cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/y2zp5xx2hg.2
title: AutoSpectral: Difficult cell controls

description: Data prepared for the 2024 Babraham Spectral Symposium.

Mouse samples stained with an unoptimized panel intended to create difficulties in spectral unmixing. Acquired on a 5-laser Cytek Aurora. In this set, only cell controls are provided for single colour stains and minimal effort has been made to unmix the data well. Unstained samples of spleen, lung and brain are provided for autofluorescence extraction options.
DOI: 10.17632/w2s8wdm3r5
title: Lammps-Model-LiYanfeng

description: Effect of surface wettability on thermal conductance of Cu-water interface: A molecular dynamics study-lammps
DOI: 10.17632/w2s8wdm3r5.1
title: Lammps-Model-LiYanfeng

description: Effect of surface wettability on thermal conductance of Cu-water interface: A molecular dynamics study-lammps
DOI: 10.17632/msd3t29rfc.2
title: Satellitosis/in-transit metastasis in cutaneous squamous cell carcinoma: Risk factors and the prognostic significance

description: Supplementary Tables S1-S3
DOI: 10.15468/dl.p5t6b6
title: Occurrence Download

description: A dataset containing 28663 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Symphyotrichum novi-belgii"
 ]
}

 The dataset includes 28663 records from 562 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012447-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rthf3y
title: Occurrence Download

description: A dataset containing 33223 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Silene dioica (L.) Clairv.",
 "MediaType is Image",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 33223 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0409349-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a98emp
title: Occurrence Download

description: A dataset containing 226 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aiouea Aubl."
 ]
}

 The dataset includes 226 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0081139-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.co9xd3
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ceratozamia mixeorum Chemnick, T.J.Greg. & Salas-Mor."
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000449-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nadesw
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Guatteria darienensis Susana Arias & Maas"
 ]
}

 The dataset includes 117 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0134681-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9hyegt
title: Occurrence Download

description: A dataset containing 63145 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Varanus Merrem, 1820"
 ]
}

 The dataset includes 63145 records from 203 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013302-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tmzqtu
title: Occurrence Download

description: A dataset containing 63108300 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 63108300 records from 4196 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004794-240202131308920/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.20673428
title: Additional file 1 of Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma

description: Additional file 1. Result of H3K9me3 Peaks.
DOI: 10.25402/fsg.20157026
title: Supplementary Tables – Methylated ZNF582 as a triage marker for occult cervical cancer and advanced cervical intraepithelial neoplasia

description: Appendix A:   
<strong>The positive rates of four detection methods in different cervical pathological stages</strong>
<br>
<strong>Appendix B:</strong>
 <strong>The positive rates of </strong><em><strong>ZNF582m</strong></em><strong> and </strong><em><strong>PAX1m</strong></em><strong> in different cervical lesions</strong>
DOI: 10.6084/m9.figshare.12292829
title: Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors

description: The SARS-CoV-2 is the causative agent of COVID-19 pandemic that is causing a global health emergency. The lack of targeted therapeutics and limited treatment options have triggered the scientific community to develop new vaccines or small molecule therapeutics against various targets of SARS-CoV-2. The main protease (Mpro) is a well characterized and attractive drug target because of its crucial role in processing of the polyproteins which are required for viral replication. In order to provide potential lead molecules against the Mpro for clinical use, we docked a set of 65 bioactive molecules of Tea plant followed by exploration of the vast conformational space of protein-ligand complexes by long term molecular dynamics (MD) simulations (1.50 µs). Top three bioactive molecules (Oolonghomobisflavan-A, Theasinensin-D, and Theaflavin-3-O-gallate) were selected by comparing their docking scores with repurposed drugs (Atazanavir, Darunavir, and Lopinavir) against SARS-CoV-2. Oolonghomobisflavan-A molecule showed a good number of hydrogen bonds with Mpro and higher MM-PBSA binding energy when compared to all three repurposed drug molecules. during the time of simulation. This study showed Oolonghomobisflavan-A as a potential bioactive molecule to act as an inhibitor for the Mpro of SARS-CoV-2. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12292829.v2
title: Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors

description: The SARS-CoV-2 is the causative agent of COVID-19 pandemic that is causing a global health emergency. The lack of targeted therapeutics and limited treatment options have triggered the scientific community to develop new vaccines or small molecule therapeutics against various targets of SARS-CoV-2. The main protease (Mpro) is a well characterized and attractive drug target because of its crucial role in processing of the polyproteins which are required for viral replication. In order to provide potential lead molecules against the Mpro for clinical use, we docked a set of 65 bioactive molecules of Tea plant followed by exploration of the vast conformational space of protein-ligand complexes by long term molecular dynamics (MD) simulations (1.50 µs). Top three bioactive molecules (Oolonghomobisflavan-A, Theasinensin-D, and Theaflavin-3-O-gallate) were selected by comparing their docking scores with repurposed drugs (Atazanavir, Darunavir, and Lopinavir) against SARS-CoV-2. Oolonghomobisflavan-A molecule showed a good number of hydrogen bonds with Mpro and higher MM-PBSA binding energy when compared to all three repurposed drug molecules. during the time of simulation. This study showed Oolonghomobisflavan-A as a potential bioactive molecule to act as an inhibitor for the Mpro of SARS-CoV-2. Communicated by Ramaswamy H. Sarma
DOI: 10.25402/fsg.20157026.v1
title: Supplementary Tables – Methylated ZNF582 as a triage marker for occult cervical cancer and advanced cervical intraepithelial neoplasia

description: Appendix A:   
<strong>The positive rates of four detection methods in different cervical pathological stages</strong>
<br>
<strong>Appendix B:</strong>
 <strong>The positive rates of </strong><em><strong>ZNF582m</strong></em><strong> and </strong><em><strong>PAX1m</strong></em><strong> in different cervical lesions</strong>
DOI: 10.6084/m9.figshare.12293066
title: Two new Yb(III)-based coordination polymers: structural characterization and treatment effect on femur fracture nonunion combined with PRP and n-HA/PA66

description: Two novel coordination polymers based on Yb(III) ion as the metal ions have been successfully prepared by using two C<sub>3</sub>-symmetrical ligands via a solvothermal synthesis approach, and their chemical formulae are [Yb<sub>1.5</sub>(TAPB)<sub>1.5</sub>(DMF)]·9DMF}<sub>n</sub> (<b>1</b>, TAPB  =  4,4′,4″-(triazine-2,4,6-triyl-tris-(benzene-4,1-diyl)) tribenzoate) and [Yb(TCBPA)·DMF]<sub>n</sub> (<b>2</b>, H<sub>3</sub>TCBPA = tris(4′-carboxybiphenyl)amine). Furthermore, the two complexes were applicated for the fracture nonunion treatment combined with plate let rich plasma (PRP) and n-HA/Polyamide66 (n-HA/PA66). Firstly, the Rat Femur Fracture Nonunion Model was constructed, and compounds <b>1</b> or <b>2</b> was used for indicated treatment combined with PRP and n-HA/PA66, the enzyme linked immunosorbent assay detection was used for the osteocalcin concentration measurement. The reverse transcription-polymerase chain reaction was carried out to determine <i>alp</i> and <i>Runx2</i> relative expression level.
DOI: 10.6084/m9.figshare.12655585
title: Additional file 10 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 10. Supplementary Table 4. Differentially expressed genes between patients and controls.
DOI: 10.6084/m9.figshare.12655585.v1
title: Additional file 10 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 10. Supplementary Table 4. Differentially expressed genes between patients and controls.
DOI: 10.6084/m9.figshare.22778351.v1
title: Design and simulation of resonant cavity-enhanced infrared detector incorporating an ultra-thin type-II superlattice

description: Raw data and graphs obtained from simulation
DOI: 10.6084/m9.figshare.12655618
title: Additional file 7 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 7 Supplementary Table 1. Regions with different H3K27ac occupancy in patients compared with the control group (adjusted p value &lt; 0.05).
DOI: 10.6084/m9.figshare.12655624
title: Additional file 9 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 9. Supplementary Table 3. a Genes in the vicinity of hyperacetylated regions using a ± 5 kb window. b Genes in the vicinity of hypoacetylated regions using a ± 5 kb window.
DOI: 10.6084/m9.figshare.22778682
title: The effects of cardiometabolic factors on the association between serum uric acid and risk of all-cause mortality in adults with congestive heart failure

