cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29036964
title: Immunoinformatic approach for designing a multi-epitope vaccine against non-typhoidal salmonellosis using starvation-stress response proteins from <i>Salmonella</i> Oranienburg

description: Non-typhoidal <i>Salmonella</i> is responsible for gastrointestinal illnesses worldwide. Therefore, it is important to implement effective therapeutic interventions for preventing these diseases. Vaccines have proven highly efficacious in the treatment and prevention of several illnesses. Nevertheless, there is currently no authorized vaccine available for non-typhoidal salmonellosis. This study aimed to employ in silico techniques to develop a multi-epitope vaccine targeting non-typhoidal salmonellosis. Specifically, we focused on proteins associated with the starvation stress response (SSR) in <i>Salmonella</i> Oranienburg. The presence of these proteins is essential for the survival and disease of the host organism. The vaccine sequence was constructed utilizing B-cell and T-cell epitopes. Linkers, adjuvants and PADRE sequences were used to establish connections between epitopes. The vaccine exhibited no allergenicity, toxigenicity and a significantly high antigenicity score. Docking analysis conducted between the designed vaccine and the TLR-1, TLR-2 and TLR-4 receptors demonstrated favorable interactions and the potential to activate these receptors. In addition, it was found through immunological simulation testing that the vaccine elicits a robust immune response. The use of these proteins in the construction of a multi-epitope vaccine shows potential in terms of both safety and immunogenicity.
DOI: 10.6084/m9.figshare.29036964.v1
title: Immunoinformatic approach for designing a multi-epitope vaccine against non-typhoidal salmonellosis using starvation-stress response proteins from <i>Salmonella</i> Oranienburg

description: Non-typhoidal <i>Salmonella</i> is responsible for gastrointestinal illnesses worldwide. Therefore, it is important to implement effective therapeutic interventions for preventing these diseases. Vaccines have proven highly efficacious in the treatment and prevention of several illnesses. Nevertheless, there is currently no authorized vaccine available for non-typhoidal salmonellosis. This study aimed to employ in silico techniques to develop a multi-epitope vaccine targeting non-typhoidal salmonellosis. Specifically, we focused on proteins associated with the starvation stress response (SSR) in <i>Salmonella</i> Oranienburg. The presence of these proteins is essential for the survival and disease of the host organism. The vaccine sequence was constructed utilizing B-cell and T-cell epitopes. Linkers, adjuvants and PADRE sequences were used to establish connections between epitopes. The vaccine exhibited no allergenicity, toxigenicity and a significantly high antigenicity score. Docking analysis conducted between the designed vaccine and the TLR-1, TLR-2 and TLR-4 receptors demonstrated favorable interactions and the potential to activate these receptors. In addition, it was found through immunological simulation testing that the vaccine elicits a robust immune response. The use of these proteins in the construction of a multi-epitope vaccine shows potential in terms of both safety and immunogenicity.
DOI: 10.6084/m9.figshare.28760537
title: Cross-variant immune shield: computational multiepitope vaccine design against B.617.2 to Omicron sub-lineages in SARS-CoV-2

description: The COVID-19 pandemic had a profound impact on global health. This study focuses on an in-depth analysis of the structural proteins (Spike (S), Nucleocapsid (N), Membrane (M), and Envelope (E) protein) of SARS-CoV-2 and its variants, aiming to develop a multiepitope vaccine construct that targets the virus independently of its variants. The analysis began by examining genetic variations in viral proteins relative to the reference strain Wuhan-Hu2, particularly in the S, M, N, and E proteins. T-cell epitope predictions for MHC Class-I and Class-II binding were conducted, shedding light on potential cytotoxic and helper T lymphocyte recognition. Identification of linear B-cell epitopes laid the groundwork for antibody-based humoral immune responses. The safety and efficacy of these epitopes were assessed for antigenicity, allergenicity, toxicity, immunogenicity, and conservancy. Population coverage analysis indicated promising global effectiveness of the designed vaccine construct. By incorporating 28 epitopes, we validated that was designed vaccine construct for stability through structural analysis. Molecular dynamics simulations and docking studies revealed its robust interaction with Toll-like receptor 4 (TLR4). Immune simulation studies suggested that the vaccine construct could induce a potent immune response by enhancing antibody titers, B-cell proliferation, memory cell development, and activation of T cells and natural killer cells upon administration. This comprehensive approach offers a promising multiepitope vaccine against SARS-CoV-2, with the potential for broad global coverage and strong immunogenicity. Further experimental validation holds the prospect of introducing a novel candidate vaccine to aid in the ongoing battle against the COVID-19 pandemic.
DOI: 10.6084/m9.figshare.28760537.v1
title: Cross-variant immune shield: computational multiepitope vaccine design against B.617.2 to Omicron sub-lineages in SARS-CoV-2

