cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10521398
title: Biodegradation of poly-3-hydroxybutyrate after soil inoculation with microbial consortium: Soil microbiome and plant responses to the changed environment; DNA sequences

description: DNA sequence reads from used for metagenomic analysis in the study.

Abstract

Biodegradable plastics can play an important role in solving global plastics disposal problems. Poly-3-hydroxybutyrate (P3HB) is a biodegradable bacterial intracellular storage polymer with a wide usage in agriculture. P3HB and its degradation products are assumed to be non-toxic. However, previous studies suggested that its biodegradation negatively affects plant growth due to their competition with microorganisms for nutrients. A solution of this

issue may hypothetically be the microbial inoculation of soil by the consortium of plant growth-promoting and N-fixing microorganisms. To verify this hypothesis, we carried out a pot experiment with lettuce (Lactuca sativa L. var. capitata L.) grown in soil amended with two doses (1% and 5% w/w) of P3HB and microbial inoculant (MI). Five experimental variants – P3HB 1%, P3HB 1% + MI, P3HB 5%, P3HB 5% + MI, MI – were tested to evaluate the effect of added microorganisms on plant growth and P3HB biodegradation. Efficient P3HB degradation, directly dependent on amended bioplastic dose, was coupled with preferential utilization of P3HB as a C source. Due to a higher demand of conditionally more abundant microbial degraders for nutrients in P3HB-amended soil, respiration and enzyme activities were enhanced, indicating increased mineralization of C as well as N, S, and P. Microbial inoculation provided functionally specific bacterial taxa, which further enhanced degradation efficiency and turnover of the nutrients (N, S, P) in P3HB-amended soil. P3HB-related soil acidification was not determinative for plant growth inhibition. However, plant biomass yield remained limited despite the MI-derived plant growth-promoting rhizobacteria (PGPR) and N2-fixing microorganisms, which were assumed to mitigate P3HB-related plant growth inhibition.
DOI: 10.5281/zenodo.10521399
title: Biodegradation of poly-3-hydroxybutyrate after soil inoculation with microbial consortium: Soil microbiome and plant responses to the changed environment; DNA sequences

description: DNA sequence reads from used for metagenomic analysis in the study.

Abstract

Biodegradable plastics can play an important role in solving global plastics disposal problems. Poly-3-hydroxybutyrate (P3HB) is a biodegradable bacterial intracellular storage polymer with a wide usage in agriculture. P3HB and its degradation products are assumed to be non-toxic. However, previous studies suggested that its biodegradation negatively affects plant growth due to their competition with microorganisms for nutrients. A solution of this

issue may hypothetically be the microbial inoculation of soil by the consortium of plant growth-promoting and N-fixing microorganisms. To verify this hypothesis, we carried out a pot experiment with lettuce (Lactuca sativa L. var. capitata L.) grown in soil amended with two doses (1% and 5% w/w) of P3HB and microbial inoculant (MI). Five experimental variants – P3HB 1%, P3HB 1% + MI, P3HB 5%, P3HB 5% + MI, MI – were tested to evaluate the effect of added microorganisms on plant growth and P3HB biodegradation. Efficient P3HB degradation, directly dependent on amended bioplastic dose, was coupled with preferential utilization of P3HB as a C source. Due to a higher demand of conditionally more abundant microbial degraders for nutrients in P3HB-amended soil, respiration and enzyme activities were enhanced, indicating increased mineralization of C as well as N, S, and P. Microbial inoculation provided functionally specific bacterial taxa, which further enhanced degradation efficiency and turnover of the nutrients (N, S, P) in P3HB-amended soil. P3HB-related soil acidification was not determinative for plant growth inhibition. However, plant biomass yield remained limited despite the MI-derived plant growth-promoting rhizobacteria (PGPR) and N2-fixing microorganisms, which were assumed to mitigate P3HB-related plant growth inhibition.
DOI: 10.6084/m9.figshare.25011050
title: Supplementary Material for: Exploring Traditional Medicine Diagnostic Classification for Parkinson’s Disease Using Hierarchical Clustering

