cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14272/qfpqagcptokobm-uhfffaoysa-n/chmo0001146
title: 1H--13C heteronuclear single quantum coherence (1H-13C HSQC) ()
title: InChI=1S/C11H15N5O/c1-8(17)15-6-9-7-16(10-4-2-3-5-10)13-11(9)12-14-15/h7,10H,2-6H2,1H3

description: dataset for 1H--13C heteronuclear single quantum coherence (1H-13C HSQC)
DOI: 10.14272/qfpqagcptokobm-uhfffaoysa-n/chmo0001148
title: 1H--13C heteronuclear multiple bond coherence (13C-1H HMBC) ()
title: InChI=1S/C11H15N5O/c1-8(17)15-6-9-7-16(10-4-2-3-5-10)13-11(9)12-14-15/h7,10H,2-6H2,1H3

description: dataset for 1H--13C heteronuclear multiple bond coherence (13C-1H HMBC)
DOI: 10.14272/qfpqagcptokobm-uhfffaoysa-n/chmo0001150
title: 1H--1H correlation spectroscopy (1H-1H COSY) ()
title: InChI=1S/C11H15N5O/c1-8(17)15-6-9-7-16(10-4-2-3-5-10)13-11(9)12-14-15/h7,10H,2-6H2,1H3

description: dataset for 1H--1H correlation spectroscopy (1H-1H COSY)
DOI: 10.14272/qfpqagcptokobm-uhfffaoysa-n/chmo0000563
title: fast-atom bombardment mass spectrometry (FABMS) ()
title: InChI=1S/C11H15N5O/c1-8(17)15-6-9-7-16(10-4-2-3-5-10)13-11(9)12-14-15/h7,10H,2-6H2,1H3

description: dataset for fast-atom bombardment mass spectrometry (FABMS) MS (FAB, Matrix: 3-NBA): m/z (%) = 235 (14) [M+2H]+, 234 (100) [M+H]+, 233 (6) [M]+, 232 (10) [M-H]+, 192 (10), 155 (15), 154 (48), 139 (10), 138 (20), 137 (30), 136 (34), 109 (11), 107 (13), 97 (11), 95 (15), 91 (13).HRMS–FAB (m/z): [M+H]+ calcd for C11H16ON5, 234.1349; found, 234.1350.
DOI: 10.14272/qfpqagcptokobm-uhfffaoysa-n/chmo0000630
title: infrared absorption spectroscopy (IR) ()
title: InChI=1S/C11H15N5O/c1-8(17)15-6-9-7-16(10-4-2-3-5-10)13-11(9)12-14-15/h7,10H,2-6H2,1H3

description: dataset for infrared absorption spectroscopy (IR) IR (ATR, ṽ) = 3370 (vw), 3129 (w), 2970 (w), 2944 (w), 2921 (w), 2873 (w), 1693 (vs), 1656 (w), 1632 (w), 1591 (w), 1538 (vw), 1503 (vw), 1475 (vs), 1456 (w), 1448 (m), 1418 (w), 1374 (vs), 1357 (s), 1332 (vs), 1286 (m), 1248 (w), 1204 (s), 1176 (w), 1159 (w), 1109 (vs), 1052 (m), 1034 (m), 1004 (vs), 953 (vs), 912 (w), 877 (vs), 827 (vs), 741 (m), 722 (s), 623 (m), 594 (w), 578 (vs), 562 (vs), 537 (m), 496 (m), 470 (w), 436 (w), 418 (w), 394 (m) cm–1.
DOI: 10.14272/qfpqagcptokobm-uhfffaoysa-n.1
title: 1-(6-cyclopentyl-4,6-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)ethan-1-one
title: InChI=1S/C11H15N5O/c1-8(17)15-6-9-7-16(10-4-2-3-5-10)13-11(9)12-14-15/h7,10H,2-6H2,1H3