description: The COVID-19 pandemic had a profound impact on global health. This study focuses on an in-depth analysis of the structural proteins (Spike (S), Nucleocapsid (N), Membrane (M), and Envelope (E) protein) of SARS-CoV-2 and its variants, aiming to develop a multiepitope vaccine construct that targets the virus independently of its variants. The analysis began by examining genetic variations in viral proteins relative to the reference strain Wuhan-Hu2, particularly in the S, M, N, and E proteins. T-cell epitope predictions for MHC Class-I and Class-II binding were conducted, shedding light on potential cytotoxic and helper T lymphocyte recognition. Identification of linear B-cell epitopes laid the groundwork for antibody-based humoral immune responses. The safety and efficacy of these epitopes were assessed for antigenicity, allergenicity, toxicity, immunogenicity, and conservancy. Population coverage analysis indicated promising global effectiveness of the designed vaccine construct. By incorporating 28 epitopes, we validated that was designed vaccine construct for stability through structural analysis. Molecular dynamics simulations and docking studies revealed its robust interaction with Toll-like receptor 4 (TLR4). Immune simulation studies suggested that the vaccine construct could induce a potent immune response by enhancing antibody titers, B-cell proliferation, memory cell development, and activation of T cells and natural killer cells upon administration. This comprehensive approach offers a promising multiepitope vaccine against SARS-CoV-2, with the potential for broad global coverage and strong immunogenicity. Further experimental validation holds the prospect of introducing a novel candidate vaccine to aid in the ongoing battle against the COVID-19 pandemic.
DOI: 10.6084/m9.figshare.27087541
title: Prognosis and immunotherapeutic implications of molecular classification of cervical cancer based on immunophenoscore-related genes

description: The immunophenoscore (IPS) is an important indicator for evaluating immunotherapy response. This work was designed to establish a prognostic model based on IPS-related genes in cervical cancer. Weighted correlation network analysis (WGCNA) was utilized to identify key modules related to IPS in cervical cancer data from The Cancer Genome Atlas (TCGA). The results show that the yellow module (158 genes) had a high correlation with both IPS_CTLA4_blocker and IPS_CTLA4_and PC1/PDL1/PDL2 blocker. Univariate cox regression analysis and LASSO regression analysis were performed based on 158 genes, and 9 characteristic genes were finally identified to construct the model. According to the differentially expressed genes, cervical cancer samples were divided into high-risk and low-risk groups and cluster 1.2.3. Higher risk scores associated with poorer prognosis. cluster2 and cluster3 were identified as cervical cancer subtypes with significant survival differences. cluster2 had higher immune cell infiltration levels and better prognosis, with greater sensitivity to Cyclopamine, Imatinib, MG-13, Paclitaxel, PHA-665752, Rapamycin, Sorafenib, Sunitinib, and VX-680. In contrast, cluster3 had higher TTN and PIK3CA mutations and greater sensitivity to AZ628, Dasatinib, Doxorubicin, HG-6-64-1, JQ12, Midostaurin, PF-562271, TAE684, and WH-4-023. In conclusion, we developed a feasible risk score model based on IPS-related genes for cervical cancer prognosis and identified potential drugs for different cervical cancer subtypes.
DOI: 10.6084/m9.figshare.27087541.v1
title: Prognosis and immunotherapeutic implications of molecular classification of cervical cancer based on immunophenoscore-related genes