description: Introduction: Personalized diagnosis and therapy for Parkinson’s disease (PD) are needed due to the clinical heterogeneity of PD. Syndrome differentiation (SD) in traditional medicine (TM) is a diagnostic method for customized therapy that comprehensively analyzes various symptoms and systemic syndromes. However, research identifying PD classification based on SD is limited. 
Methods: Ten electronic databases were systematically searched from inception to August 10, 2021. Clinical indicators, including 380 symptoms, 98 TM signs, and herbal medicine for PD diagnosed with SD, were extracted from 197 articles; frequency statistics on clinical indicators were conducted to classify several subtypes using hierarchical clustering. 
Results: Four distinct cluster groups were identified, each characterized by significant cluster-specific clinical indicators with 95% confidence intervals of distribution. Subtype 2 had the most severe progression, longest progressive duration, and highest association with greater late-stage PD-associated motor symptoms, including postural instability and gait disturbance. The action properties of the herbal formula and original SD presented in the data sources for subtype 2 were associated with Yin deficiency syndrome.
Discussion/Conclusion: Hierarchical clustering analysis distinguished various symptoms and TM signs among patients with PD. These newly identified PD subtypes may optimize the diagnosis and treatment with TM and facilitate prognosis prediction. Our findings serve as a cornerstone for evidence-based guidelines for TM diagnosis and treatment.
DOI: 10.6084/m9.figshare.25011050.v1
title: Supplementary Material for: Exploring Traditional Medicine Diagnostic Classification for Parkinson’s Disease Using Hierarchical Clustering

description: Introduction: Personalized diagnosis and therapy for Parkinson’s disease (PD) are needed due to the clinical heterogeneity of PD. Syndrome differentiation (SD) in traditional medicine (TM) is a diagnostic method for customized therapy that comprehensively analyzes various symptoms and systemic syndromes. However, research identifying PD classification based on SD is limited. 
Methods: Ten electronic databases were systematically searched from inception to August 10, 2021. Clinical indicators, including 380 symptoms, 98 TM signs, and herbal medicine for PD diagnosed with SD, were extracted from 197 articles; frequency statistics on clinical indicators were conducted to classify several subtypes using hierarchical clustering. 
Results: Four distinct cluster groups were identified, each characterized by significant cluster-specific clinical indicators with 95% confidence intervals of distribution. Subtype 2 had the most severe progression, longest progressive duration, and highest association with greater late-stage PD-associated motor symptoms, including postural instability and gait disturbance. The action properties of the herbal formula and original SD presented in the data sources for subtype 2 were associated with Yin deficiency syndrome.
Discussion/Conclusion: Hierarchical clustering analysis distinguished various symptoms and TM signs among patients with PD. These newly identified PD subtypes may optimize the diagnosis and treatment with TM and facilitate prognosis prediction. Our findings serve as a cornerstone for evidence-based guidelines for TM diagnosis and treatment.
DOI: 10.5519/qd.1icfrjze
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.h4j1nmm4
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (998 records)
DOI: 10.5281/zenodo.10521438
title: PreAlti dataset - Gas exchange maximal test
DOI: 10.5281/zenodo.10521439
title: PreAlti dataset - Gas exchange maximal test
DOI: 10.5281/zenodo.10521446
title: PreAlti dataset - Cardiac hemodynamics maximal test
DOI: 10.5281/zenodo.10521447
title: PreAlti dataset - Cardiac hemodynamics maximal test
DOI: 10.57756/fbf5wk
title: MicroCT scan of a fossil cervical vertrebra of a Perplexicervicidae (Aves) - Supplementary material to "Mayr et al. (2023): Reinterpretation of tuberculate cervical vertebrae of Eocene birds as an exceptional anti-predator adaptation against the mammalian craniocervical killing bite"

description: <p>MicroCT (x-ray
microcomputed tomography, YXLON FF35 CT) dataset of a fossil cervical vertrebrate of a Perplexicervicidae (Aves). The specimen is part of the vertebrate collection of the department of Geology and Paleontology at the Natural History Museum Vienna. </p>
DOI: 10.5281/zenodo.10521453
title: PreAlti dataset - Muscle and cerebral oxygenation maximal test
DOI: 10.5281/zenodo.10521454
title: PreAlti dataset - Muscle and cerebral oxygenation maximal test
DOI: 10.4121/af9918ff-d1f9-4e96-aece-e4fa22f6bc08.v1
title: Underwater footage of bubble curtain in Marin's Offshore Basin

