cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/zfvp2s
title: Festucalex rosa, a new species of pipefish (Teleostei: Syngnathidae) from the Seychelles, western Indian Ocean

description: This dataset contains the digitized treatments in Plazi based on the original journal article Yuki, Daijiro, Motomura, Hiroyuki (2025): Festucalex rosa, a new species of pipefish (Teleostei: Syngnathidae) from the Seychelles, western Indian Ocean. Zootaxa 5701 (5): 597-600, DOI: 10.11646/zootaxa.5701.5.8, URL: https://doi.org/10.11646/zootaxa.5701.5.8AbstractThe new pipefish Festucalex rosa sp. nov. is described from a single specimen collected from D'Arros Island, Seychelles, representing only the second species of Festucalex recorded from the western Indian Ocean. The new species is similar to other members of the genus, including F. armillatus Prokofiev 2016, F. gibbsi Dawson 1977, F. prolixus Dawson 1984, and F. wassi Dawson 1977 in possessing two ridges on the pectoral-fin base, but is distinguished from its congeners by the following combination of characters: 17 trunk rings; 34 tail rings; 21 dorsal-fin rays; 14 or 15 pectoral-fin rays; snout length 46.3% of head length; and lateral trunk ridge terminating at the anal ring. A possible conspecific record from Kosi Bay, South Africa, is noted.
DOI: 10.7910/dvn/qfnhti
title: Participant Responses to the CRiTERIA Project Questionnaire on Migration Risk Scenarios and Impact Assessments Using Frontex Data

description: This dataset contains participant responses to a questionnaire developed within the CRiTERIA project to support migration risk evaluation. The questionnaire draws on Frontex data related to migration routes across the Eastern Borders, Central Mediterranean, and Western Balkans. It includes assessments of risk scenarios, risk categories, and impact categories, and the responses provide empirical input for the project’s methodological framework for scenario-based risk analysis and prioritization.
DOI: 10.15468/tyyhxq
title: A new genus for Pycnopygius cinereus / P. ixoides (Aves: Meliphagidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Sangster, George, Marki, Petter Zahl, Gaudin, Jimmy, Irestedt, Martin, Jonsson, Knud A. (2023): A new genus for Pycnopygius cinereus / P. ixoides (Aves: Meliphagidae). Zootaxa 5330 (1): 147-150, DOI: 10.11646/zootaxa.5330.1.10, URL: http://dx.doi.org/10.11646/zootaxa.5330.1.10
DOI: 10.15468/n2vqpx
title: Staurastrum pantanale sp. nov. (Zygnematophyceae, Desmidiaceae), a new desmid species from the Brazilian Pantanal

description: This dataset contains the digitized treatments in Plazi based on the original journal article Santos, Kleber Renan De Souza, Malone, Camila Francieli Da Silva, Sant’Anna, Célia Leite, Bicudo, Carlos Eduardo De Mattos (2013): Staurastrum pantanale sp. nov. (Zygnematophyceae, Desmidiaceae), a new desmid species from the Brazilian Pantanal. Phytotaxa 90 (1): 54-60, DOI: 10.11646/phytotaxa.90.1.2, URL: http://dx.doi.org/10.11646/phytotaxa.90.1.2AbstractStaurastrum pantanale is proposed new to science and is characterized by its crenate cell wall and cell dimensions. The species was collected from the metaphyton of a shallow tropical lake (Salitrada Campo Dora Lake, 18º 58’ 02” S, 56º 38’ 59” W) with transparent water and pH 5, located in the Nhecolândia Pantanal, Mato Grosso do Sul State, Brazil. The new species’ morphology and relationship with morphologically close species are discussed.
DOI: 10.15468/8hrpc5
title: Thienemannimyia (Thienemannimyia) sinogalbina nom. n., a replacement name for Thienemannimyia galbina Cheng & Wang, 2009