description: This dataset contains experimental data from a sample (InChI=1S/C11H15N5O/c1-8(17)15-6-9-7-16(10-4-2-3-5-10)13-11(9)12-14-15/h7,10H,2-6H2,1H3). The datasets from the following experiments are available: 1H nuclear magnetic resonance spectroscopy (1H NMR) 13C nuclear magnetic resonance spectroscopy (13C NMR) distortionless enhancement with polarization transfer (DEPT) distortionless enhancement with polarization transfer (DEPT) 1H--13C heteronuclear single quantum coherence (1H-13C HSQC) 1H--13C heteronuclear multiple bond coherence (13C-1H HMBC) 1H--1H correlation spectroscopy (1H-1H COSY) fast-atom bombardment mass spectrometry (FABMS) infrared absorption spectroscopy (IR)
DOI: 10.15468/dl.q4xyvg
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Ledermanniella letouzeyi C.Cusset"
 ]
}

 The dataset includes 15 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021947-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8xdu5p
title: Occurrence Download

description: A dataset containing 398 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Machine Observation",
 "PublishingOrg is 750a8724-fa66-4c27-b645-bd58ac5ee010",
 "TaxonKey is Canis lupus Linnaeus, 1758"
 ]
}

 The dataset includes 398 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021948-250402121839773/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.7145891
title: Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

description: Age-related changes in DNA methylation were observed in cross-sectional studies, but longitudinal evidence is still limited. Here, we aimed to characterize longitudinal age-related methylation patterns using 1011 blood samples collected from 385 Swedish twins (age at entry: mean 69 and standard deviation 9.7, 73 monozygotic and 96 dizygotic pairs) up to five times (mean 2.6) over 20 years (mean 8.7). We identified 1316 age-associated methylation sites (<i>P&lt;</i>1.3×10<sup>−7</sup>) using a longitudinal epigenome-wide association study design. We measured how estimated cellular compositions changed with age and how much they confounded the age effect. We validated the results in two independent longitudinal cohorts, where 118 CpGs were replicated in Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS, 390 samples) (<i>P&lt;</i>3.9×10<sup>−5</sup>), 594 in Lothian Birth Cohort (LBC, 3018 samples) (<i>P&lt;</i>5.1×10<sup>−5</sup>) and 63 in both. Functional annotation of age-associated CpGs showed enrichment in CCCTC-binding factor (CTCF) and other transcription factor binding sites. We further investigated genetic influences on methylation and found no interaction between age and genetic effects in the 1316 age-associated CpGs. Moreover, in the same CpGs, methylation differences within twin pairs increased with 6.4% over 10 years, where monozygotic twins had smaller intra-pair differences than dizygotic twins. In conclusion, we show that age-related methylation changes persist in a longitudinal perspective, and are fairly stable across cohorts. The changes are under genetic influence, although this effect is independent of age. Moreover, methylation variability increase over time, especially in age-associated CpGs, indicating the increase of environmental contributions on DNA methylation with age.
DOI: 10.6084/m9.figshare.7145891.v1
title: Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

description: Age-related changes in DNA methylation were observed in cross-sectional studies, but longitudinal evidence is still limited. Here, we aimed to characterize longitudinal age-related methylation patterns using 1011 blood samples collected from 385 Swedish twins (age at entry: mean 69 and standard deviation 9.7, 73 monozygotic and 96 dizygotic pairs) up to five times (mean 2.6) over 20 years (mean 8.7). We identified 1316 age-associated methylation sites (<i>P&lt;</i>1.3×10<sup>−7</sup>) using a longitudinal epigenome-wide association study design. We measured how estimated cellular compositions changed with age and how much they confounded the age effect. We validated the results in two independent longitudinal cohorts, where 118 CpGs were replicated in Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS, 390 samples) (<i>P&lt;</i>3.9×10<sup>−5</sup>), 594 in Lothian Birth Cohort (LBC, 3018 samples) (<i>P&lt;</i>5.1×10<sup>−5</sup>) and 63 in both. Functional annotation of age-associated CpGs showed enrichment in CCCTC-binding factor (CTCF) and other transcription factor binding sites. We further investigated genetic influences on methylation and found no interaction between age and genetic effects in the 1316 age-associated CpGs. Moreover, in the same CpGs, methylation differences within twin pairs increased with 6.4% over 10 years, where monozygotic twins had smaller intra-pair differences than dizygotic twins. In conclusion, we show that age-related methylation changes persist in a longitudinal perspective, and are fairly stable across cohorts. The changes are under genetic influence, although this effect is independent of age. Moreover, methylation variability increase over time, especially in age-associated CpGs, indicating the increase of environmental contributions on DNA methylation with age.
DOI: 10.6084/m9.figshare.19204521
title: Additional file 1 of Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes

description: Additional file 1.
DOI: 10.6084/m9.figshare.19204521.v1
title: Additional file 1 of Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes

description: Additional file 1.
DOI: 10.5281/zenodo.5042438
title: Event logs containing deletions

description: Supplemental dataset containing deletions.
DOI: 10.5281/zenodo.5042439
title: Event logs containing deletions

description: Supplemental dataset containing deletions.
DOI: 10.6084/m9.figshare.19728824
title: Additional file 2 of Efficacy of first-line treatments in the elderly and non-elderly patients with advanced epidermal growth factor receptor mutated, non-small cell lung cancer: a network meta-analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.19728824.v1
title: Additional file 2 of Efficacy of first-line treatments in the elderly and non-elderly patients with advanced epidermal growth factor receptor mutated, non-small cell lung cancer: a network meta-analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.5573155
title: High throughput <i>in silico</i> identification and characterization of <i>Plasmodium falciparum</i> PRL phosphatase inhibitors

description: Kinases and phosphatases are involved in many essential processes in <i>Plasmodium</i> lifecycle. Among the identified 67 <i>Plasmodium falciparum</i> phosphatases, Phosphatase of Regenerating Liver (PRL) family protein homolog, PfPRL, is an essential parasite tyrosine phosphatase. PfPRL is shown to be prenylated, secreted, and involved in the host invasion process. In the present study, a structure-based high throughput <i>in silico</i> screening of PfPRL binders, using ChEMBL-NTD compounds lead to the identification of nine compounds based on binding energy, Lipinski rule of five, and QED score. The most of the shortlisted compounds are known to inhibit parasite growth at a concentration (EC50) ≤2 μm in <i>in vitro P. falciparum</i> culture assays. MD simulations were carried out on the shortlisted nine potential enzyme–inhibitor complexes to analyze specificity, stability, and to calculate the free binding energies of the complexes. The study identifies PfPRL as one of the potential drug targets for selected ChEMBL-NTD compounds that may be exploited as a scaffold to develop novel antimalarials.
DOI: 10.5281/zenodo.3989590
title: Simplified Event Logs for Sepsis Patient Trajectories

description: This dataset contains a simplified excerpt from a real event log that tracks the trajectories of patients admitted to a hospital to be treated for sepsis, a life-threatening condition. The log has been recorded by the Enterprise Resource Planning of the hospital. Additionally, the dataset contains three synthetic logs that increase the number of trajectories within the original log timespan, while maintaining other statistical characteristics.


