cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23799309.v2
title: Plant capacity notions: review, new definitions, and existence results at firm and industry levels

description: This study investigates the existence of solutions for the key plant capacity utilisation (PCU) concepts using general nonparametric technologies. This is done via a theoretical review of existing and some new PCU concepts. Focusing on short-run and long-run output-oriented, attainable output-oriented, and input-oriented PCU notions, we first investigate the existence of solutions at the firm level. Under mild axioms, this question regarding the existence of solutions for these PCU concepts at the firm level is affirmatively answered under variable and constant returns to scale as well as under convex and nonconvex assumptions. However, short-run and long-run output-oriented and attainable output-oriented PCU concepts may not be implementable depending on certain conditions. There are no such reservations for the input-oriented PCU. Then, for this same range of PCU concepts, we explore the more difficult question as to the existence of solutions at the industry level. The output-oriented and attainable output-oriented PCU exist at the industry level under strict conditions: existence and attainability are interwoven at this level. The industry input-oriented PCU is always feasible at the industry model. This theoretical review is supplemented by a semi-systematic empirical review, and an empirical application. We conclude that input-oriented PCU is clearly the best concept.
DOI: 10.5281/zenodo.10543595
title: Data used in "High-fidelity spin qubit operation and algorithmic initialisation above 1 K"

description: Corrected axes in Extended Data Figure 7a.
DOI: 10.5281/zenodo.10452860
title: Data used in "High-fidelity spin qubit operation and algorithmic initialisation above 1 K"

description: Corrected axes in Extended Data Figure 7a.
DOI: 10.5281/zenodo.10452861
title: Data used in "High-fidelity spin qubit operation and algorithmic initialisation above 1 K"
DOI: 10.5281/zenodo.10537118
title: Grapegenomics.com - Genome release: Vitis interspecific cross - Freedom cl. FPS01 - chromosome scale

description: https://www.grapegenomics.com/pages/VFreedom/
DOI: 10.5281/zenodo.10537119
title: Grapegenomics.com - Genome release: Vitis interspecific cross - Freedom cl. FPS01 - chromosome scale

description: https://www.grapegenomics.com/pages/VFreedom/
DOI: 10.5281/zenodo.10261743
title: Native MS dataset for: "Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants"

description: Native mass spectrometry dataset used in: Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants. Pavla Vankova, Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Atanasio Gómez-Mulas, Alan Kádek, José Manuel Martín-Garcia, Eduardo Salido, Petr Man and Angel L. Pey. FEBS Letters (2024)

Description:

Native mass spectrometry (MS) analysis verifying the oligomeric state of alanine:glyoxylate aminotransferase (AGT) protein and its P11L and I340M (LM) polymorphism and LM G170R mutation variants in primary hyperoxaluria type I.

Sample processing:

AGT protein as well as its LM and LM G130R mutants were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.5, MS-grade, Sigma-Aldrich) through six cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (30 kDa cut-off, Sartorius). Desalted proteins were introduced into a Synapt G2Si mass spectrometer (Waters) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (World Precision Instruments). Protein concentration in samples was determined by 280 nm absorbance measurements using DeNovix DS-11 spectrophotometer. Samples were diluted in ammonium acetate and electrosprayed at 1 and 2 µM concentration. The mass spectrometer was carefully tuned for best signal quality and intensity, while keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 80°C, sampling cone 80 V and 10 V collision voltage with 6 ml/min flow of argon in the trap region for thermalization of ions. Quadrupole was operated in a broadband transmission mode up to 8000 m/z while the spectra were acquired in mass range 500 – 20000 m/z. Spectra were externally mass recalibrated using known masses of caesium iodide clusters.

Data processing:

Raw mass spectra were averaged over 75 scans and further processed in Waters MassLynx 4.1. The averaged spectra were exported for ZENODO deposition as plain in plain m/z vs intensity .txt files as well uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.
DOI: 10.5281/zenodo.10261742
title: Native MS dataset for: "Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants"

description: Native mass spectrometry dataset used in: Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants. Pavla Vankova, Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Atanasio Gómez-Mulas, Alan Kádek, José Manuel Martín-Garcia, Eduardo Salido, Petr Man and Angel L. Pey. FEBS Letters (2024)

Description:

Native mass spectrometry (MS) analysis verifying the oligomeric state of alanine:glyoxylate aminotransferase (AGT) protein and its P11L and I340M (LM) polymorphism and LM G170R mutation variants in primary hyperoxaluria type I.