description: This dataset contains the digitized treatments in Plazi based on the original journal article Lin, Xiao-Long, Wang, Xin-Hua (2019): Thienemannimyia (Thienemannimyia) sinogalbina nom. n., a replacement name for Thienemannimyia galbina Cheng & Wang, 2009. CHIRONOMUS Journal of Chironomidae Research 32: 73-74, DOI: 10.5324/cjcr.v0i32.3318, URL: http://dx.doi.org/10.5324/cjcr.v0i32.3318AbstractThe recent transfer of Hayesomyia galbina Cheng & Wang, 2006 to Thienemannimyia (Hayesomyia) created a homonymy with Thienemannimyia (Thienemannimyia) galbina Cheng & Wang, 2009. Thienemannimyia (Hayesomyia) galbina (Cheng & Wang, 2006) has priority and Thienemannimyia (Thienemannimyia) sinogalbina nom. n. is proposed as a new replacement for the junior secondary homonymy Thienemannimyia (Thienemannimyia) galbina Cheng & Wang, 2009.
DOI: 10.17613/wxwdf-2mt65
title: All of the references to trees in The Overstory

description: This dataset captures all of the references to trees in Richard Power's The Overstory. Data from the book include page number, section, and sentence the reference appears in. Additional data include, when possible, scientific name, order, family, subfamily, genus, species, and native range.
DOI: 10.15468/dl.s6zrwj
title: Occurrence Download

description: A dataset containing 541366 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((48.34705 35.93259,56.86635 35.93259,56.86635 48.2286,48.34705 48.2286,45.99334 44.14071,48.34705 35.93259))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year 1985-2024"
 ]
}

 The dataset includes 541366 records from 322 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003478-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6ytvxs
title: Occurrence Download

description: A dataset containing 314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gopherus polyphemus (Daudin, 1801)",
 "Year 1970-2020"
 ]
}

 The dataset includes 314 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003492-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fy9ara
title: Occurrence Download

description: A dataset containing 1188 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.12_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphagneticola trilobata (L.) Pruski"
 ]
}

 The dataset includes 1188 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003493-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5255/ukda-sn-857425
title: Voicing Loss: Meanings and Implications of Participation by Bereaved People in Inquests: Qualitative Interviews and Group Discussions, 2021-2024

description: The Voicing Loss research project examined the role of bereaved people in coroners’ investigations and inquests. Research data comprise interview transcripts, interview write-ups and one written submission. The total number of interviews will differ from the number of uploaded transcripts, as participants were given the choice to opt out of having their transcript included in the repository.
DOI: 10.6084/m9.figshare.24160323
title: A comprehensive immunoinformatic analysis of chitin deacetylase’s and MP88 for designing multi-epitope vaccines against <i>Cryptococcus neoformans</i>

description: <i>Cryptococcus neoformans</i> causes life-threatening pneumonia and meningitis and is regarded as one of the leading killers of immunocompromised individuals. There is currently no vaccine against this pathogen. Recently, WHO placed it at the top among the critical priority groups in the fungal priority pathogens to accelerate the development of effective treatments. Numerous studies suggested the potential of subunit vaccines to overcome the challenges associated with live and inactivated whole-cell vaccines. Therefore, this study exploited integrated reverse vaccinology and immunoinformatic approach to construct and characterize multi-epitope vaccines targeting chitin deacetylases (Cda1, Cda2, Cda3) and MP88 of <i>C. neoformans</i>. 4 CTL, 8 HTL and 6 B cell epitopes were fused with different adjuvants and appropriate linkers to design two multi-epitope vaccines (VC1 and VC2). Both chimeric constructs were predicted to be highly antigenic, non-allergenic, non-toxic, soluble and had satisfactory physicochemical properties. Molecular docking and binding free energy calculation revealed strong binding interactions between vaccine constructs and human TLRs (TLR-2 and TLR-4). Classical MD Simulation and Normal mode analysis verified the stability of the vaccine-TLR complex in the biological environment. Codon adaptation, cloning and <i>in silico</i> expression suggested the efficient expression of recombinant vaccine proteins in <i>E. coli</i>. Both candidates also generated robust immune profiles comprising innate, adaptive and humoral immune responses. Taken together, experimental validations of our findings through extensive <i>in vitro</i> and <i>in vivo</i> testing might provide an effective vaccine for prophylactic control of <i>C. neoformans</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24160323.v1
title: A comprehensive immunoinformatic analysis of chitin deacetylase’s and MP88 for designing multi-epitope vaccines against <i>Cryptococcus neoformans</i>