In total, the dataset contains four files in .zip format and a companion that describes the statistical method used to synthesize the logs as well as the dataset content in detail. The dataset can be used in testing the performance of event-based process-mining and log (runtime) monitoring tools against an increasing load of events.
DOI: 10.6084/m9.figshare.5573155.v1
title: High throughput <i>in silico</i> identification and characterization of <i>Plasmodium falciparum</i> PRL phosphatase inhibitors

description: Kinases and phosphatases are involved in many essential processes in <i>Plasmodium</i> lifecycle. Among the identified 67 <i>Plasmodium falciparum</i> phosphatases, Phosphatase of Regenerating Liver (PRL) family protein homolog, PfPRL, is an essential parasite tyrosine phosphatase. PfPRL is shown to be prenylated, secreted, and involved in the host invasion process. In the present study, a structure-based high throughput <i>in silico</i> screening of PfPRL binders, using ChEMBL-NTD compounds lead to the identification of nine compounds based on binding energy, Lipinski rule of five, and QED score. The most of the shortlisted compounds are known to inhibit parasite growth at a concentration (EC50) ≤2 μm in <i>in vitro P. falciparum</i> culture assays. MD simulations were carried out on the shortlisted nine potential enzyme–inhibitor complexes to analyze specificity, stability, and to calculate the free binding energies of the complexes. The study identifies PfPRL as one of the potential drug targets for selected ChEMBL-NTD compounds that may be exploited as a scaffold to develop novel antimalarials.
DOI: 10.6084/m9.figshare.8194646
title: Efficacy of hyperthermic intraperitoneal chemotherapy in patients with epithelial ovarian cancer: a meta-analysis

description: <b>Objective:</b> The role of hyperthermic intraperitoneal chemotherapy (HIPEC) in epithelial ovarian cancer (EOC) is still controversial. Present analysis aims to evaluate the survival benefit of HIPEC in treatment of EOC patients. <b>Methods:</b> Articles related to ‘HIPEC’ and ‘ovarian cancer’ were comprehensively searched in four databases (PubMed, EMBASE, MEDLINE and Cochrane Library) up to 4 February 2018. Eligible studies were identified depending on the selection criteria. The survival outcome and adverse events were collected. The relationship between HIPEC and survival of EOC was assessed using random-effects models. <b>Results:</b> A total of 1464 patients from 17 trials were subjected to analysis. The pooled results showed that HIPEC significantly improved overall survival (OS, HR = 0.50, 95% CI 0.36–0.69; <i>p</i> = 0.000) and progression-free survival (PFS, HR = 0.57, 95% CI 0.47–0.69; <i>p</i> = 0.000) among EOC patients when compared with no HIPEC controls. Similar results were observed in each year rate of survival. Subgroup analysis didn’t lead to the opposite results, except no significant increased 1-year of OS in primary EOC and 1- and 2-year of PFS in recurrent EOC treated with HIPEC were observed. No significant difference existed in the adverse events and mortality between HIPEC and no HIPEC. <b>Conclusions:</b> HIPEC is associated with improved OS and PFS in both primary and recurrent EOC. However, no significant increased 1- and 2-year of PFS were reached in recurrent EOC treated with HIPEC. Further prospective randomized controlled trials are warranted.
DOI: 10.6084/m9.figshare.19728994
title: Mating loci and meiosis genes and CDS of Urocystis primulicola

description: Core meiosis genes/CDS were manually annotated in the genome of <em>Urocystis primulicola</em> using the respective genes from <em>Ustilago maydis</em>  (Gioti et al., 2013). Mating loci and mating genes/CDS were identified using the mating genes of <em>Ustilago maydis</em> and <em>Sporisorium reilianum</em>.
The dataset contains the sequences in GenBank format for the meiosis genes and both mating loci conserved in Ustilaginomycetes.
This dataset was generated in the study described in the unpublished manuscript "Comparative genomics of smut fungi suggest the ability of meiosis and mating in asexual species of the genus <em>Pseudozyma</em> (Ustilaginales)". Accession numbers of reference genes are cited in the manuscript.
Tblastn was used to identify the loci in the genome, and multiple sequence alignments (MUSCLE) of the respective reference gene and CDS with the suspected locus were used to identify the reading frames and intron positions.
DOI: 10.5281/zenodo.10677769
title: Palaungic data recordings

description: Palaungic recordings referenced in https://github.com/JeremyCollinsMPI/Thesis-Supplementary-Materials/blob/master/Chapter%204/analyses.txt.
DOI: 10.5281/zenodo.10677770
title: Palaungic data recordings

