cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19227938
title: Global, regional and national burden of non-Hodgkin lymphoma from 1990 to 2017: estimates from global burden of disease study in 2017

description: Non-Hodgkin lymphoma (NHL) is a common B/NK/T cell lymphoma. We collected detailed data about the incidence and mortality of NHL from Global Burden of Disease (GBD) Study in 2017 and extensively assessed the disease burden of NHL at the global level and also analysed its current trends according to sex, age, socio-demographic index (SDI), country and region. By obtaining relevant data from Global Burden of Disease Study in 2017, estimated annual percentage changes (EAPCs) of age-standardized rate (ASR) were calculated to assess the current trends of the rate of incidence and mortality. Globally, ASR of incidence in NHL was increased while ASR of mortality and its annual percentage change was relatively stable. EAPCs in the incidence of NHL decreased in the low SDI regions but increased in the high SDI regions. The ratio of male to female mortalities was the highest in the 50–69-year-old age group, especially in the middle and middle-high SDI regions. The incidence of NHL was increased globally, whereas the deaths and its annual percentage change were relatively stable from 1990 to 2017.Key messagesAge-standardized rate (ASR) of incidence in NHL was increased globally from 1990 to 2017.ASR of mortality and its annual percentage change in NHL were relatively stable globally from 1990 to 2017.Estimated annual percentage changes (EAPCs) in the incidence of NHL decreased in the low socio-demographic index (SDI) regions but increased in the high SDI regions. Age-standardized rate (ASR) of incidence in NHL was increased globally from 1990 to 2017. ASR of mortality and its annual percentage change in NHL were relatively stable globally from 1990 to 2017. Estimated annual percentage changes (EAPCs) in the incidence of NHL decreased in the low socio-demographic index (SDI) regions but increased in the high SDI regions.
DOI: 10.6084/m9.figshare.10315043
title: MOESM6 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 6: Data S4. Different alternative splicing events in grape leaves predicted by ASprofile software.
DOI: 10.6084/m9.figshare.10315043.v1
title: MOESM6 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 6: Data S4. Different alternative splicing events in grape leaves predicted by ASprofile software.
DOI: 10.6084/m9.figshare.10315049
title: MOESM7 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 7: Data S5. Statistics of isoform number for gene underwent alternative splicing.
DOI: 10.6084/m9.figshare.19227938.v1
title: Global, regional and national burden of non-Hodgkin lymphoma from 1990 to 2017: estimates from global burden of disease study in 2017

description: Non-Hodgkin lymphoma (NHL) is a common B/NK/T cell lymphoma. We collected detailed data about the incidence and mortality of NHL from Global Burden of Disease (GBD) Study in 2017 and extensively assessed the disease burden of NHL at the global level and also analysed its current trends according to sex, age, socio-demographic index (SDI), country and region. By obtaining relevant data from Global Burden of Disease Study in 2017, estimated annual percentage changes (EAPCs) of age-standardized rate (ASR) were calculated to assess the current trends of the rate of incidence and mortality. Globally, ASR of incidence in NHL was increased while ASR of mortality and its annual percentage change was relatively stable. EAPCs in the incidence of NHL decreased in the low SDI regions but increased in the high SDI regions. The ratio of male to female mortalities was the highest in the 50–69-year-old age group, especially in the middle and middle-high SDI regions. The incidence of NHL was increased globally, whereas the deaths and its annual percentage change were relatively stable from 1990 to 2017.Key messagesAge-standardized rate (ASR) of incidence in NHL was increased globally from 1990 to 2017.ASR of mortality and its annual percentage change in NHL were relatively stable globally from 1990 to 2017.Estimated annual percentage changes (EAPCs) in the incidence of NHL decreased in the low socio-demographic index (SDI) regions but increased in the high SDI regions. Age-standardized rate (ASR) of incidence in NHL was increased globally from 1990 to 2017. ASR of mortality and its annual percentage change in NHL were relatively stable globally from 1990 to 2017. Estimated annual percentage changes (EAPCs) in the incidence of NHL decreased in the low socio-demographic index (SDI) regions but increased in the high SDI regions.
DOI: 10.6084/m9.figshare.10315049.v1
title: MOESM7 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 7: Data S5. Statistics of isoform number for gene underwent alternative splicing.
DOI: 10.6084/m9.figshare.10315052
title: MOESM8 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 8: Data S6. LncRNAs predicated by CPAT software based on the novel genes and isoforms from SMRT data
DOI: 10.6084/m9.figshare.10315052.v1
title: MOESM8 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 8: Data S6. LncRNAs predicated by CPAT software based on the novel genes and isoforms from SMRT data
DOI: 10.6084/m9.figshare.10315058
title: MOESM9 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 9: Data S7. Fusion genes predicated based on SMRT data
DOI: 10.6084/m9.figshare.10315058.v1
title: MOESM9 of Candidate genes for grape white rot resistance based on SMRT and Illumina sequencing

