cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc27wxz1
title: CCDC 2082424: Experimental Crystal Structure Determination

description: Related Article: Tomasz Uchacz, Anna M. Maroń, Paweł Szlachcic, Andrzej Danel, Monika Pokladko-Kowar, Ewa Gondek, Przemysław Kolek, Szczepan Zapotoczny, Katarzyna M. Stadnicka|2023|Spectrochim.Acta,Part A|296|122643|doi:10.1016/j.saa.2023.122643
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc27wy03
title: CCDC 2082425: Experimental Crystal Structure Determination

description: Related Article: Tomasz Uchacz, Anna M. Maroń, Paweł Szlachcic, Andrzej Danel, Monika Pokladko-Kowar, Ewa Gondek, Przemysław Kolek, Szczepan Zapotoczny, Katarzyna M. Stadnicka|2023|Spectrochim.Acta,Part A|296|122643|doi:10.1016/j.saa.2023.122643
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cb631
title: CCDC 2184542: Experimental Crystal Structure Determination

description: Related Article: Alberto Cedillo-Cruz, Diana Cecilia Villalobos-López, María Isabel Aguilar, Pedro Josué Trejo-Soto, Alicia Hernández-Campos, Helgi Jung-Cook|2023|J.Mol.Struct.|1283|135343|doi:10.1016/j.molstruc.2023.135343
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10vhx8
title: CCDC 949000: Experimental Crystal Structure Determination

description: Related Article: Alberto Cedillo-Cruz, Diana Cecilia Villalobos-López, María Isabel Aguilar, Pedro Josué Trejo-Soto, Alicia Hernández-Campos, Helgi Jung-Cook|2023|J.Mol.Struct.|1283|135343|doi:10.1016/j.molstruc.2023.135343
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc10vhy9
title: CCDC 949001: Experimental Crystal Structure Determination

description: Related Article: Alberto Cedillo-Cruz, Diana Cecilia Villalobos-López, María Isabel Aguilar, Pedro Josué Trejo-Soto, Alicia Hernández-Campos, Helgi Jung-Cook|2023|J.Mol.Struct.|1283|135343|doi:10.1016/j.molstruc.2023.135343
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cb620
title: CCDC 2184541: Experimental Crystal Structure Determination

description: Related Article: Alberto Cedillo-Cruz, Diana Cecilia Villalobos-López, María Isabel Aguilar, Pedro Josué Trejo-Soto, Alicia Hernández-Campos, Helgi Jung-Cook|2023|J.Mol.Struct.|1283|135343|doi:10.1016/j.molstruc.2023.135343
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f7c68
title: CCDC 2241399: Experimental Crystal Structure Determination

description: Related Article: Andrés-Felipe Villamizar-Mogotocoro, Vladimir V. Kouznetsov|2023|Tetrahedron Lett.|121|154461|doi:10.1016/j.tetlet.2023.154461
description: Related Article: Andres  Villamizar|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg6v0
title: CCDC 2277782: Experimental Crystal Structure Determination

description: Related Article: T.S.A. Anupama, V. Monica, Jan Grzegorz Małecki, Rangappa S. Keri, Mohammad Azam, Saud I. Al-Resayes, Srinivasa Budagumpi|2024|J.Mol.Struct.|1301|137362|doi:10.1016/j.molstruc.2023.137362
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h69np
title: CCDC 2299972: Experimental Crystal Structure Determination

description: Related Article: Hideki Abe, Nanako Inaba, Mayu Nomura, Yuta Ogura, Naoki Fukazawa, Ryohei Saito-Moriya, Yuichiro Kawamoto, Toyoharu Kobayashi, Hisanaka Ito|2024|Tetrahedron Lett.|139|154991|doi:10.1016/j.tetlet.2024.154991
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h69rs
title: CCDC 2299975: Experimental Crystal Structure Determination

description: Related Article: Hideki Abe, Nanako Inaba, Mayu Nomura, Yuta Ogura, Naoki Fukazawa, Ryohei Saito-Moriya, Yuichiro Kawamoto, Toyoharu Kobayashi, Hisanaka Ito|2024|Tetrahedron Lett.|139|154991|doi:10.1016/j.tetlet.2024.154991
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.whv72q
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pyrrosia pannosa (Mett.) Ching"
 ]
}