description: The immunophenoscore (IPS) is an important indicator for evaluating immunotherapy response. This work was designed to establish a prognostic model based on IPS-related genes in cervical cancer. Weighted correlation network analysis (WGCNA) was utilized to identify key modules related to IPS in cervical cancer data from The Cancer Genome Atlas (TCGA). The results show that the yellow module (158 genes) had a high correlation with both IPS_CTLA4_blocker and IPS_CTLA4_and PC1/PDL1/PDL2 blocker. Univariate cox regression analysis and LASSO regression analysis were performed based on 158 genes, and 9 characteristic genes were finally identified to construct the model. According to the differentially expressed genes, cervical cancer samples were divided into high-risk and low-risk groups and cluster 1.2.3. Higher risk scores associated with poorer prognosis. cluster2 and cluster3 were identified as cervical cancer subtypes with significant survival differences. cluster2 had higher immune cell infiltration levels and better prognosis, with greater sensitivity to Cyclopamine, Imatinib, MG-13, Paclitaxel, PHA-665752, Rapamycin, Sorafenib, Sunitinib, and VX-680. In contrast, cluster3 had higher TTN and PIK3CA mutations and greater sensitivity to AZ628, Dasatinib, Doxorubicin, HG-6-64-1, JQ12, Midostaurin, PF-562271, TAE684, and WH-4-023. In conclusion, we developed a feasible risk score model based on IPS-related genes for cervical cancer prognosis and identified potential drugs for different cervical cancer subtypes.
DOI: 10.6084/m9.figshare.28023391
title: <i>In silico</i> design and discovery of pan coronavirus small molecule anti-virals targeting 3CL<sup>PRO</sup> protease

description: Coronaviruses (CoV), belonging to the family <i>Coronaviridae</i>, were not considered dangerous pathogens until the outbreaks of SARS, MERS, and more recently, COVID-19. The coronaviruses causing these respective diseases/syndromes, SARS, MERS, and SARS-CoV2, share high sequence and structural similarities. COVID-19 continues to have a global impact on human health and the economy. Human-to-human transmission is at the center of COVID-19’s ability to stall the entire world and force lockdowns across the globe. The corona viruses’ positive sense RNA genome is ∼30 kb long and encodes non-structural (ORF1ab) and structural (Spike, Envelope, Membrane, and Nucleo-capsid) proteins. The main viral protease (NSP5) is a Chymotrypsin-like protease (3CL<sup>pro</sup>) that cleaves on the carboxy side of the glutamine (Q) of the polypeptide sequence motif x-(L/F/M)-Q-(G/A/S)-x. 3CL<sup>PRO</sup> is highly conserved among coronaviruses and is critical in the replication and viral life cycle. Therefore, 3CL<sup>PRO</sup> is considered a promising drug target. We have recently reported three natural compounds, flavonoid derivatives, to target the cysteine 145 of the catalytic dyad covalently. Here, we have screened for small molecules with pan coronavirus activity to target 3CL<sup>pro</sup>. Our rigid body docking studies have identified 30 small molecules with comparable binding affinities to all the beta coronaviruses. Of these, five molecules have showed the possibility of covalently attacking the C145 of the catalytic dyad. MD simulations have revealed compounds <b>22</b> and <b>23</b> to be the most ideal lead compounds. Interestingly, one of the compounds, <b>22</b>, identified in the current study has already shown to be an ideal lead compound against SARS-CoV2 3CL<sup>PRO</sup>.
DOI: 10.6084/m9.figshare.28023391.v1
title: <i>In silico</i> design and discovery of pan coronavirus small molecule anti-virals targeting 3CL<sup>PRO</sup> protease

