cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14748007
title: STAT2-dependent restriction of Zika virus by human macrophages but not dendritic cells

description: Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that poses significant threats to global public health. Macrophages and dendritic cells are both key sentinel cells in the host immune response and play critical roles in the pathogenesis of flavivirus infections. Recent studies showed that ZIKV could productively infect monocyte-derived dendritic cells (moDCs), but the role of macrophages in ZIKV infection remains incompletely understood. In this study, we first compared ZIKV infection in monocyte-derived macrophages (MDMs) and moDCs derived from the same donors. We demonstrated that while both MDMs and moDCs were susceptible to epidemic (Puerto Rico) and pre-epidemic (Uganda) strains of ZIKV, virus replication was largely restricted in MDMs but not in moDCs. ZIKV induced significant apoptosis in moDCs but not MDMs. The restricted virus replication in MDMs was not due to inefficient virus entry but was related to post-entry events in the viral replication cycle. In stark contrast with moDCs, ZIKV failed to inhibit STAT1 and STAT2 phosphorylation in MDMs. This resulted in the lack of efficient antagonism of the host type I interferon-mediated antiviral responses. Importantly, depletion of STAT2 but not STAT1 in MDMs significantly rescued the replication of ZIKV and the prototype flavivirus yellow fever virus. Overall, our findings revealed a differential interplay between macrophages and dendritic cells with ZIKV. While dendritic cells may be exploited by ZIKV to facilitate virus replication, macrophages restricted ZIKV infection.
DOI: 10.6084/m9.figshare.14748007.v1
title: STAT2-dependent restriction of Zika virus by human macrophages but not dendritic cells

description: Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that poses significant threats to global public health. Macrophages and dendritic cells are both key sentinel cells in the host immune response and play critical roles in the pathogenesis of flavivirus infections. Recent studies showed that ZIKV could productively infect monocyte-derived dendritic cells (moDCs), but the role of macrophages in ZIKV infection remains incompletely understood. In this study, we first compared ZIKV infection in monocyte-derived macrophages (MDMs) and moDCs derived from the same donors. We demonstrated that while both MDMs and moDCs were susceptible to epidemic (Puerto Rico) and pre-epidemic (Uganda) strains of ZIKV, virus replication was largely restricted in MDMs but not in moDCs. ZIKV induced significant apoptosis in moDCs but not MDMs. The restricted virus replication in MDMs was not due to inefficient virus entry but was related to post-entry events in the viral replication cycle. In stark contrast with moDCs, ZIKV failed to inhibit STAT1 and STAT2 phosphorylation in MDMs. This resulted in the lack of efficient antagonism of the host type I interferon-mediated antiviral responses. Importantly, depletion of STAT2 but not STAT1 in MDMs significantly rescued the replication of ZIKV and the prototype flavivirus yellow fever virus. Overall, our findings revealed a differential interplay between macrophages and dendritic cells with ZIKV. While dendritic cells may be exploited by ZIKV to facilitate virus replication, macrophages restricted ZIKV infection.
DOI: 10.6084/m9.figshare.19990884
title: Exploring dielectric spectra of polymer through molecular dynamics simulations

description: In this work, poly(<i>N</i>-isopropylacrylamide) (PNIPAM) was used as a research object to explore the feasibility of molecular dynamics (MD) simulations to study the dielectric properties of polymers. A comparison of the static dielectric constants for two different calculation schemes, the applied electric field method and the dipole moment fluctuation method, has been conducted. The dielectric properties of PNIPAM aqueous solutions with different concentrations were studied as a function of temperature. The static dielectric constants derived from dipole moment fluctuation method at different temperatures can accurately describe the phase transition process. The concentration does not affect the lower critical solution temperature, but significantly affects the relaxation process of the system. According to the frequency-dependent dielectric constants, two relaxation processes are observed, namely, the dielectric relaxation process in the region of frequency less than 30 terahertz (THz) determined by the synergistic interaction of PNIPAM and water molecules, and that in the region of frequency higher than 30 THz mainly determined by water molecules beyond the solvation shell of the polymer. The calculation results suggest that the dielectric behaviour is concentration and temperature independent, similar to Debye behaviour of bulk water. This method of calculating dielectric properties using MD simulations can be used in detecting the dynamic processes of soft condensed matter and in aiding the design of materials with excellent dielectric properties.
DOI: 10.6084/m9.figshare.22607075.v1
title: Additional file 1 of The alteration of N6-methyladenosine (m6A) modification at the transcriptome-wide level in response of heat stress in bovine mammary epithelial cells

description: Additional file 1. m6A peaks in H and NH groups.
DOI: 10.6084/m9.figshare.22606945.v1
title: Additional file 3 of Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development