 The dataset includes 57 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090939-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2nhce6
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhododendron danbaense L.C.Hu"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090940-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25533358
title: PDCoV S mAb

description: Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen in pigs that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies. Here we generated and characterized a set of neutralizing antibodies targeting the S protein, shedding light on PDCoV S interdomain crosstalk and its vulnerable sites. Among the four identified antibodies, one targets the S1A domain, causing local and long-range conformational changes, resulting in partial exposure of the S1B domain. The other antibodies bind the S1B domain, disrupting binding to the APN receptor. Notably, the epitopes of these S1B-targeting antibodies are concealed in the prefusion S trimer conformation, highlighting the necessity for conformational changes for effective antibody binding. The binding footprint of one S1B binder entirely overlaps with APN-interacting residues and thus targets a highly conserved epitope. These findings provide critical structural insights into the humoral immune response against the PDCoV S protein, potentially guiding vaccine and therapeutic development for this zoonotic pathogen.
DOI: 10.6084/m9.figshare.8115674
title: CoralColonyMorphologyData_WholeColonies_MediumToHighQuality_LaserScanned

description: <br>Newest version of the data: 3DLaserScannedColonies_MedToHighQuality_2024_with_species_names.csv now includes full species names including latest taxonomy as per the World Register for Marine Species 2024. Previous versions only included a short form species code.<br>Morphological data generated from 3D laser scans of coral colonies.Dataset consists of 162 coral skeletons from museum collections that covered seven major growth forms and over three orders of magnitude in size, representing a broad subsample of coral morphological variation.Date are from whole colony scans considered medium to high quality.All units are in mm unless stated otherwise.Sphericity, convexity, fractal dimension and packing are all dimensionless.
DOI: 10.6084/m9.figshare.8115674.v2
title: CoralColonyMorphologyData_WholeColonies_MediumToHighQuality_LaserScanned

description: Newest version of the data: 3DLaserScannedColonies_MedToHighQuality_updatedFractalDimension.csv has updated fractal dimension data that is more accurate and used in a newer manuscript. The old version is still here for compatibility with already published manuscripts. Both fractal dimension data are present in the latest version.<br><br>Morphological data generated from 3D laser scans of coral colonies.<br>Dataset consists of 162 coral skeletons from museum collections that covered seven major growth forms and over three orders of magnitude in size, representing a broad subsample of coral morphological variation.<br><br>Date are from whole colony scans considered medium to high quality.<br>All units are in mm unless stated otherwise.<br>Sphericity, convexity, fractal dimension and packing are all dimensionless.
DOI: 10.48597/eq6m-suev
title: Measurement of Aerosol_absorption_coefficient at Birkenes II

description: Measurement of Aerosol_absorption_coefficient at Birkenes II
DOI: 10.6084/m9.figshare.25533370
title: Supplementary Material for: HSPA8 chaperone complex drives chaperone-mediated autophagy regulation in acute promyelocytic leukemia cell differentiation

description: Introduction: Acute myeloid leukemia (AML) is a cancer of the hematopoietic system characterized by hyperproliferation of undifferentiated cells of the myeloid lineage. While most of AML therapies are focused towards tumor debulking, all-trans retinoic acid (ATRA) induces neutrophil differentiation in the AML subtype acute promyelocytic leukemia (APL). Macroautophagy has been extensively investigated in the context of various cancers and is often dysregulated in AML where it can have context-dependent pro- or anti-leukemogenic effects. On the contrary, the implications of chaperone-mediated autophagy (CMA) on the pathophysiology of diseases are still being explored and its role in AML has remains elusive. Methods: We took advantages of human AML primary samples and databases to analyze CMA gene expression and activity. Furthermore, we used ATRA-sensitive (NB4) and -resistant (NB4-R1) cells to further dissect a potential function for CMA in ATRA-mediated neutrophil differentiation. NB4-R1 cells are unique in that they do respond to retinoic acid transcriptionally, but do not mature in response to retinoid signaling alone unless maturation is triggered by adding cAMP. Results: Here, we report that CMA related mRNA transcripts are significantly higher expressed in immature hematopoietic cells as compared to neutrophils, contrasting the macroautophagy gene expression patterns. Accordingly, lysosomal degradation of an mCherry-KFERQ CMA reporter decreases during ATRA-induced differentiation of APL cells. On the other hand, using NB4-R1 cells we found that macroautophagy flux primed ATRA resistant NB4-R1 cells to differentiate upon ATRA treatment, but reduced association of lysosome-associated membrane protein type 2A (LAMP-2A) and heat shock protein family A (Hsp70) member 8 (HSPA8), which are necessary for complete neutrophil maturation. Accordingly, depletion of HSPA8 attenuated CMA activity and facilitated APL cell differentiation. In contrast, maintaining high CMA activity by ectopic expression of LAMP-2A impeded APL differentiation. Conclusion: Overall, our findings suggest that APL neutrophil differentiation requires CMA inactivation and that this pathway predominantly depends on HSPA8 and is possibly assisted by other co-chaperones.
DOI: 10.6084/m9.figshare.25533370.v1
title: Supplementary Material for: HSPA8 chaperone complex drives chaperone-mediated autophagy regulation in acute promyelocytic leukemia cell differentiation