description: Palaungic recordings referenced in https://github.com/JeremyCollinsMPI/Thesis-Supplementary-Materials/blob/master/Chapter%204/analyses.txt.
DOI: 10.6084/m9.figshare.19204716
title: Supplement Information0220.docx

description: Supplement 1
DOI: 10.6084/m9.figshare.19204716.v1
title: Supplement Information0220.docx

description: Supplement 1
DOI: 10.25402/fsg.22350568
title: A sensitive, robust and high-throughput isotope dilution LC–MS/MS method for quantifying three folate forms in serum: Supplementary data

description: This study aimed to establish an isotope dilution LC–MS/MS method for the determination of folic acid,
5-formyltetrahydrofolate and 5-methyltetrahydrofolate in human serum. This method was then used to
quantify these three folate forms in the healthy adult population and supplement users. A stable 96-
well solid-phase extraction system was used to prepare serum samples. The highly sensitive method was
established using a Shimadzu LCMS-8060NX. The linearity was good in the range of 0.1–10 nmol/l for
folic acid and 5-formyltetrahydrofolate and 1.0–100 nmol/l for 5-methyltetrahydrofolate. The accuracy
and precision were good. The method was sensitive, robust and high-throughput and could be used for
the routine clinical monitoring of these three folate forms in the Chinese population.
DOI: 10.25402/fsg.22350568.v1
title: A sensitive, robust and high-throughput isotope dilution LC–MS/MS method for quantifying three folate forms in serum: Supplementary data

description: This study aimed to establish an isotope dilution LC–MS/MS method for the determination of folic acid,
5-formyltetrahydrofolate and 5-methyltetrahydrofolate in human serum. This method was then used to
quantify these three folate forms in the healthy adult population and supplement users. A stable 96-
well solid-phase extraction system was used to prepare serum samples. The highly sensitive method was
established using a Shimadzu LCMS-8060NX. The linearity was good in the range of 0.1–10 nmol/l for
folic acid and 5-formyltetrahydrofolate and 1.0–100 nmol/l for 5-methyltetrahydrofolate. The accuracy
and precision were good. The method was sensitive, robust and high-throughput and could be used for
the routine clinical monitoring of these three folate forms in the Chinese population.
DOI: 10.6084/m9.figshare.19204862
title: Ultrasound-targeted microbubble destruction-mediated miR-144-5p overexpression enhances the anti-tumor effect of paclitaxel on thyroid carcinoma by targeting STON2

description: The effects of miR-144-5p and paclitaxel (PTX) on thyroid carcinoma were less explored. Thus, we investigated the effects of miR-144-5p and PTX on thyroid carcinoma. The expression and target gene of miR-144-5p in thyroid carcinoma were analyzed by bioinformatics, y qRT-PCR and dual-luciferase reporter assay. After the transfection mediated by ultrasound-targeted microbubble destruction (UTMD) or liposome, or the treatment of PTX, the viability, proliferation, migration, and invasion of thyroid carcinoma cells were detected by MTT, colony formation, wound-healing, and transwell assays. The expressions of miR-144-5p, STON2, MMP-9, E-cadherin, and N-cadherin in cells were calculated via qRT-PCR or Western blotting. After a subcutaneous-xenotransplant tumor model was established using BALB/c nude mice and further treated with PTX and UTMD-mediated miR-144-5p, the volume, weight, and Ki67 level of tumor were recorded or evaluated by immunohistochemical assays. MiR-144-5p, which was low-expressed in thyroid carcinoma, directly down-regulated STON2 level. MiR-144-5p overexpression and PTX inhibited the viability, proliferation, migration, and invasion of thyroid carcinoma cells, while miR-144-5p silencing caused the opposite results. MiR-144-5p overexpression and PTX further up-regulated E-cadherin level and down-regulated those of MMP-9 and N-cadherin in thyroid carcinoma cells. STON2 overexpression reversed the effects of miR-144-5p overexpression.. MiR-144-5p overexpression enhanced the inhibiting effect of PTX on tumor volume, weight, and Ki67 level of xenotransplant tumor, and the effects of UTMD-mediated miR-144-5p overexpression were stronger than those mediated by liposome. Collectively, UTMD-mediated miR-144-5p overexpression enhanced the anti-tumor effect of PTX on thyroid carcinoma by targeting STON2.
DOI: 10.6084/m9.figshare.19204862.v1
title: Ultrasound-targeted microbubble destruction-mediated miR-144-5p overexpression enhances the anti-tumor effect of paclitaxel on thyroid carcinoma by targeting STON2