description: Additional file 9: Data S7. Fusion genes predicated based on SMRT data
DOI: 10.5281/zenodo.10672844
title: IODP Expedition 393 Spectrophotometry

description: Interstitial water constitutents were measured by UV-VIS spectrometry using colorimetric methods (e.g., ammonium, nitrate, nitrite, phosphate, silica, and sulfide) by an Agilent CARY 100 UV-VIS spectrophotometer.
DOI: 10.5281/zenodo.10672845
title: IODP Expedition 393 Spectrophotometry

description: Interstitial water constitutents were measured by UV-VIS spectrometry using colorimetric methods (e.g., ammonium, nitrate, nitrite, phosphate, silica, and sulfide) by an Agilent CARY 100 UV-VIS spectrophotometer.
DOI: 10.25345/c58w38d0s
title: MassIVE MSV000094117 - Screening Metarhizium on plates-HZI
title: Screening metabolites from different Metarhizium species inoculated on YM and GYM plates
DOI: 10.6073/pasta/6b5dcd67d90e65397642eefd68a2eb43
title: Periphyton Net Primary Productivity and Respiration Rates from the Taylor Slough, just outside Everglades National Park (FCE), South Florida from December 1998 to December 2004

description: Periphyton metabolism is being measured at TS/Ph1b, TS/Ph2, TS/Ph3, TS/Ph4, and TS/Ph5 every 6-8 weeks during the wet season. We quantify metabolic rates of periphyton assemblages using standard oxygen change techniques in 300mL light and dark BOD bottles in triplicate. Using YSI dissolved oxygen probes and meters, we measure dissolved oxygen change as the difference of initial and final oxygen concentrations during a two hour incubation period. We calculate net primary productivity and respiration rates in units of oxygen and carbon, then normalize to the organic content (ash free dry weight) of the incubated periphyton.
DOI: 10.6084/m9.figshare.22625947
title: Additional file 16 of N,N-Dimethyl-3β-hydroxycholenamide attenuates neuronal death and retinal inflammation in retinal ischemia/reperfusion injury by inhibiting Ninjurin 1

description: Additional file 16. Table S11. Table of GO analysis of DEGs of microglia in DMHCA group compared to RIR group.
DOI: 10.6084/m9.figshare.22625947.v1
title: Additional file 16 of N,N-Dimethyl-3β-hydroxycholenamide attenuates neuronal death and retinal inflammation in retinal ischemia/reperfusion injury by inhibiting Ninjurin 1

description: Additional file 16. Table S11. Table of GO analysis of DEGs of microglia in DMHCA group compared to RIR group.
DOI: 10.5281/zenodo.10672842
title: IODP Expedition 393 Scanning electron microscope images

description: Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
DOI: 10.5281/zenodo.10672843
title: IODP Expedition 393 Scanning electron microscope images

description: Microscopic images of discrete samples were acquired using a scanning electron microscope (SEM) and captured as image files. These files were uploaded along with a brief description and a record of the microscopic conditions when the image was taken.
DOI: 10.6084/m9.figshare.10315145
title: MOESM1 of Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape

description: Additional file 1: Table S1. Genes on the candidate region of chromosome C05 of Brassica napus.
DOI: 10.6084/m9.figshare.10315145.v1
title: MOESM1 of Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape

description: Additional file 1: Table S1. Genes on the candidate region of chromosome C05 of Brassica napus.
DOI: 10.6084/m9.figshare.10315151
title: MOESM2 of Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape

description: Additional file 2: Table S2. Primers used in this study.
DOI: 10.6084/m9.figshare.10315151.v1
title: MOESM2 of Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape

description: Additional file 2: Table S2. Primers used in this study.
DOI: 10.6084/m9.figshare.8218007
title: Human aging DNA methylation signatures are conserved but accelerated in cultured fibroblasts

description: Aging is associated with progressive and site-specific changes in DNA methylation (DNAm). These global changes are captured by DNAm clocks that accurately predict chronological age in humans but relatively little is known about how clocks perform <i>in vitro</i>. Here we culture primary human fibroblasts across the cellular lifespan (~6 months) and use four different DNAm clocks to show that age-related DNAm signatures are conserved and accelerated <i>in vitro</i>. The Skin & Blood clock shows the best linear correlation with chronological time (r = 0.90), including during replicative senescence. Although similar in nature, the rate of epigenetic aging is approximately 62x times faster in cultured cells than in the human body. Consistent with <i>in vivo</i> data, cells aged under hyperglycemic conditions exhibit an approximately three years elevation in baseline DNAm age. Moreover, candidate gene-based analyses further corroborate the conserved but accelerated biological aging process in cultured fibroblasts. Fibroblasts mirror the established DNAm topology of the age-related <i>ELOVL2</i> gene in human blood and the rapid hypermethylation of its promoter cg16867657, which correlates with a linear decrease in ELOVL2 mRNA levels across the lifespan. Using generalized additive modeling on twelve timepoints across the lifespan, we also show how single CpGs exhibit loci-specific, linear and nonlinear trajectories that reach rates up to −47% (hypomethylation) to +23% (hypermethylation) per month. Together, these high-temporal resolution global, gene-specific, and single CpG data highlight the conserved and accelerated nature of epigenetic aging in cultured fibroblasts, which may constitute a system to evaluate age-modifying interventions across the lifespan.
DOI: 10.5281/zenodo.10672838
title: IODP Expedition 393 Section summary

description: Report includes data for individual core sections: coring/drilling depths and recovery, database identifiers for the whole section and section halves, and number of samples taken from the section before and after splitting.
DOI: 10.5281/zenodo.10672839
title: IODP Expedition 393 Section summary

description: Report includes data for individual core sections: coring/drilling depths and recovery, database identifiers for the whole section and section halves, and number of samples taken from the section before and after splitting.
DOI: 10.6084/m9.figshare.8218007.v2
title: Human aging DNA methylation signatures are conserved but accelerated in cultured fibroblasts

description: Aging is associated with progressive and site-specific changes in DNA methylation (DNAm). These global changes are captured by DNAm clocks that accurately predict chronological age in humans but relatively little is known about how clocks perform <i>in vitro</i>. Here we culture primary human fibroblasts across the cellular lifespan (~6 months) and use four different DNAm clocks to show that age-related DNAm signatures are conserved and accelerated <i>in vitro</i>. The Skin & Blood clock shows the best linear correlation with chronological time (r = 0.90), including during replicative senescence. Although similar in nature, the rate of epigenetic aging is approximately 62x times faster in cultured cells than in the human body. Consistent with <i>in vivo</i> data, cells aged under hyperglycemic conditions exhibit an approximately three years elevation in baseline DNAm age. Moreover, candidate gene-based analyses further corroborate the conserved but accelerated biological aging process in cultured fibroblasts. Fibroblasts mirror the established DNAm topology of the age-related <i>ELOVL2</i> gene in human blood and the rapid hypermethylation of its promoter cg16867657, which correlates with a linear decrease in ELOVL2 mRNA levels across the lifespan. Using generalized additive modeling on twelve timepoints across the lifespan, we also show how single CpGs exhibit loci-specific, linear and nonlinear trajectories that reach rates up to −47% (hypomethylation) to +23% (hypermethylation) per month. Together, these high-temporal resolution global, gene-specific, and single CpG data highlight the conserved and accelerated nature of epigenetic aging in cultured fibroblasts, which may constitute a system to evaluate age-modifying interventions across the lifespan.
DOI: 10.6084/m9.figshare.8218007.v1
title: Human Aging DNA Methylation Signatures are Conserved but Accelerated in Cultured Fibroblasts