description: Additional file 3: Table S3. Sequencing data of the 75 GIT samples of sika deer among the three stages. Table S4. The significantly changed metabolic pathways at KEGG level 1 in five GIT regions among the three time points. Table S5. The significantly changed metabolic pathways at KEGG level 3 in the rumen and colon among the three time points. Table S6. Enrichment analysis of the increased KOs in the rumen and colon microbiota between the comparison of Day 70 vs Day 1.
DOI: 10.6084/m9.figshare.22606948.v1
title: Additional file 4 of Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development

description: Additional file 4: Table S7. Summary of genome assembly of Sika deer. Table S8. Summary of RNA-seq data from 75 GIT epithelium samples of sika deer. Table S9. Enrichment analysis at KEGG level 3 of up regulated DEGs in rumen epithelium.
DOI: 10.6084/m9.figshare.22612399.v1
title: Additional file 6 of Systematic analysis identifies XRCC4 as a potential immunological and prognostic biomarker associated with pan-cancer

description: Additional file 6. Association between XRCC4 expression and marker genes of immune cells.
DOI: 10.6084/m9.figshare.22607018.v1
title: Additional file 1 of Interactions between the gut micro-community and transcriptome of Culex pipiens pallens under low-temperature stress

description: Additional file 1: Table S1. Basic information of 16S rRNA sequencing of gut bacteria. Table S2. Basic information of transcriptome sequencing. Table S3. DEGs. Table S4. GO level_2 statistics. Table S5. Top 20 enriched KEGG pathways. Table S6. Pearson’s correlation analysis of the data and statistics.
DOI: 10.5281/zenodo.8423432
title: CMLs vs VMLs DIMS

description: Data derived from a direct infusion mass spectrometry (DIMS) analysis of Vitamaize lines (VMLs), derived from backcrossing the pigmented aleurone trait into the CIMMYT Maize Lines (CMLs).

Title:  Backcrossing Modulates the Metabolic Profiles of Anthocyanin-Pigmented ‘Vitamaize’ Lines Derived from Elite Maize Lines

DOI:  10.1007/s11130-024-01155-0

Article type: Research

Journal: Plant Foods for Human Nutrition
DOI: 10.5281/zenodo.8423433
title: CMLs vs VMLs DIMS

description: Data derived from a direct infusion mass spectrometry (DIMS) analysis of Vitamaize lines (VMLs), derived from backcrossing the pigmented aleurone trait into the CIMMYT Maize Lines (CMLs).

Title:  Backcrossing Modulates the Metabolic Profiles of Anthocyanin-Pigmented ‘Vitamaize’ Lines Derived from Elite Maize Lines

DOI:  10.1007/s11130-024-01155-0

Article type: Research

Journal: Plant Foods for Human Nutrition
DOI: 10.6084/m9.figshare.22606942
title: Additional file 2 of Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development

description: Additional file 2: Table S1. Summary of RNA-seq data from liver tissue of sika deer among the three stages. Table S2. Enrichment analysis at KEGG level 3 of up regulated DEGs in liver among the three stages.
DOI: 10.6084/m9.figshare.21563880
title: Additional file 8 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 8: Table S7. PPI network parameters.
DOI: 10.6084/m9.figshare.21563877
title: Additional file 7 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 7: Table S6. Pathway enrichment analysis.
DOI: 10.6084/m9.figshare.21563865
title: Additional file 3 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 3: Table S2. Differentially expressed genes for simple steatosis.
DOI: 10.6084/m9.figshare.21563871.v1
title: Additional file 5 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 5: Table S4. Common differentially expressed genes of SS, NASH, and COVID-19 (n = 62).
DOI: 10.6084/m9.figshare.21563883.v1
title: Additional file 9 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 9: Table S8. TFs-DEGs interaction network parameters.
DOI: 10.6084/m9.figshare.21563856.v1
title: Additional file 11 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 11: Table S10. Parameters of the disease-DEGs network.
DOI: 10.6084/m9.figshare.21563868.v1
title: Additional file 4 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 4: Table S3. Differentially expressed genes for NASH.
DOI: 10.6084/m9.figshare.21563853.v1
title: Additional file 10 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 10: Table S9. Parameters of miRNAs-DEGs interaction network.
DOI: 10.6084/m9.figshare.21563862.v1
title: Additional file 2 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 2: Table S1. Differentially expressed genes for COVID-19.
DOI: 10.6084/m9.figshare.21563868
title: Additional file 4 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 4: Table S3. Differentially expressed genes for NASH.
DOI: 10.6084/m9.figshare.21563877.v1
title: Additional file 7 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 7: Table S6. Pathway enrichment analysis.
DOI: 10.6084/m9.figshare.22612283.v1
title: Additional file 1 of Differential miRNA expression profiles in the bone marrow of Beagle dogs at different stages of Toxocara canis infection

