cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fpp8dc
title: Occurrence Download

description: A dataset containing 1966 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Seriola rivoliana Valenciennes, 1833"
 ]
}

 The dataset includes 1966 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013024-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mvjeeg
title: Occurrence Download

description: A dataset containing 345 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hibbertia wagapii Gilg"
 ]
}

 The dataset includes 345 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020359-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nx2w43
title: Occurrence Download

description: A dataset containing 26105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Quercus alba L."
 ]
}

 The dataset includes 26105 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019252-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25582/data.2020-02.1946663/2363111
title: Data for EMSL Project 50076 from February 2020
DOI: 10.15468/dl.hb7afc
title: Occurrence Download

description: A dataset containing 612 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Weinmannia tomentosa L.fil.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 612 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0059634-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5aaq8j
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trichodactylus harttii Rathbun, 1905"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019160-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bjxp58
title: Occurrence Download

description: A dataset containing 5105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carthamus tinctorius L.",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5105 records from 213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020350-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ahj8ck
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Festuca stricta subsp. sulcata (Hack.) Patzke ex Joch.Müll.",
 "HasCoordinate is true",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019260-240216155721649/datasets/export for details.
DOI: 10.25582/data.2020-02.1946649/2363112
title: Data for EMSL Project 50076 from February 2020
DOI: 10.15468/dl.5cgyux
title: Occurrence Download

description: A dataset containing 167 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium doronicifolium Arv.-Touv."
 ]
}

 The dataset includes 167 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020334-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evawqe
title: Occurrence Download

description: A dataset containing 647251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((27 -30,27 -25,27.5 -25,27.5 -30,27 -30))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 647251 records from 111 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013024-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mr2zmv
title: Occurrence Download

description: A dataset containing 8629 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((120 53.55059, 126 53.55059, 126 54.85811, 120 54.85811, 120 53.55059))"
 ]
}

 The dataset includes 8629 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038059-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.spdaql
title: Occurrence Download

description: A dataset containing 1227 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 {
 "or" : [
 "TaxonKey is Moehringia fontqueri Pau",
 "TaxonKey is Moehringia intricata subsp. tejedensis (Willk.) J.M.Monts.",
 "TaxonKey is Monanthes wildpretii Bañares & S.Scholz",
 "TaxonKey is Moricandia moricandioides subsp. pseudofoetida Sánchez-Gómez, M.A.Carrión, A.Hern. & J.Guerra",
 "TaxonKey is Myrica gale L.",
 "TaxonKey is Myrica rivas-martinezii A.Santos",
 "TaxonKey is Narcissus alcaracensis S.Ríos, D.Rivera, Alcaraz & Obón",
 "TaxonKey is Narcissus bugei (Fern.Casas) Fern.Casas",
 "TaxonKey is Narcissus cyclamineus DC.",
 "TaxonKey is Narcissus eugeniae Fern.Casas",
 "TaxonKey is Narcissus juressianus Fern.Casas",
 "TaxonKey is Narcissus longispathus Degen & Hervier ex Pugsley",
 "TaxonKey is Narcissus nevadensis subsp. nevadensis Pugsley",
 "TaxonKey is Narcissus nevadensis subsp. enemeritoi Sánchez-Gómez, A.F.Carrillo, A.Hern., M.A.Carrión & Güemes",
 "TaxonKey is Narcissus perez-chiscanoi Fern.Casas",
 "TaxonKey is Narcissus radinganorum Fern.Casas",
 "TaxonKey is Narcissus segurensis S.Ríos, D.Rivera, Alcaraz & Obón",
 "TaxonKey is Narcissus yepesii S.Ríos, D.Rivera, Alcaraz & Obón",
 "TaxonKey is Naufraga balearica Constance & Cannon",
 "TaxonKey is Nauplius graveolens subsp. odorus (Schousb.) Wiklund",
 "TaxonKey is Nauplius graveolens subsp. stenophyllus (Link) Wiklund",
 "TaxonKey is Nauplius schultzii (Bolle) Wiklund",
 "TaxonKey is Nepeta amethystina subsp. anticaria (Ladero & Rivas Goday ex Ubera & Valdés) Cabezudo, Nieto Caldera & T.Navarro",
 "TaxonKey is Nepeta hispanica Boiss. & Reut.",
 "TaxonKey is Nepeta hispanica Boiss. & Reut."
 ]
 }
 ]
}

 The dataset includes 1227 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013025-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25582/data.2020-03.1973182/2363113
title: Data for EMSL Project 50076 from March 2020
DOI: 10.15468/dl.e9y56z
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eurya hebbemensis Kobuski"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049041-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.whswxy
title: Occurrence Download

description: A dataset containing 62892 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cotinus coggygria Scop.",
 "Year is greater than or equal to 1900",
 "HasCoordinate is true"
 ]
}