description: The effects of miR-144-5p and paclitaxel (PTX) on thyroid carcinoma were less explored. Thus, we investigated the effects of miR-144-5p and PTX on thyroid carcinoma. The expression and target gene of miR-144-5p in thyroid carcinoma were analyzed by bioinformatics, y qRT-PCR and dual-luciferase reporter assay. After the transfection mediated by ultrasound-targeted microbubble destruction (UTMD) or liposome, or the treatment of PTX, the viability, proliferation, migration, and invasion of thyroid carcinoma cells were detected by MTT, colony formation, wound-healing, and transwell assays. The expressions of miR-144-5p, STON2, MMP-9, E-cadherin, and N-cadherin in cells were calculated via qRT-PCR or Western blotting. After a subcutaneous-xenotransplant tumor model was established using BALB/c nude mice and further treated with PTX and UTMD-mediated miR-144-5p, the volume, weight, and Ki67 level of tumor were recorded or evaluated by immunohistochemical assays. MiR-144-5p, which was low-expressed in thyroid carcinoma, directly down-regulated STON2 level. MiR-144-5p overexpression and PTX inhibited the viability, proliferation, migration, and invasion of thyroid carcinoma cells, while miR-144-5p silencing caused the opposite results. MiR-144-5p overexpression and PTX further up-regulated E-cadherin level and down-regulated those of MMP-9 and N-cadherin in thyroid carcinoma cells. STON2 overexpression reversed the effects of miR-144-5p overexpression.. MiR-144-5p overexpression enhanced the inhibiting effect of PTX on tumor volume, weight, and Ki67 level of xenotransplant tumor, and the effects of UTMD-mediated miR-144-5p overexpression were stronger than those mediated by liposome. Collectively, UTMD-mediated miR-144-5p overexpression enhanced the anti-tumor effect of PTX on thyroid carcinoma by targeting STON2.
DOI: 10.6084/m9.figshare.9767783
title: High-throughput sequencing reveals biofluid exosomal miRNAs associated with immunity in pigs

description: Large numbers of miRNAs are found in biofluid exosomes. We isolated ~50–200 nm diameter exosomes from four types of porcine biofluid (urine, plasma, semen, and bile) using serial centrifugation and ultracentrifugation procedures. A total of 42.15 M raw data were generated from four small RNA libraries. This produced 40.17 M map-able sequences, of which we identified 204 conserved miRNAs, and 190 novel candidate miRNAs. Furthermore, we identified 34 miRNAs specifically expressed in only one library, all with well-characterized immune-related functions. A set of five universally abundant miRNAs (miR-148a-3p, miR-21-5p, let-7f-5p, let-7i-5p, and miR-99a-5p) across all four biofluids was also found. Function enrichment analysis revealed that the target genes of the five ubiquitous miRNAs are primarily involved in immune and RNA metabolic processes. In summary, our findings suggest that porcine biofluid exosomes contain a large number of miRNAs, many of which may be crucial regulators of the immune system. High-throughput sequencing evidence indicates that porcine biofluid exosomes contain a large number of miRNAs, many of which may be crucial regulators of the immune system.