Sample processing:

AGT protein as well as its LM and LM G130R mutants were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.5, MS-grade, Sigma-Aldrich) through six cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (30 kDa cut-off, Sartorius). Desalted proteins were introduced into a Synapt G2Si mass spectrometer (Waters) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (World Precision Instruments). Protein concentration in samples was determined by 280 nm absorbance measurements using DeNovix DS-11 spectrophotometer. Samples were diluted in ammonium acetate and electrosprayed at 1 and 2 µM concentration. The mass spectrometer was carefully tuned for best signal quality and intensity, while keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 80°C, sampling cone 80 V and 10 V collision voltage with 6 ml/min flow of argon in the trap region for thermalization of ions. Quadrupole was operated in a broadband transmission mode up to 8000 m/z while the spectra were acquired in mass range 500 – 20000 m/z. Spectra were externally mass recalibrated using known masses of caesium iodide clusters.

Data processing:

Raw mass spectra were averaged over 75 scans and further processed in Waters MassLynx 4.1. The averaged spectra were exported for ZENODO deposition as plain in plain m/z vs intensity .txt files as well uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.
DOI: 10.5281/zenodo.5652931
title: Native MS dataset for: "Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines."

description: Native mass spectrometry dataset used in: Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines. Anja Konietzny, Jasper Grendel, Alan Kadek, Michael Bucher, Yuhao Han, Nathalie Hertrich, Dick H. W. Dekkers, Jeroen A. A. Demmers, Kay Grünewald, Charlotte Uetrecht and Marina Mikhaylova. The EMBO Journal (2021) e106523. doi:10.15252/embj.2020106523
 
Description:
Native mass spectrometry (MS) analysis of the stoichiometry and ion occupancy of recombinant human calmodulin (CaM) and recombinant rat caldendrin (CaD) complex with synthetic mouse myosinV IQ1 (myoIQ) motif in the presence / absence of excess Ca2+ and Mg2+ ions.
Sample processing:
Full-length CaD and CaM as well as the synthetic myoVa peptide were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.4). CaM was twice passed through a Bio-Spin P-6 gel filtration spin column (6 kDa cut-off, Bio-Rad), CaD and the myoVa peptide were buffer exchanged through five cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (10 kDa cut-off, Sartorius) or Amicon Ultra 0.5mL (3 kDa cut-off, Merck/Millipore), respectively. Desalted proteins were introduced into an Orbitrap Q Exactive UHMR mass spectrometer (Thermo Scientific) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (World Precision Instruments). Proteins were sprayed and analysed at 8.5 µM concentration in ammonium acetate alone or supplemented with 200 µM calcium acetate and 100 µM magnesium acetate (both for trace metal analysis, Sigma-Aldrich). For interaction analysis, CaM and/or caldendrin were mixed with myoVa peptide which had final concentration of 8.5 µM (low concentration) or 34 µM (high concentration). The mass spectrometer was tuned for best signal quality and intensity, keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 250°C, in-source desolvation -50 V, ion transfer profile "high m/z", analyzer profile "low m/z", analyzer target resolution 12500 acquiring in mass range 500 – 9000 m/z. Nitrogen was used as collision gas in HCD cell at relative gas pressure setting 7.0 with gentle collisional activation by 10 V HCD voltage gradient.
Data processing:
Raw spectra were averaged over at least 50 scans for mass deconvolution and peak assignment in UniDec 4.4.1 package (Marty et al., 2015). The averaged spectra were exported for ZENODO deposition using Thermo Scientific FreeStyle 1.5.93.34 as single-scan Thermo .raw files (including instrumental parameters metadata) as well as in plain m/z vs intensity .txt files.
DOI: 10.5281/zenodo.5652932
title: Native MS dataset for: "Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines."

