cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16856291
title: TABLE 2 in The wood-decaying fungal diversity unveiled by morphology and phylogeny in Ailaoshan Mountain, Yunnan, China

description: TABLE 2. The taxonomic position of 103 corticioid fungal basidiomycetous species in the Ailaoshan Mountains.
ClassOrderFamilyNumber of generaNumber of speciesAgaricomycetesAgaricalesCystostereaceae11Physalacriaceae11AuricularialesAuriculariaceae11CantharellalesHydnaceae11CorticialesPunctulariaceae11HymenochaetalesHymenochaetaceae618Rickenellaceae11Schizoporaceae211PolyporalesAdustoporiaceae11Dacryobolaceae11Fomitopsidaceae11Fragiliporiaceae11Ganodermataceae11Grammotheleaceae11Hyphodermataceae24Irpicaceae24Laetiporaceae11Meruliaceae810Phaeophlebiopsis11Phanerochaetaceae47Podoscyphaceae11Polyporaceae1619Steccherinaceae26RussulalesBondarzewiaceae11Hericiaceae11Peniophoraceae12Stereaceae25SistotrematalesSistotremastraceae11XenasmatalesXenasmataceae11
description: Published as part of Wang, Lu, Yang, Xin & Zhao, Changlin, 2024, The wood-decaying fungal diversity unveiled by morphology and phylogeny in Ailaoshan Mountain, Yunnan, China, pp. 20 in Phytotaxa 661 (1) on page 20, DOI: 10.11646/phytotaxa.661.1.1, http://zenodo.org/record/13218270
DOI: 10.3535/6c1-f57-5ma
title: Macrogastra attenuata modulata (A. Schmidt, 1856)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nbj-w9e-bhs
title: Alinda biplicata biplicata (Montagu, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/48h-5zr-mkf
title: Albinaria praeclara parallelifera (O. Boettger, 1878)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jc6-ybw-lwk
title: Albinaria brevicollis anaphiensis (O. Boettger, 1878)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jzb-pjv-hds
title: Albinaria arcadica dorica (O. Boettger, 1889)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6kx-tvf-890
title: Ellobium stagnale (A. d'Orbigny, 1835)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b8s-88v-de4
title: Abida polyodon (Draparnaud, 1801)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6p2-dd7-pve
title: Ladislavella catascopium (Say, 1817)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/hpl-evf-3se
title: Graniberia braunii (Rossmässler, 1842)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9ve-l45-qhb
title: Lauria J. E. Gray, 1840

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g5n-r44-phx
title: Gittenedouardia drakensbergensis (E. A. Smith, 1877)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/34k-xc1-bca
title: Acanthinula aculeata (O. F. Müller, 1774)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4dl-5rf-tyl
title: Ancylus fluviatilis O. F. Müller, 1774

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mjc-22a-w4h
title: Chondrina avenacea avenacea (Bruguière, 1792)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d0g-pmk-qwa
title: Brachypodella morini (Morelet, 1849)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dk2-fd1-2k5
title: Fusulus interruptus (C. Pfeiffer, 1828)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/05g-w0m-ygq
title: Nesopupa maaseni van Regteren Altena, 1975

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q6n-akg-89l
title: Ocinebrina aciculata (Lamarck, 1822)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/evs-8wb-28z
title: Laciniaria plicata (Draparnaud, 1801)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cse-pke-xxe
title: Charpentieria Stabile, 1864

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rt0-qtv-723
title: Cochlodina laminata laminata (Montagu, 1803)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mhy-607-yks
title: Arion ater rufus (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m31-s2a-ef6
title: Allopeas gracile (T. Hutton, 1834)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pm4-03j-wry
title: Williamia krebsii (Mörch, 1877)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q7f-qzb-e7w
title: Orcula dolium dolium (Draparnaud, 1801)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zfq-dq3-e2e
title: Macrogastra plicatula (Draparnaud, 1801)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f8z-6r7-fxq
title: Columella edentula (Draparnaud, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gdx-g6r-124
title: Tricolia azorica (Dautzenberg, 1889)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2vx-vst-wgy
title: Leiostracus Albers, 1850