description: Additional file 1: Table S1. The differently expressed miRNAs (DEmiRNAs) (P &lt; 0.05) in puppy bone marrow at different infection stages. Table S2. The potential target genes of the differentially expressed miRNAs (DEmiRNAs) at different infection stages. Table S3. The differential enriched Gene Ontology (GO) terms of potential target genes of the differentially expressed miRNAs. Table S4. The KEGG pathways of the differentially expressed miRNAs (DEmiRNAs) at different infection stages. Table S5. The primers used in the qRT-PCR experiment.
DOI: 10.6084/m9.figshare.21563871
title: Additional file 5 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 5: Table S4. Common differentially expressed genes of SS, NASH, and COVID-19 (n = 62).
DOI: 10.6084/m9.figshare.22607078.v1
title: Additional file 2 of The alteration of N6-methyladenosine (m6A) modification at the transcriptome-wide level in response of heat stress in bovine mammary epithelial cells

description: Additional file 2. m6A peaks related genes in H and NH groups.
DOI: 10.6084/m9.figshare.24233629.v6
title: <b>Efficient Object-Relational Database Design Optimization through Learning-Powered Systematic Tradeoff Analysis</b>

description: Optimizing object-relational database mapping (ORM) design is essential for software system performance. However, current ORM design tools widely used in practice offer limited support for evaluating performance implications. State-of-the-art relying on systematic tradeoff analysis provides greater assistance but becomes impractical for large-scale, real-world systems. In this paper, we introduce an innovative solution grounded in machine learning to efficiently and scalably identify optimal ORM database tradeoffs.Our approach involves training a transformer model using a dataset of formally analyzed object-relational database designs to identify Pareto-optimal design tradeoffs, significantly reducing the number of design candidates. The extensive experiments across various software database systems demonstrate the high effectiveness of the approach in identifying optimal design alternatives overlooked by leading ORM tools. Additionally, our results show a remarkable 98.21\% improvement in analysis efficiency compared to the current state-of-the-art, reducing tradeoff analysis time from over 15 days to around 18 minutes on average.<br><br>
DOI: 10.6084/m9.figshare.21563874.v1
title: Additional file 6 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 6: Table S5. Gene ontology analysis.
DOI: 10.6084/m9.figshare.10029539.v2
title: Metadata record for: A de novo genome assembly of the dwarfing pear rootstock Zhongai 1

description: This dataset contains key characteristics about the data described in the Data Descriptor A de novo genome assembly of the dwarfing pear rootstock Zhongai 1. <br>
 Contents: <br>
 
 1. human readable metadata summary table in CSV format
 
 
 2. machine readable metadata file in JSON format<br><br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.21563865.v1
title: Additional file 3 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 3: Table S2. Differentially expressed genes for simple steatosis.
DOI: 10.6084/m9.figshare.21563882.v1
title: Additional file 12 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

description: Additional file 12: Table S3. The downregulated genes in malaria-infected relative to noninfected individuals in the discovery datasets.
DOI: 10.6084/m9.figshare.21563876.v1
title: Additional file 10 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

description: Additional file 10: Table S1. The subsets of genes and immune cell types identified from the ImmPort database.
DOI: 10.6084/m9.figshare.21563874
title: Additional file 6 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 6: Table S5. Gene ontology analysis.
DOI: 10.6084/m9.figshare.21563880.v1
title: Additional file 8 of Systems biology approach reveals a common molecular basis for COVID-19 and non-alcoholic fatty liver disease (NAFLD)

description: Additional file 8: Table S7. PPI network parameters.
DOI: 10.6084/m9.figshare.21563879
title: Additional file 11 of Multicohort transcriptome analysis of whole blood identifies robust human response signatures in Plasmodium falciparum infections

description: Additional file 11: Table S2. The upregulated genes in malaria-infected relative to noninfected individuals in the discovery datasets.
DOI: 10.15468/dl.h9vwrn
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meistera tomrey (Gagnep.) Škorničk. & M.F.Newman"
 ]
}

 The dataset includes 47 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057723-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kjub99
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nemesia lanceolata Hiern"
 ]
}