description: Aging is associated with progressive and site-specific changes in DNA methylation (DNAm). These global changes are captured by DNAm clocks that accurately predict chronological age in humans but relatively little is known about how clocks perform <i>in vitro</i>. Here we culture primary human fibroblasts across the cellular lifespan (~6 months) and use four different DNAm clocks to show that age-related DNAm signatures are conserved and accelerated <i>in vitro</i>. The Skin & Blood clock shows the best linear correlation with chronological time (r=0.90), including during replicative senescence. Although similar in nature, the rate of epigenetic aging is approximately 62x times faster in cultured cells than in the human body. Consistent with <i>in vivo</i> data, cells aged under hyperglycemic conditions exhibit an approximately three years elevation in baseline DNAm age. Moreover, candidate gene-based analyses further corroborate the conserved but accelerated biological aging process in cultured fibroblasts. Fibroblasts mirror the established DNAm topology of the age-related <i>ELOVL2</i> gene in human blood and the rapid hypermethylation of its promoter cg16867657, which correlates with a linear decrease in ELOVL2 mRNA levels across the lifespan. Using generalized additive modeling on twelve timepoints across the lifespan, we also show how single CpGs exhibit loci-specific, linear and nonlinear trajectories that reach rates up to -47% (hypomethylation) to +23% (hypermethylation) per month. Together, these high temporal resolution global, gene-specific, and single CpG data highlight the conserved and accelerated nature of epigenetic aging in cultured fibroblasts, which may constitute a system to evaluate age-modifying interventions across the lifespan.
DOI: 10.5281/zenodo.10672836
title: IODP Expedition 393 Sample report

description: Report includes detailed information about samples taken for testing: location/depth, type/form factor, test, request number, and database identifier.
DOI: 10.5281/zenodo.10672837
title: IODP Expedition 393 Sample report

description: Report includes detailed information about samples taken for testing: location/depth, type/form factor, test, request number, and database identifier.
DOI: 10.6084/m9.figshare.25245604
title: Data for BI course

description: Some materials for a brain imaging course. Referenced in notebooks in git@github.com:tknapen/brainimaging_VU.git
DOI: 10.6084/m9.figshare.25245604.v1
title: Data for BI course

description: Some materials for a brain imaging course. Referenced in notebooks in git@github.com:tknapen/brainimaging_VU.git
DOI: 10.6084/m9.figshare.14509501
title: Additional file 2 of The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure

description: Additional file 2. List of predictive markers.
DOI: 10.6084/m9.figshare.14509498.v1
title: Additional file 1 of The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure

description: Additional file 1. GO and KEGG annotation.
DOI: 10.6084/m9.figshare.14509498
title: Additional file 1 of The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure

description: Additional file 1. GO and KEGG annotation.
DOI: 10.6084/m9.figshare.14509500
title: Additional file 2 of Nitric oxide donor sodium nitroprusside-induced transcriptional changes and hypocrellin biosynthesis of Shiraia sp. S9

description: Additional file 2: Table S3. Annotation of DEGs using NR, SWISS-Prot, KEGG, KOG and GO databases and their fold change with SNP treatment. Table S4. GO enrichment of Shiraia sp. S9 with SNP treatment. Table S5. Differentially expressed genes (DEGs) involved in hypocrellin biosynthesis of Shiraia sp. S9 under SNP treatment. Table S6. Differentially expressed genes (DEGs) involved in hypocrellin transport of Shiraia sp. S9 under SNP treatment. Table S7. Annotation of transcription factors in Shiraia sp. S9. Table S8. Differentially expressed genes (DEGs) involved in transcription factors of Shiraia sp. S9 under SNP treatment.
DOI: 10.6084/m9.figshare.14509501.v1
title: Additional file 2 of The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure

description: Additional file 2. List of predictive markers.
DOI: 10.6084/m9.figshare.14509500.v1
title: Additional file 2 of Nitric oxide donor sodium nitroprusside-induced transcriptional changes and hypocrellin biosynthesis of Shiraia sp. S9