 The dataset includes 62892 records from 359 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022784-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ytgohp
title: Occurrence Download

description: A dataset containing 212 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alisterus amboinensis (Linnaeus, 1766)",
 "Country is Indonesia"
 ]
}

 The dataset includes 212 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013025-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wrug2e
title: Occurrence Download

description: A dataset containing 1272697 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "Geometry POLYGON((-242.04464 37.4622,-240.35447 29.79125,-235.84733 28.49965,-229.50918 29.73012,-232.46698 35.42292,-233.59376 38.12998,-234.79097 40.20452,-237.18539 39.77286,-237.60793 41.64114,-241.12913 41.0065,-243.73482 39.5017,-242.04464 37.4622))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1272697 records from 522 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007794-240216155721649/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.26232076
title: <i>Helicobacter pylori</i> East Asian type CagA hijacks more SHIP2 by its EPIYA-D motif to potentiate the oncogenicity

description: CagA is a significant oncogenic factor injected into host cells by <i>Helicobacter pylori</i>, which is divided into two subtypes: East Asian type (CagA<sup>E</sup>), characterized by the EPIYA-D motif, and western type (CagA<sup>W</sup>), harboring the EPIYA-C motif. CagA<sup>E</sup> has been reported to have higher carcinogenicity than CagA<sup>W</sup>, although the underlying reason is not fully understood. SHIP2 is an intracellular phosphatase that can be recruited by CagA to perturb the homeostasis of intracellular signaling pathways. In this study, we found that SHIP2 contributes to the higher oncogenicity of CagA<sup>E</sup>. Co-Immunoprecipitation and Pull-down assays showed that CagA<sup>E</sup> bind more SHIP2 than CagA<sup>W</sup>. Immunofluorescence staining showed that a higher amount of SHIP2 recruited by CagA<sup>E</sup> to the plasma membrane catalyzes the conversion of PI(3,4,5)P<sub>3</sub> into PI(3,4)P<sub>2</sub>. This alteration causes higher activation of Akt signaling, which results in enhanced IL-8 secretion, migration, and invasion of the infected cells. SPR analysis showed that this stronger interaction between CagA<sup>E</sup> and SHIP2 stems from the higher affinity between the EPIYA-D motif of CagA<sup>E</sup> and the SH2 domain of SHIP2. Structural analysis revealed the crucial role of the Phe residue at the Y + 5 position in EPIYA-D. After mutating Phe of CagA<sup>E</sup> into Asp (the corresponding residue in the EPIYA-C motif) or Ala, the activation of downstream Akt signaling was reduced and the malignant transformation of infected cells was alleviated. These findings revealed that CagA<sup>E</sup> hijacks SHIP2 through its EPIYA-D motif to enhance its carcinogenicity, which provides a better understanding of the higher oncogenic risk of <i>H. pylori</i> CagA<sup>E</sup>.
DOI: 10.6084/m9.figshare.26232076.v1
title: <i>Helicobacter pylori</i> East Asian type CagA hijacks more SHIP2 by its EPIYA-D motif to potentiate the oncogenicity

description: CagA is a significant oncogenic factor injected into host cells by <i>Helicobacter pylori</i>, which is divided into two subtypes: East Asian type (CagA<sup>E</sup>), characterized by the EPIYA-D motif, and western type (CagA<sup>W</sup>), harboring the EPIYA-C motif. CagA<sup>E</sup> has been reported to have higher carcinogenicity than CagA<sup>W</sup>, although the underlying reason is not fully understood. SHIP2 is an intracellular phosphatase that can be recruited by CagA to perturb the homeostasis of intracellular signaling pathways. In this study, we found that SHIP2 contributes to the higher oncogenicity of CagA<sup>E</sup>. Co-Immunoprecipitation and Pull-down assays showed that CagA<sup>E</sup> bind more SHIP2 than CagA<sup>W</sup>. Immunofluorescence staining showed that a higher amount of SHIP2 recruited by CagA<sup>E</sup> to the plasma membrane catalyzes the conversion of PI(3,4,5)P<sub>3</sub> into PI(3,4)P<sub>2</sub>. This alteration causes higher activation of Akt signaling, which results in enhanced IL-8 secretion, migration, and invasion of the infected cells. SPR analysis showed that this stronger interaction between CagA<sup>E</sup> and SHIP2 stems from the higher affinity between the EPIYA-D motif of CagA<sup>E</sup> and the SH2 domain of SHIP2. Structural analysis revealed the crucial role of the Phe residue at the Y + 5 position in EPIYA-D. After mutating Phe of CagA<sup>E</sup> into Asp (the corresponding residue in the EPIYA-C motif) or Ala, the activation of downstream Akt signaling was reduced and the malignant transformation of infected cells was alleviated. These findings revealed that CagA<sup>E</sup> hijacks SHIP2 through its EPIYA-D motif to enhance its carcinogenicity, which provides a better understanding of the higher oncogenic risk of <i>H. pylori</i> CagA<sup>E</sup>.
DOI: 10.6084/m9.figshare.27036603
title: Detection and differentiation of antinuclear antibodies in serum of dengue suspected patients with or without systemic autoimmune disease in Kolkata, India