description: Introduction: Acute myeloid leukemia (AML) is a cancer of the hematopoietic system characterized by hyperproliferation of undifferentiated cells of the myeloid lineage. While most of AML therapies are focused towards tumor debulking, all-trans retinoic acid (ATRA) induces neutrophil differentiation in the AML subtype acute promyelocytic leukemia (APL). Macroautophagy has been extensively investigated in the context of various cancers and is often dysregulated in AML where it can have context-dependent pro- or anti-leukemogenic effects. On the contrary, the implications of chaperone-mediated autophagy (CMA) on the pathophysiology of diseases are still being explored and its role in AML has remains elusive. Methods: We took advantages of human AML primary samples and databases to analyze CMA gene expression and activity. Furthermore, we used ATRA-sensitive (NB4) and -resistant (NB4-R1) cells to further dissect a potential function for CMA in ATRA-mediated neutrophil differentiation. NB4-R1 cells are unique in that they do respond to retinoic acid transcriptionally, but do not mature in response to retinoid signaling alone unless maturation is triggered by adding cAMP. Results: Here, we report that CMA related mRNA transcripts are significantly higher expressed in immature hematopoietic cells as compared to neutrophils, contrasting the macroautophagy gene expression patterns. Accordingly, lysosomal degradation of an mCherry-KFERQ CMA reporter decreases during ATRA-induced differentiation of APL cells. On the other hand, using NB4-R1 cells we found that macroautophagy flux primed ATRA resistant NB4-R1 cells to differentiate upon ATRA treatment, but reduced association of lysosome-associated membrane protein type 2A (LAMP-2A) and heat shock protein family A (Hsp70) member 8 (HSPA8), which are necessary for complete neutrophil maturation. Accordingly, depletion of HSPA8 attenuated CMA activity and facilitated APL cell differentiation. In contrast, maintaining high CMA activity by ectopic expression of LAMP-2A impeded APL differentiation. Conclusion: Overall, our findings suggest that APL neutrophil differentiation requires CMA inactivation and that this pathway predominantly depends on HSPA8 and is possibly assisted by other co-chaperones.
DOI: 10.48597/9s59-xscq
title: Measurement of Aerosol_absorption_coefficient at Birkenes II

description: Measurement of Aerosol_absorption_coefficient at Birkenes II
DOI: 10.48597/dg5u-pfjp
title: Measurement of Aerosol_absorption_coefficient at Birkenes II

description: Measurement of Aerosol_absorption_coefficient at Birkenes II
DOI: 10.57755/dy4w-4p07
title: Multienzymatic biotransformation of flavokawain B by entomopathogenic filamentous fungi

description: The record contains raw data regarding the publication: Chlipała P,* Tronina T, Dymarska M, Urbaniak M, Kozłowska E, Stępień Ł, Kostrzewa-Susłow E, Janeczko T.* "Multienzymatic biotransformation of flavokawain B by entomopathogenic filamentous fungi: structural modifications and pharmacological predictions." Microbial Cell Factories, 2024, 23:65. https://doi.org/10.1186/s12934-024-02338-9.

In the "UPLC data" folder, chromatograms are available depicting substrate conversions in cultures of investigated microorganisms over time. In the "NMR data of isolated biotransformation products" folder, NMR spectra of substrates and isolated/purified biotransformation products are provided.
DOI: 10.5281/zenodo.10686851
title: Host aphid immunosuppression by Aphidius ervi venom

description: Dataset referred to the manuscript: 

Host aphid immunosuppression by Aphidius ervi venom

Elia Russo1§, Andrea Becchimanzi1,2§, Giulia Magoga1, Matteo Montagna1,2, Ilaria Di Lelio1,2* & Francesco Pennacchio1,2*

 

