Hilaire, 1831), Macacus rufescens Anderson, 1872, Papio melanotus Ogilby, 1839, Macacus brunneus Anderson, 1871, Macacus harmandi Trouessart, 1897, Macacus arctoides (Geoffroy, 1831), Macacus ursinus Gervais, 1854, Macacus arctoides melli Matschie, 1912)",
 "Year 1970-2024"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087003-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/1002
title: Data for "An evaluation of the heat test for the ice-nucleating ability of minerals and biological material"

description: Mineral dust and particles of biological origin are important types of ice-nucleating particles (INPs) that can trigger ice formation of supercooled cloud droplets. Heat treatments are used to detect the presence of biological INPs in samples collected from the environment as the activity of mineral INPs is assumed unchanged, although not fully assessed. We show that the ice-nucleating ability of some minerals can change after heating and discuss how INP heat tests should be interpreted. This dataset contains the droplet freezing assay data used in this study.
DOI: 10.15468/dl.jv35yf
title: Occurrence Download

description: A dataset containing 124153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cystopteris fragilis (L.) Bernh.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 124153 records from 919 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0086969-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qndw7p
title: Occurrence Download

description: A dataset containing 3248 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Melaleuca thymifolia Sm.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3248 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087004-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.892531
title: Physical oceanography during SONNE cruise SO239
DOI: 10.5281/zenodo.7982554
title: Biosynthesis of Furfurylamines in Batch and Continuous Flow by Immobilized Amine Transaminases

description: Building blocks with amine functionality are crucial in the chemical industry. Biocatalytic syntheses and chemicals derived from renewable resources are increasingly desired to achieve sustainable production of these amines. As a result, renewable materials such as furfurals, especially furfurylamines like 5-(hydroxymethyl)furfurylamine (HMFA) and 2,5-di(aminomethyl)furan (DAF), are gaining increasing attention. In this study, we identified four different amine transaminases (ATAs) that catalyze the reductive amination of 5-(hydroxymethyl)furfural (HMF) and 2,5-diformylfuran (DFF). We successfully immobilized these ATAs on glutaraldehyde-functionalized amine beads using multiple binding and on amine beads by site-selective binding of the unique Cα-formylglycine within an aldehyde tag. All immobilized ATAs were efficiently reused in five repetitive cycles of reductive amination of HMF with alanine as co-substrate, while the ATA from Silicibacter pomeroyi (ATA-Spo) also exhibited high stability for reuse when isopropylamine was used as an amine donor. Additionally, immobilized ATA-Spo yielded high conversion in the batch syntheses of HMFA and DAF using alanine (87% and 87%, respectively) or isopropylamine (99% and 98%, respectively) as amine donors. We further demonstrated that ATA-Spo was effective for the reductive amination of HMF with alanine or isopropylamine in continuous-flow catalysis with high conversion up to 12 days (48% and 41%, respectively).
DOI: 10.5281/zenodo.7982555
title: Biosynthesis of Furfurylamines in Batch and Continuous Flow by Immobilized Amine Transaminases

description: Building blocks with amine functionality are crucial in the chemical industry. Biocatalytic syntheses and chemicals derived from renewable resources are increasingly desired to achieve sustainable production of these amines. As a result, renewable materials such as furfurals, especially furfurylamines like 5-(hydroxymethyl)furfurylamine (HMFA) and 2,5-di(aminomethyl)furan (DAF), are gaining increasing attention. In this study, we identified four different amine transaminases (ATAs) that catalyze the reductive amination of 5-(hydroxymethyl)furfural (HMF) and 2,5-diformylfuran (DFF). We successfully immobilized these ATAs on glutaraldehyde-functionalized amine beads using multiple binding and on amine beads by site-selective binding of the unique Cα-formylglycine within an aldehyde tag. All immobilized ATAs were efficiently reused in five repetitive cycles of reductive amination of HMF with alanine as co-substrate, while the ATA from Silicibacter pomeroyi (ATA-Spo) also exhibited high stability for reuse when isopropylamine was used as an amine donor. Additionally, immobilized ATA-Spo yielded high conversion in the batch syntheses of HMFA and DAF using alanine (87% and 87%, respectively) or isopropylamine (99% and 98%, respectively) as amine donors. We further demonstrated that ATA-Spo was effective for the reductive amination of HMF with alanine or isopropylamine in continuous-flow catalysis with high conversion up to 12 days (48% and 41%, respectively).
DOI: 10.5281/zenodo.7947609
title: A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors

description: The development of methods to engineer and immobilize amine transaminases (ATAs) to improve their functionality and operational stability is gaining momentum. The quest for robust, fast, and easy-to-use methods to screen the activity of large collections of transaminases, is essential. This work presents a novel and multiplex fluorescence-based kinetic assay to assess ATA activity using 4-dimethylamino-1-naphthaldehyde as an amine acceptor. The developed assay allowed us to screen a battery of amine donors using free and immobilized ATAs from different microbial sources as biocatalysts. As a result, using chromatographic methods, 4-hydroxybenzylamine was identified as the best amine donor for the amination of hydroxy methyl furfural. Finally, we adapted this method to determine the apparent Michaelis-Menten parameters of a model immobilized ATA at the microscopic (single-particle) level. Our studies promote the use of this multiplex, multidimensional assay to screen ATAs for further improvement.
DOI: 10.5281/zenodo.7947610
title: A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors

description: The development of methods to engineer and immobilize amine transaminases (ATAs) to improve their functionality and operational stability is gaining momentum. The quest for robust, fast, and easy-to-use methods to screen the activity of large collections of transaminases, is essential. This work presents a novel and multiplex fluorescence-based kinetic assay to assess ATA activity using 4-dimethylamino-1-naphthaldehyde as an amine acceptor. The developed assay allowed us to screen a battery of amine donors using free and immobilized ATAs from different microbial sources as biocatalysts. As a result, using chromatographic methods, 4-hydroxybenzylamine was identified as the best amine donor for the amination of hydroxy methyl furfural. Finally, we adapted this method to determine the apparent Michaelis-Menten parameters of a model immobilized ATA at the microscopic (single-particle) level. Our studies promote the use of this multiplex, multidimensional assay to screen ATAs for further improvement.
DOI: 10.48364/isimip.364229
title: ISIMIP3 marine ecosystems masks

description: This dataset contains masks for large marine ecosystems (LME) and regional marine ecosystems (RME) to be used in the fisheries & marine ecosystems sector of ISIMIP3a and 3b (Frieler et al. 2023, Frieler et al. 2024, in prep.).<br>While the LME masks originate from Sherman et al. (2017), the RME masks were provided by the modelling groups already participating in ISIMIP.
DOI: 10.15468/dl.wh69bn
title: Occurrence Download

description: A dataset containing 5146 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Melaleuca styphelioides Sm.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5146 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087005-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12165736
title: AI Tool Use and Adoption in Software Development by Individuals and Organizations: A Grounded Theory Study

description: This data represents four artifacts from our research in studying what impacts AI adoption and use in SE. It includes our interview questions, the codebook with example quotes, survey questions, and table with the code to category generation.

This page includes supplementary materials associated with our paper entitled "AI Tool Use and Adoption in Software Development by Individuals and Organizations: A Grounded Theory Study".
DOI: 10.5281/zenodo.12165737
title: AI Tool Use and Adoption in Software Development by Individuals and Organizations: A Grounded Theory Study

description: This data represents four artifacts from our research in studying what impacts AI adoption and use in SE. It includes our interview questions, the codebook with example quotes, survey questions, and table with the code to category generation.

This page includes supplementary materials associated with our paper entitled "AI Tool Use and Adoption in Software Development by Individuals and Organizations: A Grounded Theory Study".
DOI: 10.15468/dl.pqa3qe
title: Occurrence Download

description: A dataset containing 8843 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cyrtomium fortunei J.Sm.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8843 records from 151 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087007-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vrd4at
title: Occurrence Download

description: A dataset containing 1365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Abutilon abutiloides (Jacq.) Garcke, Abutilon abutiloides (Jacq.) Garcke ex Hochr.)"
 ]
}

 The dataset includes 1365 records from 100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087006-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.892532
title: Physical oceanography during SONNE cruise SO242/1