description: The pathophysiology of dengue may be influenced by antibodies released during infection. Several autoimmune diseases are accompanied by antinuclear antibodies (ANAs) but 8–10% of the general population have positive ANA tests. To test the hypothesis that an ANA-positive test indicates an immune dysregulated state that modifies the risk for certain clinical disorders in people with or without an autoimmune disease, we examined the various ANA profiles and their relationships to various autoimmune disorders, as well as the severity of these relationships, in patients infected with dengue fever. Enzyme-linked immunosorbent assay (ELISA) and reverse transcription-polymerase chain reaction (RT-PCR) methods were used. Indirect immunofluorescence assay (IIFA) and line immunoassay (LIA) were performed to detect and differentiate the ANAs among dengue infected patients. Out of 135 dengue virus-positive patients, 94.07% were positive by ELISA and 5.93% positive by RT-PCR method. ANAs by IIFA and LIA were detected in 54.8% and 18.5% of the dengue positive patients, respectively, and 10.3% and 7.1% of the 126 dengue negative patients, respectively. This study showed that dengue was associated with an increased risk of autoimmune myositis and mixed connective tissue disease (MCTD), a rare complication of dengue. The risk of other autoimmune diseases did not seem to increase after DENV infection.
DOI: 10.6084/m9.figshare.27036603.v1
title: Detection and differentiation of antinuclear antibodies in serum of dengue suspected patients with or without systemic autoimmune disease in Kolkata, India

description: The pathophysiology of dengue may be influenced by antibodies released during infection. Several autoimmune diseases are accompanied by antinuclear antibodies (ANAs) but 8–10% of the general population have positive ANA tests. To test the hypothesis that an ANA-positive test indicates an immune dysregulated state that modifies the risk for certain clinical disorders in people with or without an autoimmune disease, we examined the various ANA profiles and their relationships to various autoimmune disorders, as well as the severity of these relationships, in patients infected with dengue fever. Enzyme-linked immunosorbent assay (ELISA) and reverse transcription-polymerase chain reaction (RT-PCR) methods were used. Indirect immunofluorescence assay (IIFA) and line immunoassay (LIA) were performed to detect and differentiate the ANAs among dengue infected patients. Out of 135 dengue virus-positive patients, 94.07% were positive by ELISA and 5.93% positive by RT-PCR method. ANAs by IIFA and LIA were detected in 54.8% and 18.5% of the dengue positive patients, respectively, and 10.3% and 7.1% of the 126 dengue negative patients, respectively. This study showed that dengue was associated with an increased risk of autoimmune myositis and mixed connective tissue disease (MCTD), a rare complication of dengue. The risk of other autoimmune diseases did not seem to increase after DENV infection.
DOI: 10.6084/m9.figshare.27922564
title: Xylose utilization promotes <i>Salmonella</i> replication within macrophages and systemic infection in mice

description: The intracellular pathogen <i>Salmonella</i> can cause systemic diseases via its survival and replication in host macrophages. Xylose is the second most abundant sugar in nature and <i>Salmonella</i> can use xylose as its sole carbon source for growth. However, whether xylose utilization contributes to the pathogenicity and intracellular growth of <i>Salmonella</i> has not yet been determined. In this study, we observed that the xylose concentration in macrophages increased during <i>Salmonella</i> infection. Moreover, there was an increase in expression of <i>Salmonella</i> xylose catabolic genes (<i>xylA</i> and <i>xylB)</i> and the transcriptional regulatory gene of xylose metabolism (<i>xylR</i>) in macrophages, revealing the possibility of using host-accumulated xylose by <i>Salmonella</i> for intracellular growth. Mutation of either <i>xylAB</i> or <i>xylR</i> reduced <i>Salmonella</i> replication in macrophages and attenuated the colonization of mouse systemic loci (e.g. the liver and spleen), indicating that xylose utilization promotes <i>Salmonella</i> replication within macrophages and systemic infection in mice. Moreover, we found that xylose utilization by intracellular <i>Salmonella</i> was activated by the cAMP-CRP complex upon detection of low glucose levels in the infected macrophages. Collectively, these findings reveal that although the available glucose decreases during infection, <i>Salmonella</i> can use xylose, which accumulates in infected macrophages, as an alternative carbon source to promote intracellular replication and virulence.
DOI: 10.6084/m9.figshare.27922564.v1
title: Xylose utilization promotes <i>Salmonella</i> replication within macrophages and systemic infection in mice