description: <i>Cryptococcus neoformans</i> causes life-threatening pneumonia and meningitis and is regarded as one of the leading killers of immunocompromised individuals. There is currently no vaccine against this pathogen. Recently, WHO placed it at the top among the critical priority groups in the fungal priority pathogens to accelerate the development of effective treatments. Numerous studies suggested the potential of subunit vaccines to overcome the challenges associated with live and inactivated whole-cell vaccines. Therefore, this study exploited integrated reverse vaccinology and immunoinformatic approach to construct and characterize multi-epitope vaccines targeting chitin deacetylases (Cda1, Cda2, Cda3) and MP88 of <i>C. neoformans</i>. 4 CTL, 8 HTL and 6 B cell epitopes were fused with different adjuvants and appropriate linkers to design two multi-epitope vaccines (VC1 and VC2). Both chimeric constructs were predicted to be highly antigenic, non-allergenic, non-toxic, soluble and had satisfactory physicochemical properties. Molecular docking and binding free energy calculation revealed strong binding interactions between vaccine constructs and human TLRs (TLR-2 and TLR-4). Classical MD Simulation and Normal mode analysis verified the stability of the vaccine-TLR complex in the biological environment. Codon adaptation, cloning and <i>in silico</i> expression suggested the efficient expression of recombinant vaccine proteins in <i>E. coli</i>. Both candidates also generated robust immune profiles comprising innate, adaptive and humoral immune responses. Taken together, experimental validations of our findings through extensive <i>in vitro</i> and <i>in vivo</i> testing might provide an effective vaccine for prophylactic control of <i>C. neoformans</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24174367
title: RAGE: a potential target for Epimedium’s anti-neuroinflammation role in vascular dementia—insights from network pharmacology and molecular simulation

description: Vascular dementia (VaD), a cognitive impairment resulting from cerebrovascular issues, could be mitigated by Epimedium. This study investigates Epimedium's efficacy in VaD management through a systematic review, network pharmacology, molecular docking, and molecular dynamic simulations (MDS). Comprehensive literature searches were conducted across various databases. Epimedium's pharmacological properties were analyzed using the TCMSP database. Integration with the Aging Atlas database enabled the identification of shared targets between Epimedium and VaD. A protein-protein interaction (PPI) network was constructed, and central targets' topological attributes were analyzed using Cytoscape 3.9.1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using “ClusterProfiler” R package. The interactions between Epimedium and central targets were assessed by Molecular docking and MDS. Epimedium and its 23 bioactive components counteracted oxidative stress, neuroinflammation, and neuronal damage, thereby attenuating cognitive deterioration in VaD. A total of 78 common targets were identified, with 22 being significantly related to aging. Enrichment analysis identified 1769 GO terms and 139 KEGG pathways, highlighting the AGE-RAGE signaling pathway. Molecular docking revealed that 23 bioactive components, except Linoleyl acetate, effectively interacted with top central targets (JUN, MAPK14, IL6, FOS, TNF). MDS demonstrated that flavonoids Icariin, Kaempferol, Luteolin, and Quercetin formed stable complexes with RAGE. The study identifies RAGE as a novel therapeutic target for Epimedium in the mitigation of VaD via its anti-inflammatory properties.
DOI: 10.6084/m9.figshare.24174367.v1
title: RAGE: a potential target for Epimedium’s anti-neuroinflammation role in vascular dementia—insights from network pharmacology and molecular simulation