description: One video shows the underwater drone filming the bubble curtain. The second video shows an overview of the bubble curtain. The bubble curtain was 31 m wide and 10 m high with 2 mm holes drilled every 100mm. This research was carried out in the light of sound mitigation by bubble curtains. Both the hydrodynamic and acoustic properties of the bubble curtain were measured. The data was collected using an underwater drone with a camera and a stationary underwater camera.
DOI: 10.6084/m9.figshare.25001768.v3
title: <b>Bright and stable monomeric fluorescent protein derived from StayGold</b>

description: High brightness and photostability of StayGold make it a particularly attractive probe for long-term live cell imaging. However, its dimeric nature precludes its application as a fluorescent tag for some proteins. Here, we report the development and X-ray structures of a monomeric variant of StayGold (mBaoJin), which preserves the beneficial properties of its precursor while serving as a tag for structural proteins and membranes. We compare mBaoJin to other state-of-art GFPs and utilize it for super-resolution long-term live cell imaging and expansion microscopy.
DOI: 10.5281/zenodo.10521482
title: Projects' Statistical Information

description: The dataset contains statistical information about the projects we used in our experiments.
DOI: 10.5281/zenodo.10521483
title: Projects' Statistical Information

description: The dataset contains statistical information about the projects we used in our experiments.
DOI: 10.5281/zenodo.10521491
title: Project and Versions

description: The dataset contains a list of the projects and versions used in our experiments.
DOI: 10.5281/zenodo.10521492
title: Project and Versions

description: The dataset contains a list of the projects and versions used in our experiments.
DOI: 10.5281/zenodo.8163498
title: Dataset for paper "A Close-Range Photogrammetric Surface Scanner and its Evaluation"

description: This dataset is supplementary material to the submission “A low-cost close-range photogrammetric surface scanner”, by Panagiotis Koutlemanis, Xenophon Zabulis, Nikolaos Stivaktakis, Nikolaos Partarakis, Emmanouil Zidianakis, and Ioanna Demeridou. The dataset contains 3D reconstructions that show the results of a close-range photogrammetric approach and its implementation using a low-cost CNC device.
DOI: 10.5281/zenodo.8163499
title: Dataset for paper "A Close-Range Photogrammetric Surface Scanner and its Evaluation"

description: This dataset is supplementary material to the submission “A low-cost close-range photogrammetric surface scanner”, by Panagiotis Koutlemanis, Xenophon Zabulis, Nikolaos Stivaktakis, Nikolaos Partarakis, Emmanouil Zidianakis, and Ioanna Demeridou. The dataset contains 3D reconstructions that show the results of a close-range photogrammetric approach and its implementation using a low-cost CNC device.
DOI: 10.5281/zenodo.7998391
title: NMR and structure calculation data of the TccC3 toxin from Photorhabdus luminescens

description: NMR and structure calculation data of the protein TcART (a section of TccC3 from Photorhabdus luminescens) as presented in the publication

Belyy, A., Lindemann, F., Roderer, D. et al. Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin. Nat Commun 13, 4202 (2022). https://doi.org/10.1038/s41467-022-31836-w

and my thesis

"A Structural View on Mechanisms of Bacterial Communal Life and Toxicity" submitted to the Free University Berlin (http://dx.doi.org/10.17169/refubium-41725).
description: Detailed overview:
ARIA_structure_calc.tar.gz - Input and structure calculation data of two consensus runs to determine an NMR ensemble
Belyy_Lindemann_NatCommun_2022.tar.gz - My data published in 2022
solutionNMR_TcART.tar.gz - Assignment project incl. input data for structure calculation
TcART_dialysis_comparison.tar.gz - Comparison of dialyzed and non-dialyzed TcART (CH spectra)
TcART_NAD+binding.tar.gz - NMR data of TcART titration with NAD+ (NH spectra, TcART)
TcART_NAD+binding_31P.tar.gz - NMR data of TcART titration with NAD+ (31P spectra, NAD+)
TcART_relaxation_data.tar.gz - Relaxation data recorded on TcART to determine local flexibility
TcB_TcC_solids_data.tar.gz - Solid-state NMR data of the TcdB2-TccC3 complex from Photorhabdus luminescens
TcHVR_TcART_comparison.tar.gz - Comparison of two constructs arising from TccC3
DOI: 10.5281/zenodo.7998392
title: NMR and structure calculation data of the TccC3 toxin from Photorhabdus luminescens

description: NMR and structure calculation data of the protein TcART (a section of TccC3 from Photorhabdus luminescens) as presented in the publication