description: The intracellular pathogen <i>Salmonella</i> can cause systemic diseases via its survival and replication in host macrophages. Xylose is the second most abundant sugar in nature and <i>Salmonella</i> can use xylose as its sole carbon source for growth. However, whether xylose utilization contributes to the pathogenicity and intracellular growth of <i>Salmonella</i> has not yet been determined. In this study, we observed that the xylose concentration in macrophages increased during <i>Salmonella</i> infection. Moreover, there was an increase in expression of <i>Salmonella</i> xylose catabolic genes (<i>xylA</i> and <i>xylB)</i> and the transcriptional regulatory gene of xylose metabolism (<i>xylR</i>) in macrophages, revealing the possibility of using host-accumulated xylose by <i>Salmonella</i> for intracellular growth. Mutation of either <i>xylAB</i> or <i>xylR</i> reduced <i>Salmonella</i> replication in macrophages and attenuated the colonization of mouse systemic loci (e.g. the liver and spleen), indicating that xylose utilization promotes <i>Salmonella</i> replication within macrophages and systemic infection in mice. Moreover, we found that xylose utilization by intracellular <i>Salmonella</i> was activated by the cAMP-CRP complex upon detection of low glucose levels in the infected macrophages. Collectively, these findings reveal that although the available glucose decreases during infection, <i>Salmonella</i> can use xylose, which accumulates in infected macrophages, as an alternative carbon source to promote intracellular replication and virulence.
DOI: 10.6084/m9.figshare.25040361
title: HylS’, a fragment of truncated hyaluronidase of <i>Streptococcus suis</i>, contributes to immune evasion by interaction with host complement factor C3b

description: Pathogenic bacteria have evolved many strategies to evade surveillance and attack by complements. <i>Streptococcus suis</i> is an important zoonotic pathogen that infects humans and pigs. Hyaluronidase (HylA) has been reported to be a potential virulence factor of <i>S. suis</i>. However, in this study, it was discovered that the genomic region encoding HylA of the virulent <i>S. suis</i> strain SC19 and other ST1 strains was truncated into four fragments when aligned with a strain containing intact HylA and possessing hyaluronidase activity. As a result, SC19 had no hyaluronidase activity, but one truncated HylA fragment, designated as HylS,’ directly interacted with complement C3b, as confirmed by western ligand blotting, pull-down, and ELISA assays. The deposition of C3b and membrane attack complex (MAC) formation on the surface of a HylS’-deleted mutant (Δ<i>hylS’</i>) was significantly increased compared to wild-type SC19. In human sera and whole blood, Δ<i>hylS’</i> survival was significantly reduced compared to that in SC19. The resistance of Δ<i>hylS’</i> to macrophages and human polymorphonuclear neutrophil PMNs also decreased. In a mouse infection model, Δ<i>hylS’</i> showed reduced lethality and lower bacterial load in the organs compared to that of SC19. We conclude that the truncated hyaluronidase HylS’ fragment contributes to complement evasion and the pathogenesis of <i>S. suis</i>.
DOI: 10.6084/m9.figshare.25040361.v2
title: HylS’, a fragment of truncated hyaluronidase of <i>Streptococcus suis</i>, contributes to immune evasion by interaction with host complement factor C3b

description: Pathogenic bacteria have evolved many strategies to evade surveillance and attack by complements. <i>Streptococcus suis</i> is an important zoonotic pathogen that infects humans and pigs. Hyaluronidase (HylA) has been reported to be a potential virulence factor of <i>S. suis</i>. However, in this study, it was discovered that the genomic region encoding HylA of the virulent <i>S. suis</i> strain SC19 and other ST1 strains was truncated into four fragments when aligned with a strain containing intact HylA and possessing hyaluronidase activity. As a result, SC19 had no hyaluronidase activity, but one truncated HylA fragment, designated as HylS,’ directly interacted with complement C3b, as confirmed by western ligand blotting, pull-down, and ELISA assays. The deposition of C3b and membrane attack complex (MAC) formation on the surface of a HylS’-deleted mutant (Δ<i>hylS’</i>) was significantly increased compared to wild-type SC19. In human sera and whole blood, Δ<i>hylS’</i> survival was significantly reduced compared to that in SC19. The resistance of Δ<i>hylS’</i> to macrophages and human polymorphonuclear neutrophil PMNs also decreased. In a mouse infection model, Δ<i>hylS’</i> showed reduced lethality and lower bacterial load in the organs compared to that of SC19. We conclude that the truncated hyaluronidase HylS’ fragment contributes to complement evasion and the pathogenesis of <i>S. suis</i>.