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l3a-t7a-ptk
title: Subulina mamillata (Craven, 1880)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gw9-g87-rd3
title: Partula otaheitana (Bruguière, 1792)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q3w-9t9-1rz
title: Cochlodina liburnica (A. J. Wagner, 1919)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z20-04y-qfh
title: Cerion martinianum (Küster, 1844)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ag4-az1-3hg
title: Medora agnata agnata (L. Pfeiffer, 1842)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c7v-dzt-082
title: Muticaria macrostoma oscitans (Charpentier, 1852)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b0y-8qy-lve
title: Albinaria contaminata periporon Kemperman & E. Gittenberger, 1992

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.yxg7hp
title: Occurrence Download

description: A dataset containing 365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Myrica californica)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 365 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011241-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d5yvdq
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "DatasetKey is one of (iNaturalist Research-grade Observations, eButterfly Surveys)",
 "Geometry POLYGON((-111.952 33.447,-111.94 33.447,-111.94 33.453,-111.952 33.453,-111.952 33.447))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera",
 "Year 2000-2025"
 ]
}

 The dataset includes 33 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032145-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mdhvp4
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arundo donax",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032146-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26188/28844174.v1
title: Supplementary video S1: Major intramural arteries of the mouse urinary bladder

description: Cleared lower urinary tract from an adult C57Bl/6 female mouse, perfused intracardially with a DY649 conjugate of Tomato lectin, immunostained for vascular markers PECAM and PODXL and viewed with light sheet microscopy (Ultramicroscope II, Miltenyi Biotec, Germany). Segmentations (Imaris) of the intramural arteries in the bladder [superficial ventrolateral artery (SVLA), deep ventral arteries (DVA) and deep dorsal arteries (DDA)]. This demonstrates the stereotypical branching and location of these major arteries.
DOI: 10.6084/m9.figshare.25152165
title: Enzyme engineering of choline oxidase for improving stability

description: Functioning as a flavoprotein, choline oxidase facilitates the transformation of choline into glycine betaine. Notably, choline oxidase and its resultant product, glycine betaine, find extensive applications across various industries and fields of study. However, its high sensitivity and tendency to lose functional activity at high temperatures reduces its industrial usage. MD simulation and mutation studies have revealed the role of certain residues responsible for the enzyme’s thermal instability. This study focuses on inducing thermal stability to choline oxidase of A. <i>globiformis</i> through computational approaches at a maximum temperature of 60 °C. MD simulation analysis showed that Trp 331, Val 464 and Ser 101 contribute to structural instability, leading to the instability at 60 °C. Mutation of these residues with phenylalanine residues and simulation of the mutated enzyme at 60 °C exhibited thermostability and insignificant residual fluctuation. The re-docking and MM/GBSA analyses further validated the mutated enzyme’s binding affinity and catalytic activity.
DOI: 10.6084/m9.figshare.25152165.v1
title: Enzyme engineering of choline oxidase for improving stability

description: Functioning as a flavoprotein, choline oxidase facilitates the transformation of choline into glycine betaine. Notably, choline oxidase and its resultant product, glycine betaine, find extensive applications across various industries and fields of study. However, its high sensitivity and tendency to lose functional activity at high temperatures reduces its industrial usage. MD simulation and mutation studies have revealed the role of certain residues responsible for the enzyme’s thermal instability. This study focuses on inducing thermal stability to choline oxidase of A. <i>globiformis</i> through computational approaches at a maximum temperature of 60 °C. MD simulation analysis showed that Trp 331, Val 464 and Ser 101 contribute to structural instability, leading to the instability at 60 °C. Mutation of these residues with phenylalanine residues and simulation of the mutated enzyme at 60 °C exhibited thermostability and insignificant residual fluctuation. The re-docking and MM/GBSA analyses further validated the mutated enzyme’s binding affinity and catalytic activity.
DOI: 10.6084/m9.figshare.25093440
title: Association of cuproptosis-related signature with the prognosis of patients with head and neck squamous cell carcinoma