Belyy, A., Lindemann, F., Roderer, D. et al. Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin. Nat Commun 13, 4202 (2022). https://doi.org/10.1038/s41467-022-31836-w

and my thesis

"A Structural View on Mechanisms of Bacterial Communal Life and Toxicity" submitted to the Free University Berlin (http://dx.doi.org/10.17169/refubium-41725).
description: Detailed overview:
ARIA_structure_calc.tar.gz - Input and structure calculation data of two consensus runs to determine an NMR ensemble
Belyy_Lindemann_NatCommun_2022.tar.gz - My data published in 2022
solutionNMR_TcART.tar.gz - Assignment project incl. input data for structure calculation
TcART_dialysis_comparison.tar.gz - Comparison of dialyzed and non-dialyzed TcART (CH spectra)
TcART_NAD+binding.tar.gz - NMR data of TcART titration with NAD+ (NH spectra, TcART)
TcART_NAD+binding_31P.tar.gz - NMR data of TcART titration with NAD+ (31P spectra, NAD+)
TcART_relaxation_data.tar.gz - Relaxation data recorded on TcART to determine local flexibility
TcB_TcC_solids_data.tar.gz - Solid-state NMR data of the TcdB2-TccC3 complex from Photorhabdus luminescens
TcHVR_TcART_comparison.tar.gz - Comparison of two constructs arising from TccC3
DOI: 10.5519/qd.ueyks2yw
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (41 records)
DOI: 10.5281/zenodo.8359465
title: Dataset #2 for paper "A Close-Range Photogrammetric Surface Scanner and its Evaluation"

description: This dataset is supplementary material to the submission “A low-cost close-range photogrammetric surface scanner”, by Panagiotis Koutlemanis, Xenophon Zabulis, Nikolaos Stivaktakis, Nikolaos Partarakis, Emmanouil Zidianakis, and Ioanna Demeridou. The dataset contains 3D reconstructions that show the results of a close-range photogrammetric approach and its implementation using a low-cost CNC device.
DOI: 10.5281/zenodo.8359466
title: Dataset #2 for paper "A Close-Range Photogrammetric Surface Scanner and its Evaluation"

description: This dataset is supplementary material to the submission “A low-cost close-range photogrammetric surface scanner”, by Panagiotis Koutlemanis, Xenophon Zabulis, Nikolaos Stivaktakis, Nikolaos Partarakis, Emmanouil Zidianakis, and Ioanna Demeridou. The dataset contains 3D reconstructions that show the results of a close-range photogrammetric approach and its implementation using a low-cost CNC device.
DOI: 10.6084/m9.figshare.25011150
title: S6_species_trait_groupings.xlsx from The influence of scale-dependent geodiversity on species distribution models in a biodiversity hotspot

description: Improving models of species' distributions is essential for conservation, especially in light of global change. Species distribution models (SDMs) often rely on mean environmental conditions, yet species distributions are also a function of environmental heterogeneity and filtering acting at multiple spatial scales. Geodiversity, which we define as the variation of abiotic features and processes of Earth's entire geosphere (inclusive of climate), has potential to improve SDMs and conservation assessments, as they capture multiple abiotic dimensions of species niches, however they have not been sufficiently tested in SDMs. We tested a range of geodiversity variables computed at varying scales using climate and elevation data. We compared predictive performance of MaxEnt SDMs generated using CHELSA bioclimatic variables to those also including geodiversity variables for 31 mammalian species in Colombia. Results show the spatial grain of geodiversity variables affects SDM performance. Some variables consistently exhibited an increasing or decreasing trend in variable importance with spatial grain, showing slight scale-dependence and indicating that some geodiversity variables are more relevant at particular scales for some species. Incorporating geodiversity variables into SDMs, and doing so at the appropriate spatial scales, enhances the ability to model species-environment relationships, thereby contributing to the conservation and management of biodiversity.This article is part of the Theo Murphy meeting issue ‘Geodiversity science for society’.
DOI: 10.6084/m9.figshare.25011150.v1
title: S6_species_trait_groupings.xlsx from The influence of scale-dependent geodiversity on species distribution models in a biodiversity hotspot