1University of Naples ‘Federico II’ - Department of Agricultural Sciences, Naples, Italy, and 2BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples ‘Federico II’, Naples, Italy

 

bstract 

The host immunosuppression by parasitic wasps is an important component of the host regulation strategy. The venom injected at the oviposition is one of the key-factors involved in this host alteration and, in some parasitoids, its immunosuppressive role is complemented by wasp’s symbionts. Most studies in this research area are related to hosts belonging to Lepidoptera and Diptera, for which a strong immune response is observed, whereas little is known for hemimetabolous host species, characterized by apparently much weaker defense barriers. To fill this research gap, here we focus on the host–parasitoid system Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae) – Aphidius ervi Haliday (Hymenoptera: Braconidae). We functionally characterized a serine protease homolog (AeSPH) protein in vivo, identified in the venom of the aphid endoparasitoid A. ervi, generating AeSPH-depleted female wasps by RNA interference and evaluating their capacity to successfully parasitize the host. Parasitism success rate was negatively affected by AeSPH knockdown and associated with an increased phenoloxidase (PO) cascade activation in aphids, scored by measuring PO enzymatic activity and the expression of phenoloxidase activating factor 2, a proPO-activating gene upregulated in response to A. ervi parasitism. Our results indicate that AeSPH contributes to parasitism success by inhibiting the melanization response of the host, which is therefore an important component of the defense barriers involved in the parasitoid egg suppression. The undergoing studies on other virulence factors in A. ervi venom will allow to further characterize the immunosuppression strategy and its possible broader role in the host regulation through its action on aphid symbiont development.
DOI: 10.5281/zenodo.10686852
title: Host aphid immunosuppression by Aphidius ervi venom

description: Dataset referred to the manuscript: 

Host aphid immunosuppression by Aphidius ervi venom

Elia Russo1§, Andrea Becchimanzi1,2§, Giulia Magoga1, Matteo Montagna1,2, Ilaria Di Lelio1,2* & Francesco Pennacchio1,2*

 

1University of Naples ‘Federico II’ - Department of Agricultural Sciences, Naples, Italy, and 2BAT Center - Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples ‘Federico II’, Naples, Italy

 

bstract 

The host immunosuppression by parasitic wasps is an important component of the host regulation strategy. The venom injected at the oviposition is one of the key-factors involved in this host alteration and, in some parasitoids, its immunosuppressive role is complemented by wasp’s symbionts. Most studies in this research area are related to hosts belonging to Lepidoptera and Diptera, for which a strong immune response is observed, whereas little is known for hemimetabolous host species, characterized by apparently much weaker defense barriers. To fill this research gap, here we focus on the host–parasitoid system Acyrthosiphon pisum (Harris) (Hemiptera: Aphididae) – Aphidius ervi Haliday (Hymenoptera: Braconidae). We functionally characterized a serine protease homolog (AeSPH) protein in vivo, identified in the venom of the aphid endoparasitoid A. ervi, generating AeSPH-depleted female wasps by RNA interference and evaluating their capacity to successfully parasitize the host. Parasitism success rate was negatively affected by AeSPH knockdown and associated with an increased phenoloxidase (PO) cascade activation in aphids, scored by measuring PO enzymatic activity and the expression of phenoloxidase activating factor 2, a proPO-activating gene upregulated in response to A. ervi parasitism. Our results indicate that AeSPH contributes to parasitism success by inhibiting the melanization response of the host, which is therefore an important component of the defense barriers involved in the parasitoid egg suppression. The undergoing studies on other virulence factors in A. ervi venom will allow to further characterize the immunosuppression strategy and its possible broader role in the host regulation through its action on aphid symbiont development.
DOI: 10.15468/dl.5k2sr8
title: Occurrence Download

description: A dataset containing 407304 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Lotus pedunculatus Cav.)"
 ]
}

 The dataset includes 407304 records from 1744 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0090879-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9phxa7
title: Occurrence Download

description: A dataset containing 30588 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erica multiflora"
 ]
}

 The dataset includes 30588 records from 217 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014841-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17909/g0bh-7854
title: Tanaka et al. 2024

description: COSMOS-Web NIRCam + PRIMER-COSMOS NIRCam dataset used in Tanaka et al. 2024, arXiv:2401.13742
DOI: 10.15468/dl.gur7pk
title: Occurrence Download

description: A dataset containing 30985 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Spodoptera exigua (Hübner, 1808)"
 ]
}

 The dataset includes 30985 records from 313 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107325-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.