description: Serum uric acid (SUA) has been shown to increase all-cause mortality from cardiovascular disease. However, limited studies have examined the mediating effect of dyslipidemia, hyperglycemia, or hypertension on the association between SUA and all-cause mortality in patients with congestive heart failure (CHF). Participants in the present investigation were 620 US adults with CHF from the NHANES database (1999–2014). The relationship between SUA and all-cause mortality was evaluated utilizing multivariable Cox proportional hazards models. Additionally, the nonlinearity between SUA and mortality was investigated utilizing Restricted Cubic Splines (RCS) and 2-piecewise Cox proportional hazards models. Finally, the mediating role of cardiometabolic factors on the relationship between SUA and all-cause mortality was investigated utilizing the mediation analysis. During a mean follow-up of 7.6 years, 391 (63.1%) all-cause deaths occurred. Furthermore, we found a U-shaped association between SUA and all-cause mortality. The inflection point for the RCS curve was found at a SUA level of 363 umol/L. The hazard ratios (95% confidence intervals) for all-cause mortality were 0.998 (0.995–1.000) and 1.003 (1.002–1.005) to the left and right of the inflection point, respectively. This U-shaped association was also observed in both subgroups of sex and age. Moreover, the effect of SUA on all-cause mortality was not mediated by hypertension, hyperglycemia, or dyslipidemia (all P-values&gt;0.05). The association between SUA level and all-cause mortality followed a U-shaped curve, and this association was not mediated by hypertension, hyperglycemia, or dyslipidemia.
DOI: 10.5281/zenodo.10657576
title: LCDM_nonflat_3x2pt
DOI: 10.5281/zenodo.10657577
title: LCDM_nonflat_3x2pt
DOI: 10.6084/m9.figshare.12655588
title: Additional file 11 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 11. Supplementary Table 5. Identified transcription binding motifs from differentially acetylated regions.
DOI: 10.6084/m9.figshare.22778682.v1
title: The effects of cardiometabolic factors on the association between serum uric acid and risk of all-cause mortality in adults with congestive heart failure

description: Serum uric acid (SUA) has been shown to increase all-cause mortality from cardiovascular disease. However, limited studies have examined the mediating effect of dyslipidemia, hyperglycemia, or hypertension on the association between SUA and all-cause mortality in patients with congestive heart failure (CHF). Participants in the present investigation were 620 US adults with CHF from the NHANES database (1999–2014). The relationship between SUA and all-cause mortality was evaluated utilizing multivariable Cox proportional hazards models. Additionally, the nonlinearity between SUA and mortality was investigated utilizing Restricted Cubic Splines (RCS) and 2-piecewise Cox proportional hazards models. Finally, the mediating role of cardiometabolic factors on the relationship between SUA and all-cause mortality was investigated utilizing the mediation analysis. During a mean follow-up of 7.6 years, 391 (63.1%) all-cause deaths occurred. Furthermore, we found a U-shaped association between SUA and all-cause mortality. The inflection point for the RCS curve was found at a SUA level of 363 umol/L. The hazard ratios (95% confidence intervals) for all-cause mortality were 0.998 (0.995–1.000) and 1.003 (1.002–1.005) to the left and right of the inflection point, respectively. This U-shaped association was also observed in both subgroups of sex and age. Moreover, the effect of SUA on all-cause mortality was not mediated by hypertension, hyperglycemia, or dyslipidemia (all P-values&gt;0.05). The association between SUA level and all-cause mortality followed a U-shaped curve, and this association was not mediated by hypertension, hyperglycemia, or dyslipidemia.
DOI: 10.6084/m9.figshare.7050086
title: Heterothallic sexual reproduction in three canker-inducing tree pathogens within the <i>Fusarium torreyae</i> species complex

description: <i>Fusarium zanthoxyli</i> and <i>F. continuum</i> are sister taxa that are the etiological agents of canker disease of prickly ash (<i>Zanthoxylum bungeanum</i>) in northern China. These two pathogens, together with <i>F. torreyae</i>, the causal agent of canker disease of the critically endangered conifer Florida torreya (<i>Torreya taxifolia</i>) from northern Florida and southwestern Georgia, constitute a novel clade, the <i>F. torreyae</i> species complex. To assess their reproductive mode, a polymerase chain reaction (PCR) assay targeting the <i>MAT1-1</i> and <i>MAT1-2</i> idiomorphs was designed and validated, using <i>MAT</i> sequences mined from the whole-genome sequence of the three <i>F. torreyae</i> clade pathogens and several closely related fusaria. Results of the <i>MAT</i> idiomorph PCR assay indicated that isolates of the three pathogens were <i>MAT1-1</i> or <i>MAT1-2</i>. When <i>MAT1-1</i> and <i>MAT1-2</i> isolates of each species were crossed on carrot agar, all of the <i>F. zanthoxyli</i> (N = 30) and <i>F. continuum</i> (N = 3) isolates tested were female fertile, yielding mature perithecia with viable ascospores. By comparison, only one pairing of the five different isolates of <i>F. torreyae</i> produced perithecia; however, the majority of the asci in this cross aborted or produced fewer than eight ascospores. Of the three temperatures tested (i.e., 22, 25, and 27 C), the optimal temperature for perithecium production was 22–25 C in <i>F. zanthoxyli</i> and 25 C in <i>F. continuum</i> and <i>F. torreyae</i>. Ascospore progeny from three separate crosses of <i>F. zanthoxyli</i> and <i>F. continuum</i> and one cross of <i>F. torreyae</i> were genotyped to assess whether they were the products of genetic recombination and sexual reproduction. Genotyping of 34–40 progeny from the <i>F. zanthoxyli</i> and <i>F. continuum</i> crosses confirmed that they were the products of sexual reproduction. However, only 36% of the progeny in the <i>F. torreyae</i> cross were recombinant, which was roughly half of the nonparental progeny expected with three markers segregating.
DOI: 10.6084/m9.figshare.7050086.v1
title: Heterothallic sexual reproduction in three canker-inducing tree pathogens within the <i>Fusarium torreyae</i> species complex