description: Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis because of their high recurrence and metastasis rates. Cuproptosis is a novel type of copper-dependent cell death that differs from apoptosis, necroptosis, and cytosolic scorch death. We designed and validated an individualized cuproptosis-related gene (CRG) signature for risk evaluation and prognostic prediction in HNSCC patients. Ninety differentially expressed CRGs were found in HNSCC. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses were performed to investigate the functional involvement of CRGs in the Cancer Genome Atlas (TCGA) HNSCC cohort. A CRG signature was created using 10 genes after univariate and multivariate analysis. Kaplan Meier (KM) analysis showed that the survival rate of the high-risk group was significantly lower than that of the low-risk group. Multivariate regression analysis identified risk scores based on prognostic characteristics as independent prognostic indicators of HNSCC. Moreover, risk models are related to tumor mutational burden (TMB), tumor-infiltrating immune cells (TICs), immune checkpoints, clinical characteristics, and antitumor drug susceptibility. Furthermore, we found that CuCl<sub>2</sub> treatment promoted cuproptosis in HNSCC cells, and that the expression levels of cuproptosis-related genes were altered by different doses of CuCl<sub>2</sub>. In summary, understanding the detailed molecular mechanisms of cuproptosis and its impact on overall survival (OS), and identifying potential therapeutic targets for HNSCC will provide potential insights for treatment.
DOI: 10.6084/m9.figshare.25093440.v1
title: Association of cuproptosis-related signature with the prognosis of patients with head and neck squamous cell carcinoma

description: Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis because of their high recurrence and metastasis rates. Cuproptosis is a novel type of copper-dependent cell death that differs from apoptosis, necroptosis, and cytosolic scorch death. We designed and validated an individualized cuproptosis-related gene (CRG) signature for risk evaluation and prognostic prediction in HNSCC patients. Ninety differentially expressed CRGs were found in HNSCC. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses were performed to investigate the functional involvement of CRGs in the Cancer Genome Atlas (TCGA) HNSCC cohort. A CRG signature was created using 10 genes after univariate and multivariate analysis. Kaplan Meier (KM) analysis showed that the survival rate of the high-risk group was significantly lower than that of the low-risk group. Multivariate regression analysis identified risk scores based on prognostic characteristics as independent prognostic indicators of HNSCC. Moreover, risk models are related to tumor mutational burden (TMB), tumor-infiltrating immune cells (TICs), immune checkpoints, clinical characteristics, and antitumor drug susceptibility. Furthermore, we found that CuCl<sub>2</sub> treatment promoted cuproptosis in HNSCC cells, and that the expression levels of cuproptosis-related genes were altered by different doses of CuCl<sub>2</sub>. In summary, understanding the detailed molecular mechanisms of cuproptosis and its impact on overall survival (OS), and identifying potential therapeutic targets for HNSCC will provide potential insights for treatment.
DOI: 10.6084/m9.figshare.25102238
title: A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers

description: PROTACs (Proteolysis Targeting Chimeras), heterobifunctional molecules, exhibit selectivity in degrading target proteins through E3 ubiquitin ligases. Designing effective PROTACs requires a deep understanding of the intricate binding interactions in the ternary complex (POI/PROTAC/E3 ligase), crucial for efficient target protein degradation. To address this challenge, we introduce a novel computational virtual screening method that considers essential amino acid interactions between the protein of interest and the chosen E3 ligase. This approach enhances accuracy and reliability, facilitating the strategic development of potent PROTACs. Utilizing a crystallized model of the VHL:PROTAC:SMARCA2<sup>BD</sup> ternary complex (PDB: 7Z6L), we assessed the effectiveness of our method. Our study reveals that increasing the number of essential restraints between the two proteins reduces the generated docking poses, leading to closer alignment with the experimental ternary complex. Specifically, utilizing three restraints showed the closest resemblance to the published complex, highlighting crucial interactions such as an H-bond between A:Gln 89 and B:Asn 67, along with two hydrophobic interactions: A:Gly 22 with B:Arg 69 and A:Glu 37 with B:Pro 99. This resulted in a significant decrease in the mean RMSD value from 31.8 and 31.0 Å to 24.4 Å, respectively. This underscores the importance of incorporating multiple essential restraints to enhance docking accuracy. Building on this progress, we introduce a systematic approach to design potential PROTACs between the Estrogen receptor and the E3 ligase, utilizing bridging intermediates with 4, 6, or 7 carbon atoms. By providing a more accurate and efficient means of identifying optimal PROTAC candidates, this approach has the potential to accelerate the development of targeted therapies and reduce the time and costs associated with drug discovery.
DOI: 10.6084/m9.figshare.25102238.v1
title: A close-up shot of protein-protein docking, from experiment to theory and reverse with the PROTAC performers