description: Coronaviruses (CoV), belonging to the family <i>Coronaviridae</i>, were not considered dangerous pathogens until the outbreaks of SARS, MERS, and more recently, COVID-19. The coronaviruses causing these respective diseases/syndromes, SARS, MERS, and SARS-CoV2, share high sequence and structural similarities. COVID-19 continues to have a global impact on human health and the economy. Human-to-human transmission is at the center of COVID-19’s ability to stall the entire world and force lockdowns across the globe. The corona viruses’ positive sense RNA genome is ∼30 kb long and encodes non-structural (ORF1ab) and structural (Spike, Envelope, Membrane, and Nucleo-capsid) proteins. The main viral protease (NSP5) is a Chymotrypsin-like protease (3CL<sup>pro</sup>) that cleaves on the carboxy side of the glutamine (Q) of the polypeptide sequence motif x-(L/F/M)-Q-(G/A/S)-x. 3CL<sup>PRO</sup> is highly conserved among coronaviruses and is critical in the replication and viral life cycle. Therefore, 3CL<sup>PRO</sup> is considered a promising drug target. We have recently reported three natural compounds, flavonoid derivatives, to target the cysteine 145 of the catalytic dyad covalently. Here, we have screened for small molecules with pan coronavirus activity to target 3CL<sup>pro</sup>. Our rigid body docking studies have identified 30 small molecules with comparable binding affinities to all the beta coronaviruses. Of these, five molecules have showed the possibility of covalently attacking the C145 of the catalytic dyad. MD simulations have revealed compounds <b>22</b> and <b>23</b> to be the most ideal lead compounds. Interestingly, one of the compounds, <b>22</b>, identified in the current study has already shown to be an ideal lead compound against SARS-CoV2 3CL<sup>PRO</sup>.
DOI: 10.6084/m9.figshare.28028129
title: Deubiquitinating enzymes in breast cancer: <i>in silico</i> analysis of gene expression and metastatic correlation

description: Breast cancer, the most prevalent cancer in females, is a heterogeneous disease with various molecular subtypes, which presents challenges in diagnosis and treatment. Ubiquitination is one of the most critical post-translational protein modifications, that plays regulatory roles in numerous cellular processes including cell cycle progression, DNA replication & repair, apoptosis, transcription regulation, protein localization, trafficking and signal transduction. This modification can be reversed by deubiquitinases, or DUBs, a superfamily of cysteine proteases and metalloproteases that cleave ubiquitin-protein bonds. Dysregulation of DUBs has been associated to various diseases including cancer, making them promising targets for cancer therapy. We leveraged publicly available breast cancer datasets and employed various bioinformatics tools to identify differentially expressed DUBs in breast cancer. Our analysis identified six genes (COPS5, EIF3H, MINDY1, MINDY2, PSMD14 and USP26) with significant differential expression and survival implications. We further validated our findings experimentally and found upregulation of COPS5, EIF3H and MINDY 1 in MCF-7 and T47D breast cancer cell lines using qPCR analysis. To identify the role of these genes, EIF3H and COPS5, in disease progression, we constructed a protein-protein interaction (PPI) network with genes associated with metastasis and explored their correlation at the gene expression level in breast cancer patients. Together, this comprehensive study sheds light on DUB gene expression patterns in breast cancer with the potential to identify novel targets for therapeutic interventions.
DOI: 10.6084/m9.figshare.28028129.v1
title: Deubiquitinating enzymes in breast cancer: <i>in silico</i> analysis of gene expression and metastatic correlation

description: Breast cancer, the most prevalent cancer in females, is a heterogeneous disease with various molecular subtypes, which presents challenges in diagnosis and treatment. Ubiquitination is one of the most critical post-translational protein modifications, that plays regulatory roles in numerous cellular processes including cell cycle progression, DNA replication & repair, apoptosis, transcription regulation, protein localization, trafficking and signal transduction. This modification can be reversed by deubiquitinases, or DUBs, a superfamily of cysteine proteases and metalloproteases that cleave ubiquitin-protein bonds. Dysregulation of DUBs has been associated to various diseases including cancer, making them promising targets for cancer therapy. We leveraged publicly available breast cancer datasets and employed various bioinformatics tools to identify differentially expressed DUBs in breast cancer. Our analysis identified six genes (COPS5, EIF3H, MINDY1, MINDY2, PSMD14 and USP26) with significant differential expression and survival implications. We further validated our findings experimentally and found upregulation of COPS5, EIF3H and MINDY 1 in MCF-7 and T47D breast cancer cell lines using qPCR analysis. To identify the role of these genes, EIF3H and COPS5, in disease progression, we constructed a protein-protein interaction (PPI) network with genes associated with metastasis and explored their correlation at the gene expression level in breast cancer patients. Together, this comprehensive study sheds light on DUB gene expression patterns in breast cancer with the potential to identify novel targets for therapeutic interventions.
DOI: 10.15468/dl.enur2f
title: Occurrence Download