description: Vascular dementia (VaD), a cognitive impairment resulting from cerebrovascular issues, could be mitigated by Epimedium. This study investigates Epimedium's efficacy in VaD management through a systematic review, network pharmacology, molecular docking, and molecular dynamic simulations (MDS). Comprehensive literature searches were conducted across various databases. Epimedium's pharmacological properties were analyzed using the TCMSP database. Integration with the Aging Atlas database enabled the identification of shared targets between Epimedium and VaD. A protein-protein interaction (PPI) network was constructed, and central targets' topological attributes were analyzed using Cytoscape 3.9.1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using “ClusterProfiler” R package. The interactions between Epimedium and central targets were assessed by Molecular docking and MDS. Epimedium and its 23 bioactive components counteracted oxidative stress, neuroinflammation, and neuronal damage, thereby attenuating cognitive deterioration in VaD. A total of 78 common targets were identified, with 22 being significantly related to aging. Enrichment analysis identified 1769 GO terms and 139 KEGG pathways, highlighting the AGE-RAGE signaling pathway. Molecular docking revealed that 23 bioactive components, except Linoleyl acetate, effectively interacted with top central targets (JUN, MAPK14, IL6, FOS, TNF). MDS demonstrated that flavonoids Icariin, Kaempferol, Luteolin, and Quercetin formed stable complexes with RAGE. The study identifies RAGE as a novel therapeutic target for Epimedium in the mitigation of VaD via its anti-inflammatory properties.
DOI: 10.15468/dl.8sfukz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dreissena rostriformis (Deshayes, 1838)",
 "Country is Canada",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003494-241107131044228/datasets/export for details.
DOI: 10.6084/m9.figshare.24224060.v1
title: Computational insights of the molecular recognition between volatile molecules and odorant binding proteins from the red palm weevil <i>Rhynchophorus ferrugineus</i>

description: The red palm weevil <i>Rhynchophorus ferrugineus</i> (Coleoptera: Curculionidae) is one of the most harmful pests for palm trees, causing serious economic damage worldwide. The present work aims to model and study the 3D structures of highly expressed odorant binding proteins from <i>R. ferrugineus</i> (RferOBPs) and identify possible binding modes and ligand release mechanism by docking and molecular dynamics. Highly confident 3D structures of a total of 11 odorant binding proteins (OBPs) were obtained with AlphaFold2. All 3D RferOBPs modeled structures displayed six characteristic α-helices, except for RfeOBP7 and RfeOBP10, which had an extra terminal α-helix. Among the eleven modeled RferOBPs, RferOBP4 was highly expressed in the antennae and subsequently selected for further analyses. Molecular docking analyses demonstrated that ferruginol, α-pinene, DEET, and picaridin can favorably bind the RferOBP4 cavity with low affinity energies. Molecular dynamic simulations of RferOBP4 bound to ferruginol at different pH values showed that low pH environments dictate a structural change into an apo-state that modifies the number of tunnels where the ligand can coexist, further triggering ligand release by a pH-dependent mechanism. This is the first report concerning the modelling and study of ligand binding modes and release mechanism of <i>R. ferrugineus</i> OBPs. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24212819
title: Permeability of antioxidants through a lipid bilayer model with coarse-grained simulations

description: Oxidative stress caused by pollution and lifestyle changes causes an excess of free radicals that react chemically with cell constituents leading to irreversible damage. There are molecules known as antioxidants that reduce the levels of free radicals. Some pigments of fruits and vegetables known as anthocyanins have antioxidant properties. Their interaction with the cell membrane becomes a crucial step in studying these substances. In this research, molecular dynamics simulations, particularly, coarse-grained molecular dynamics (CGMD) were used. This technique aims to replace functional groups with corresponding beads that represent their level of polarity and affinities to other chemical groups. Also, umbrella sampling was carried out to obtain free energy profiles that describe well the orientation and location of antioxidants in a membrane considering Trolox, Cyanidin, Gallic Acid, and Resveratrol molecules to study the structural effects they cause on it. It was concluded in this study that an antioxidant when crossing the membrane does not cause either damage to the structural properties or the loss of packing and stratification of phospholipids. it was also observed that the most reactive part of the molecules could easily approach area A prone to lipid oxidation, which can describe the antioxidant capacity of these molecules. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24212819.v1
title: Permeability of antioxidants through a lipid bilayer model with coarse-grained simulations