 The dataset includes 35 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057724-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xbudtn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cetraria fastigiata (Delise ex Nyl.) Kärnefelt, Cetraria halei W.L.Culb. & C.F.Culb., Cetraria laii Divakar, A.Crespo & Lumbsch, Cetraria islandica subsp. orientalis (Asah.) Kärnef., Cetraria islandica var. orientalis Asah., Cetraria nigricans Nyl., Cetraria nigricascens (Nyl.) Elenkin, Cetraria nivalis (L.) Ach., Cetraria richardsonii Hook., Cetraria tilesii Ach., Cetrelia cetrarioides (Delise) W.L.Culb. & C.F.Culb., Chaenotheca brunneola (Ach.) Müll.Arg., Chaenotheca ferruginea (Turner ex Sm.) Mig., Chaenotheca gracillima (Vain.) Tibell, Chaenotheca trichialis (Ach.) Hellb., Chaenotheca trichialis (Ach.) Th.Fr., Chaenotheca xyloxena Nádv., Chaenotheca xylogena Nádv., Chaenothecopsis aeruginosa Goward & E.B.Peterson, Chaenothecopsis Vain., Chaenothecopsis consociata (Nádv.) A.F.W.Schmidt, Chaenothecopsis lecanactidis Tibell, Chaenothecopsis nana Tibell, Chaenothecopsis pusiola (Ach.) Vain., Chaenothecopsis pusilla (Ach.) A.F.W.Schmidt, Chaenothecopsis savonica (Räsänen) Tibell, Chaenothecopsis tasmanica Tibell, Chaenothecopsis viridireagens (Nádv.) A.F.W.Schmidt, Cheiromycina petri D.Hawksw. & Poelt, Cirrenalia lichenicola Pérez-Ort., Cladonia P.Browne, 1756, Cladina mitis (Sandst.) Hale & W.Culb., Cladina mitis (Sandst.) Hustich, Cladina mitis (Sandst.) Mong., Cladina mitis Sandst., 1918, Cladonia mitis Sandst., Cladina stellaris (Opiz) Brodo, Cladonia stellaris (Opiz) Pouzar & Vĕzda, Cladonia alpestris (L.) Rabenh., Cladina alpestris (L.) Nyl., Cladonia conista (Nyl.) Robbins, Cladonia conista Robbins ex A.Evans, Cladonia conistea (Delise) Asahina, Cladonia cristatella Tuck., Cladonia crispatula (Nyl.) Ahti, Cladonia farinacea (Vain.) A.Evans, Cladonia impexa Harm., Cladina impexa (Harm.) B.de Lesd., Cladonia kanewskii Oxner, Cladonia lepidota Nyl., Cladonia lepidula Kremp., Cladonia multiformis G.K.Kerr., Cladonia multiformis G.Merr., 1908, Cladonia norrlinii Vain., Cladonia pseudorangiformis Asah., Cladonia straminea (Sommerf.) Flörke, Cladonia straminea (Sommerf.) Fr., Cladonia subcariosa Nyl., Cladonia subcaryana, Cladonia P.Browne, 1756, Cladonia verruculosa (Vainio) Ahti, Cliostomum griffithii (Sm.) Coppins, Cliostomum leprosum (Räsänen) Holien & Tønsberg, Clypeococcum placopsiiphilus Øvst. & D.Hawksw., Coccotrema hahriae T.Sprib. & Tønsberg, Coccotrema pocillarium (Cummings) Brodo, Coelocaulon muricatum (Ach.) J.R.Laundon, Coelocaulon muricatum (Ach.) Eckfeldt, Collema bachmanianum (Fink) Degel., Collema ceraniscum Nyl., Collema fuscovirens (With.) J.R.Laundon)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation, Literature Occurrence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-180 50,-180 55,180 55,180 50,-180 50))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057557-240321170329656/datasets/export for details.
DOI: 10.15468/dl.v996na
title: Occurrence Download

description: A dataset containing 120 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ocotea humblotii Baill."
 ]
}

 The dataset includes 120 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057725-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c322hu
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Musa ingens N.W.Simmonds"
 ]
}

 The dataset includes 37 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057726-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22003/xfel.eu-data-007116-00
title: Pulsed Magnetic Field COMMISSIONING
DOI: 10.22003/xfel.eu-data-005721-00
title: Observation of charge transfer in sliding charge density wave system in a quasi-2D material
DOI: 10.22003/xfel.eu-data-005659-00
title: JINXED: In the footsteps of protein crystal nucleation
DOI: 10.22003/xfel.eu-data-005701-00
title: Polarized femtosecond time-resolved electronic structure of aqueous solutions of vitamin B12
DOI: 10.22003/xfel.eu-data-006922-00
title: LTP - Dynamics of nanoscale phenomena in solids and liquids studied with X-ray Transient Gratings at European XFEL (joint FXE/MID) (derived from 3323)
DOI: 10.15468/dl.qh5k2y
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Meistera trichostachya (Alston) Škorničk. & M.F.Newman"
 ]
}

 The dataset includes 11 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057727-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qgxhja
title: Occurrence Download

description: A dataset containing 103 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nemesia leipoldtii Hiern"
 ]
}

 The dataset includes 103 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057728-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mwfpru
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ocotea involuta Kosterm."
 ]
}

 The dataset includes 33 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057729-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.