description: A dataset containing 6949 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phengaris teleius"
 ]
}

 The dataset includes 6949 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021909-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pg5bwp
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Croton echinulatus"
 ]
}

 The dataset includes 52 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021911-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/kufgmh
title: Soundscape - The Symphony of Birds in Montpellier

description: This dataset documents bird communities along urbanization and green space gradients within the Montpellier metropolitan area (southern France). Surveys were conducted using standardized point count protocols as part of an exploratory ecoacoustic research project aimed at assessing the contribution of avifauna to urban soundscapes.

The dataset includes ornithological occurrence data describing species composition and abundance recorded at each sampling site. Acoustic recordings and environmental variables were also collected during the surveys but are not included in this dataset.
DOI: 10.15468/dl.db7qcv
title: Occurrence Download

description: A dataset containing 431 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-20 -38,55 -38,55 38,-20 38,-20 -38))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anthocerotophyta"
 ]
}

 The dataset includes 431 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021913-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aswt7k
title: Occurrence Download

description: A dataset containing 28589 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Phengaris nausithous"
 ]
}

 The dataset includes 28589 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021912-260208012135463/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.31346683
title: Northern Bohai Bay

description: 11111111111111111111
DOI: 10.6084/m9.figshare.31346683.v2
title: Northern Bohai Bay

description: 11111111111111111111
DOI: 10.6084/m9.figshare.31346683.v1
title: Zhen

description: 11111111111111111111
DOI: 10.6084/m9.figshare.31347037
title: <b>Evolutionary Adaptations in Iron Capture via Type II Pyoverdine in XDR</b><b> </b><b><i>Pseudomonas aeruginosa ST235</i></b>_v2

description: <i>Pseudomonas aeruginosa</i> ST235 is a globally disseminated, high-risk clone associated with multidrug resistance and increased virulence. This study explores structural and functional modifications in the pyoverdine synthesis system of the ST235 clone.
DOI: 10.6084/m9.figshare.31347037.v1
title: <b>Evolutionary Adaptations in Iron Capture via Type II Pyoverdine in XDR</b><b> </b><b><i>Pseudomonas aeruginosa ST235</i></b>_v2

description: <i>Pseudomonas aeruginosa</i> ST235 is a globally disseminated, high-risk clone associated with multidrug resistance and increased virulence. This study explores structural and functional modifications in the pyoverdine synthesis system of the ST235 clone.
DOI: 10.5281/zenodo.18659367
title: Freshwater conservation priority areas are threatened by global mining activities

description: Code and data supporting the article: Braz Pires, M., Baltus, N., Marques, A., Kleijn, R., Buxton, M., Maus, V., & Barbarossa, V. (2026). Freshwater conservation priority areas are threatened by global mining activities. Global Change Biology.
DOI: 10.5281/zenodo.18659366
title: Freshwater conservation priority areas are threatened by global mining activities

description: Code and data supporting the article: Braz Pires, M., Baltus, N., Marques, A., Kleijn, R., Buxton, M., Maus, V., & Barbarossa, V. (2026). Freshwater conservation priority areas are threatened by global mining activities. Global Change Biology.
DOI: 10.15468/dl.geu38r
title: Occurrence Download

description: A dataset containing 7723 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Epipactis leptochila"
 ]
}

 The dataset includes 7723 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021914-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.