description: Additional file 2: Table S3. Annotation of DEGs using NR, SWISS-Prot, KEGG, KOG and GO databases and their fold change with SNP treatment. Table S4. GO enrichment of Shiraia sp. S9 with SNP treatment. Table S5. Differentially expressed genes (DEGs) involved in hypocrellin biosynthesis of Shiraia sp. S9 under SNP treatment. Table S6. Differentially expressed genes (DEGs) involved in hypocrellin transport of Shiraia sp. S9 under SNP treatment. Table S7. Annotation of transcription factors in Shiraia sp. S9. Table S8. Differentially expressed genes (DEGs) involved in transcription factors of Shiraia sp. S9 under SNP treatment.
DOI: 10.5281/zenodo.10672834
title: IODP Expedition 393 Salinity

description: Salinity was measured on interstitial water (IW) samples using an optical refractometer.
DOI: 10.5281/zenodo.10672835
title: IODP Expedition 393 Salinity

description: Salinity was measured on interstitial water (IW) samples using an optical refractometer.
DOI: 10.6084/m9.figshare.11888118
title: A chromosome-scale genome assembly of the Mongolian oak (Quercus mongolica)

description: Mongolian oak
(Quercus mongolica Fisch.) is an ecologically and economically important white
oak species native to and widespread in the temperate zone of East Asia. Here,
we present a chromosome-scale reference genome assembly of Q. mongolica, a
representative white oak species, by combining Illumina and PacBio data with
Hi-C mapping technologies that is the first reference genome created for an
Asian oak. Our results showed that the PacBio draft genome size was 809.84 Mb,
with a BUSCO complete gene percentage of 92.71%. Hi-C scaffolding anchored
774.59 Mb contigs (95.65% of draft assembly) onto 12 pseudochromosomes. The
contig N50 and scaffold N50 were 2.64 Mb and 66.74 Mb, respectively. We further
annotated 36,553 protein-coding genes and 435.34 Mb (53.75% of the genome)
repetitive sequences. The non-coding RNAs were identified, including 129 miRNAs, 768 tRNAs, 4,896
rRNAs, and 371 snRNAs. This pioneering Asian oak genome resource represents an
important supplement to the oak genomics community and will improve our
understanding of Asian white oak biology and evolution.
DOI: 10.5281/zenodo.10672832
title: IODP Expedition 393 Color reflectance

description: Color reflectance data were measured on section halves using an integration sphere and a UV-VIS spectrophotometer mounted on the Section Half Multisensor Logger (SHMSL). Spectral counts are recorded in the range of 380 to 700 nm, covering the visible spectrum, and binned in ~2 nm bins. Spectral data are reduced from spectra and recorded in tristimulus XYZ values, CieLAB L*a*b* values, and other units.
DOI: 10.5281/zenodo.10672833
title: IODP Expedition 393 Color reflectance

description: Color reflectance data were measured on section halves using an integration sphere and a UV-VIS spectrophotometer mounted on the Section Half Multisensor Logger (SHMSL). Spectral counts are recorded in the range of 380 to 700 nm, covering the visible spectrum, and binned in ~2 nm bins. Spectral data are reduced from spectra and recorded in tristimulus XYZ values, CieLAB L*a*b* values, and other units.
DOI: 10.6084/m9.figshare.25245466.v1
title: Finding Large Independent Sets in Networks Using Competitive Dynamics

description: Many decision-making algorithms were inspired by the inner working of individual biological systems. However, it is less clear whether collective behaviour of biological species can also be interpreted as a mechanism for solving computational tasks. By studying coexistence of species interacting through simple rules on a complex network, we demonstrate that the underlying dynamical system recovers near-optimal solutions to the maximum independent set problem -- one of the fundamental computationally hard problems in graph theory. Furthermore, through illuminating an unexpected connection between bifurcation points in the underlying dynamical system and the Katz centrality in the network, we introduce an algorithm for approximating the maximum independent set problem on a graph. Because of fundamental positioning of this problem in science, our results have multi-fold relevance for biology, economics, complex systems, as well as computer science, including the identification of optimal error-correcting codes.<br><br>These files contain the numerical study performed for the article Finding Large Independent Sets in Networks Using Competitive Dynamics by M.N. Mooij & I. Kryven.