description: Native mass spectrometry dataset used in: Caldendrin and myosin V regulate synaptic spine apparatus localization via ER stabilization in dendritic spines. Anja Konietzny, Jasper Grendel, Alan Kadek, Michael Bucher, Yuhao Han, Nathalie Hertrich, Dick H. W. Dekkers, Jeroen A. A. Demmers, Kay Grünewald, Charlotte Uetrecht and Marina Mikhaylova. The EMBO Journal (2021) e106523. doi:10.15252/embj.2020106523
 
Description:
Native mass spectrometry (MS) analysis of the stoichiometry and ion occupancy of recombinant human calmodulin (CaM) and recombinant rat caldendrin (CaD) complex with synthetic mouse myosinV IQ1 (myoIQ) motif in the presence / absence of excess Ca2+ and Mg2+ ions.
Sample processing:
Full-length CaD and CaM as well as the synthetic myoVa peptide were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.4). CaM was twice passed through a Bio-Spin P-6 gel filtration spin column (6 kDa cut-off, Bio-Rad), CaD and the myoVa peptide were buffer exchanged through five cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (10 kDa cut-off, Sartorius) or Amicon Ultra 0.5mL (3 kDa cut-off, Merck/Millipore), respectively. Desalted proteins were introduced into an Orbitrap Q Exactive UHMR mass spectrometer (Thermo Scientific) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (World Precision Instruments). Proteins were sprayed and analysed at 8.5 µM concentration in ammonium acetate alone or supplemented with 200 µM calcium acetate and 100 µM magnesium acetate (both for trace metal analysis, Sigma-Aldrich). For interaction analysis, CaM and/or caldendrin were mixed with myoVa peptide which had final concentration of 8.5 µM (low concentration) or 34 µM (high concentration). The mass spectrometer was tuned for best signal quality and intensity, keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 250°C, in-source desolvation -50 V, ion transfer profile "high m/z", analyzer profile "low m/z", analyzer target resolution 12500 acquiring in mass range 500 – 9000 m/z. Nitrogen was used as collision gas in HCD cell at relative gas pressure setting 7.0 with gentle collisional activation by 10 V HCD voltage gradient.
Data processing:
Raw spectra were averaged over at least 50 scans for mass deconvolution and peak assignment in UniDec 4.4.1 package (Marty et al., 2015). The averaged spectra were exported for ZENODO deposition using Thermo Scientific FreeStyle 1.5.93.34 as single-scan Thermo .raw files (including instrumental parameters metadata) as well as in plain m/z vs intensity .txt files.
DOI: 10.5281/zenodo.10543620
title: Base de datos sobre ensayo de citotoxicidad de extractos de Pleurotus ostreatus en diferentes líneas celulares para aplicaciones inmunonutricionales

description: Base de datos sobre investigación de ensayo donde se evaluó la citotoxicidad de los bioproductos de Pleurotus ostreatus, por el ensayo de reducción del colorante resazurina, en tres líneas celulares. Se utilizaron células no adherentes THP-1 (pre-monocitos de leucemia humana), células adherentes Caco-2 (epitelio de adenocarcinoma de colon humano) y células adherentes RAW 264.7 (macrófagos murinos).
DOI: 10.5281/zenodo.10543621
title: Base de datos sobre ensayo de citotoxicidad de extractos de Pleurotus ostreatus en diferentes líneas celulares para aplicaciones inmunonutricionales

description: Base de datos sobre investigación de ensayo donde se evaluó la citotoxicidad de los bioproductos de Pleurotus ostreatus, por el ensayo de reducción del colorante resazurina, en tres líneas celulares. Se utilizaron células no adherentes THP-1 (pre-monocitos de leucemia humana), células adherentes Caco-2 (epitelio de adenocarcinoma de colon humano) y células adherentes RAW 264.7 (macrófagos murinos).
DOI: 10.34740/kaggle/dsv/7444282
title: BBC News
DOI: 10.15156/bio/sh3290953.08fu
title: SH3290953.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3290954.08fu
title: SH3290954.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3290955.08fu
title: SH3290955.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3290956.08fu
title: SH3290956.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3290957.08fu
title: SH3290957.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3290958.08fu
title: SH3290958.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3290959.08fu
title: SH3290959.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh3290960.08fu
title: SH3290960.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.