description: <i>Fusarium zanthoxyli</i> and <i>F. continuum</i> are sister taxa that are the etiological agents of canker disease of prickly ash (<i>Zanthoxylum bungeanum</i>) in northern China. These two pathogens, together with <i>F. torreyae</i>, the causal agent of canker disease of the critically endangered conifer Florida torreya (<i>Torreya taxifolia</i>) from northern Florida and southwestern Georgia, constitute a novel clade, the <i>F. torreyae</i> species complex. To assess their reproductive mode, a polymerase chain reaction (PCR) assay targeting the <i>MAT1-1</i> and <i>MAT1-2</i> idiomorphs was designed and validated, using <i>MAT</i> sequences mined from the whole-genome sequence of the three <i>F. torreyae</i> clade pathogens and several closely related fusaria. Results of the <i>MAT</i> idiomorph PCR assay indicated that isolates of the three pathogens were <i>MAT1-1</i> or <i>MAT1-2</i>. When <i>MAT1-1</i> and <i>MAT1-2</i> isolates of each species were crossed on carrot agar, all of the <i>F. zanthoxyli</i> (N = 30) and <i>F. continuum</i> (N = 3) isolates tested were female fertile, yielding mature perithecia with viable ascospores. By comparison, only one pairing of the five different isolates of <i>F. torreyae</i> produced perithecia; however, the majority of the asci in this cross aborted or produced fewer than eight ascospores. Of the three temperatures tested (i.e., 22, 25, and 27 C), the optimal temperature for perithecium production was 22–25 C in <i>F. zanthoxyli</i> and 25 C in <i>F. continuum</i> and <i>F. torreyae</i>. Ascospore progeny from three separate crosses of <i>F. zanthoxyli</i> and <i>F. continuum</i> and one cross of <i>F. torreyae</i> were genotyped to assess whether they were the products of genetic recombination and sexual reproduction. Genotyping of 34–40 progeny from the <i>F. zanthoxyli</i> and <i>F. continuum</i> crosses confirmed that they were the products of sexual reproduction. However, only 36% of the progeny in the <i>F. torreyae</i> cross were recombinant, which was roughly half of the nonparental progeny expected with three markers segregating.
DOI: 10.6084/m9.figshare.14390324.v1
title: Transcriptomic analysis of Pinellia ternata (Thunb.) Breit T2 plus line provides insights in host responses resist Pectobacterium carotovorum infection

description: Transcriptome is used to determine the induction response of <i>Pinellia ternata (Thunb.) Breit</i> T2 plus line (abbreviated as <i>PT2P</i> line) infected with <i>Pectobacterium carotovorum</i>. The main objective of the study was to deal with the transcriptome database of <i>PT2P</i> line resistance to soft rot pathogens to provide a new perspective for identifying the resistance-related genes and understanding the molecular mechanism. Results indicated that water soaking and tissue collapse started at 20 h after <i>PT2P</i> line was infected by <i>P. carotovorum</i>. A total of 1360 and 5768 differentially expressed genes (DEGs) were identified at 0 h and 20 h, respectively. After 20 h of infection, growth and development-related pathways were inhibited. Meanwhile, DEGs were promoted the colonization of <i>P. carotovorum</i> pathogens in specific cell wall modification processes at the early infected stage. A shift to a defensive response was triggered at 0 h. A large number of DEGs were mainly up-controlled at 20 h and were substantially used in the pathogen recognition and the introduction of signal transformation cascades, secondary metabolites biosynthesis, pathogenic proteins activation, transcription aspects and numerous transporters. Furthermore, our data provided novel insights into the transcript reprogramming of <i>PT2P</i> line in response to <i>P. carotovorum</i> infestation.
DOI: 10.6084/m9.figshare.12655624.v1
title: Additional file 9 of H3K27ac acetylome signatures reveal the epigenomic reorganization in remodeled non-failing human hearts

description: Additional file 9. Supplementary Table 3. a Genes in the vicinity of hyperacetylated regions using a ± 5 kb window. b Genes in the vicinity of hypoacetylated regions using a ± 5 kb window.