description: PROTACs (Proteolysis Targeting Chimeras), heterobifunctional molecules, exhibit selectivity in degrading target proteins through E3 ubiquitin ligases. Designing effective PROTACs requires a deep understanding of the intricate binding interactions in the ternary complex (POI/PROTAC/E3 ligase), crucial for efficient target protein degradation. To address this challenge, we introduce a novel computational virtual screening method that considers essential amino acid interactions between the protein of interest and the chosen E3 ligase. This approach enhances accuracy and reliability, facilitating the strategic development of potent PROTACs. Utilizing a crystallized model of the VHL:PROTAC:SMARCA2<sup>BD</sup> ternary complex (PDB: 7Z6L), we assessed the effectiveness of our method. Our study reveals that increasing the number of essential restraints between the two proteins reduces the generated docking poses, leading to closer alignment with the experimental ternary complex. Specifically, utilizing three restraints showed the closest resemblance to the published complex, highlighting crucial interactions such as an H-bond between A:Gln 89 and B:Asn 67, along with two hydrophobic interactions: A:Gly 22 with B:Arg 69 and A:Glu 37 with B:Pro 99. This resulted in a significant decrease in the mean RMSD value from 31.8 and 31.0 Å to 24.4 Å, respectively. This underscores the importance of incorporating multiple essential restraints to enhance docking accuracy. Building on this progress, we introduce a systematic approach to design potential PROTACs between the Estrogen receptor and the E3 ligase, utilizing bridging intermediates with 4, 6, or 7 carbon atoms. By providing a more accurate and efficient means of identifying optimal PROTAC candidates, this approach has the potential to accelerate the development of targeted therapies and reduce the time and costs associated with drug discovery.
DOI: 10.6084/m9.figshare.25152167
title: Decoding the structural integrity and multifunctional role of Era protein in the survival of <i>Mycobacterium tuberculosis</i> H<sub>37</sub>Rv

description: Era, a widely known GTP binding protein found in many organisms including prokaryotes and eukaryotes and plays a significant role in many fundamental cellular processes like cell growth, differentiation and signaling. In <i>Mycobacterium tuberculosis</i> (Mtb) H<sub>37</sub>Rv, Era protein had been proved as a GTPase protein but its structural and functional insights are still lacking. Through comparative analysis, structural modeling, docking and using various bioinformatic tools, a detailed investigation of Era was carried out to deduce the structure, function and residues involved in the activity of the protein. Intriguingly, docking results revealed high binding affinity of Era not only with GTP but also with ATP. Myristoylation modifications and phosphorylations on Era were predicted to possibly aid in regulating Era activity and localization; and also the role of Era in translation regulation was foreseen by showing its association with 16s rRNA. Moreover, point mutation of Era residues revealed the effect of W288G and K19G in highly destabilizing the protein structure and activity. Additionally, Era protein was docked with 25 GTPase/ATPase inhibitors, where, Dynasore inhibitor showed the highest affinity for the protein’s GTP binding sites and can be used for further drug trials to inhibit growth of mycobacteria. MtEra protein carries five GTP binding motifs (G1, G2, G3, G4 and G5) and one KH domain for RNA binding.Multifunctional role of MtEra predicted in processes like catabolic, metabolic and ribosome biogenesis.Point mutation analysis showed the importance of tryptophan (W) and lysine (K) residues at position 288 and 19 in stability and activity of the protein, respectively.Dynasore inhibitor showed the highest binding energy of −9 kcal/mol for MtEra. MtEra protein carries five GTP binding motifs (G1, G2, G3, G4 and G5) and one KH domain for RNA binding. Multifunctional role of MtEra predicted in processes like catabolic, metabolic and ribosome biogenesis. Point mutation analysis showed the importance of tryptophan (W) and lysine (K) residues at position 288 and 19 in stability and activity of the protein, respectively. Dynasore inhibitor showed the highest binding energy of −9 kcal/mol for MtEra.