description: Improving models of species' distributions is essential for conservation, especially in light of global change. Species distribution models (SDMs) often rely on mean environmental conditions, yet species distributions are also a function of environmental heterogeneity and filtering acting at multiple spatial scales. Geodiversity, which we define as the variation of abiotic features and processes of Earth's entire geosphere (inclusive of climate), has potential to improve SDMs and conservation assessments, as they capture multiple abiotic dimensions of species niches, however they have not been sufficiently tested in SDMs. We tested a range of geodiversity variables computed at varying scales using climate and elevation data. We compared predictive performance of MaxEnt SDMs generated using CHELSA bioclimatic variables to those also including geodiversity variables for 31 mammalian species in Colombia. Results show the spatial grain of geodiversity variables affects SDM performance. Some variables consistently exhibited an increasing or decreasing trend in variable importance with spatial grain, showing slight scale-dependence and indicating that some geodiversity variables are more relevant at particular scales for some species. Incorporating geodiversity variables into SDMs, and doing so at the appropriate spatial scales, enhances the ability to model species-environment relationships, thereby contributing to the conservation and management of biodiversity.This article is part of the Theo Murphy meeting issue ‘Geodiversity science for society’.
DOI: 10.6084/m9.figshare.25011153
title: S4_imp_mean.csv from The influence of scale-dependent geodiversity on species distribution models in a biodiversity hotspot

description: Improving models of species' distributions is essential for conservation, especially in light of global change. Species distribution models (SDMs) often rely on mean environmental conditions, yet species distributions are also a function of environmental heterogeneity and filtering acting at multiple spatial scales. Geodiversity, which we define as the variation of abiotic features and processes of Earth's entire geosphere (inclusive of climate), has potential to improve SDMs and conservation assessments, as they capture multiple abiotic dimensions of species niches, however they have not been sufficiently tested in SDMs. We tested a range of geodiversity variables computed at varying scales using climate and elevation data. We compared predictive performance of MaxEnt SDMs generated using CHELSA bioclimatic variables to those also including geodiversity variables for 31 mammalian species in Colombia. Results show the spatial grain of geodiversity variables affects SDM performance. Some variables consistently exhibited an increasing or decreasing trend in variable importance with spatial grain, showing slight scale-dependence and indicating that some geodiversity variables are more relevant at particular scales for some species. Incorporating geodiversity variables into SDMs, and doing so at the appropriate spatial scales, enhances the ability to model species-environment relationships, thereby contributing to the conservation and management of biodiversity.This article is part of the Theo Murphy meeting issue ‘Geodiversity science for society’.
DOI: 10.6084/m9.figshare.25011153.v1
title: S4_imp_mean.csv from The influence of scale-dependent geodiversity on species distribution models in a biodiversity hotspot

description: Improving models of species' distributions is essential for conservation, especially in light of global change. Species distribution models (SDMs) often rely on mean environmental conditions, yet species distributions are also a function of environmental heterogeneity and filtering acting at multiple spatial scales. Geodiversity, which we define as the variation of abiotic features and processes of Earth's entire geosphere (inclusive of climate), has potential to improve SDMs and conservation assessments, as they capture multiple abiotic dimensions of species niches, however they have not been sufficiently tested in SDMs. We tested a range of geodiversity variables computed at varying scales using climate and elevation data. We compared predictive performance of MaxEnt SDMs generated using CHELSA bioclimatic variables to those also including geodiversity variables for 31 mammalian species in Colombia. Results show the spatial grain of geodiversity variables affects SDM performance. Some variables consistently exhibited an increasing or decreasing trend in variable importance with spatial grain, showing slight scale-dependence and indicating that some geodiversity variables are more relevant at particular scales for some species. Incorporating geodiversity variables into SDMs, and doing so at the appropriate spatial scales, enhances the ability to model species-environment relationships, thereby contributing to the conservation and management of biodiversity.This article is part of the Theo Murphy meeting issue ‘Geodiversity science for society’.