description: Oxidative stress caused by pollution and lifestyle changes causes an excess of free radicals that react chemically with cell constituents leading to irreversible damage. There are molecules known as antioxidants that reduce the levels of free radicals. Some pigments of fruits and vegetables known as anthocyanins have antioxidant properties. Their interaction with the cell membrane becomes a crucial step in studying these substances. In this research, molecular dynamics simulations, particularly, coarse-grained molecular dynamics (CGMD) were used. This technique aims to replace functional groups with corresponding beads that represent their level of polarity and affinities to other chemical groups. Also, umbrella sampling was carried out to obtain free energy profiles that describe well the orientation and location of antioxidants in a membrane considering Trolox, Cyanidin, Gallic Acid, and Resveratrol molecules to study the structural effects they cause on it. It was concluded in this study that an antioxidant when crossing the membrane does not cause either damage to the structural properties or the loss of packing and stratification of phospholipids. it was also observed that the most reactive part of the molecules could easily approach area A prone to lipid oxidation, which can describe the antioxidant capacity of these molecules. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24224060
title: Computational insights of the molecular recognition between volatile molecules and odorant binding proteins from the red palm weevil <i>Rhynchophorus ferrugineus</i>

description: The red palm weevil <i>Rhynchophorus ferrugineus</i> (Coleoptera: Curculionidae) is one of the most harmful pests for palm trees, causing serious economic damage worldwide. The present work aims to model and study the 3D structures of highly expressed odorant binding proteins from <i>R. ferrugineus</i> (RferOBPs) and identify possible binding modes and ligand release mechanism by docking and molecular dynamics. Highly confident 3D structures of a total of 11 odorant binding proteins (OBPs) were obtained with AlphaFold2. All 3D RferOBPs modeled structures displayed six characteristic α-helices, except for RfeOBP7 and RfeOBP10, which had an extra terminal α-helix. Among the eleven modeled RferOBPs, RferOBP4 was highly expressed in the antennae and subsequently selected for further analyses. Molecular docking analyses demonstrated that ferruginol, α-pinene, DEET, and picaridin can favorably bind the RferOBP4 cavity with low affinity energies. Molecular dynamic simulations of RferOBP4 bound to ferruginol at different pH values showed that low pH environments dictate a structural change into an apo-state that modifies the number of tunnels where the ligand can coexist, further triggering ligand release by a pH-dependent mechanism. This is the first report concerning the modelling and study of ligand binding modes and release mechanism of <i>R. ferrugineus</i> OBPs. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.27637930
title: Designing a novel multi-epitopes pan-vaccine against SARS-CoV-2 and seasonal influenza: <i>in silico</i> and immunoinformatics approach

description: The merger of COVID-19 and seasonal influenza infections is considered a potentially serious threat to public health. These two viral agents can cause extensive and severe lower and upper respiratory tract infections with lung damage with host factors. Today, the development of vaccination has been shown to reduce the risk of hospitalization and mortality from the COVID-19 virus and influenza epidemics. Therefore, this study contributes to an immunoinformatics approach to producing a vaccine that can elicit strong and specific immune responses against COVID-19 and influenza A and B viruses. The NCBI, GISAID, and Uniprot databases were used to retrieve sequences. Linear B cell, Cytotoxic T lymphocyte, and Helper T lymphocyte epitopes were predicted using the online servers. Population coverage of MHC I epitopes worldwide for SARS-CoV-2, Influenza virus H3N2, H3N2, and Yamagata/Victoria were 99.93%, 68.67%, 68.38%, and 85.45%, respectively. Candidate epitopes were linked by GGGGS, GPGPG, and KK linkers. Different epitopes were permutated several times to form different peptides and then screened for antigenicity, allergenicity, and toxicity. The vaccine construct was analyzed for physicochemical properties, conformational B-cell epitopes, interaction with Toll-like receptors, and IFN-gamma-induced. Immune stimulation response of final construct was evaluated using C-IMMSIM. Eventually, the final construct sequence was codon-optimized for <i>Escherichia coli</i> K12 and <i>Homo sapiens</i> to design a multi-epitope vaccine and mRNA vaccine. In conclusion, due to the variable nature of SARS-CoV-2 and influenza proteins, the design of a multi-epitope vaccine can protect against all their standard variants, but laboratory validation is required. Communicated by Ramaswamy H. Sarma