cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4008561
title: KM1906_Gradients3_Surface_O2Ar_NCP

description: This data set gives values of dissolved gas saturation and calculated rates of net community production implied from those observations in the North Pacific Ocean. Data were collected between April 10, 2019 and April 29, 2019 using an equilibrated inlet mass spectrometer (EIMS, Cassar et al., 2009) connected to the surface uncontaminated seawater supply of the Research Vessel Kilo Moana on Cruise ID KM1906. Data were collected near-continuously over the cruise track which departed and returned from Honolulu, HI and sampled waters of the North Pacific subtropical gyre and transition zone.
DOI: 10.6084/m9.figshare.5867154
title: MOESM2 of Improvement of malaria diagnostic system based on acridine orange staining

description: Additional file 2. AO_Giemsa_PCR diagnoses data for 1018 samples.
DOI: 10.6084/m9.figshare.5867154.v1
title: MOESM2 of Improvement of malaria diagnostic system based on acridine orange staining

description: Additional file 2. AO_Giemsa_PCR diagnoses data for 1018 samples.
DOI: 10.6084/m9.figshare.5867148
title: Additional file 3: of Correction to: A statistical framework for analyzing deep mutational scanning data

description: Replicate correlation tables. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5867148.v1
title: Additional file 3: of Correction to: A statistical framework for analyzing deep mutational scanning data

description: Replicate correlation tables. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.5867139
title: Additional file 12: Tables S15 and S16. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

description: Full list of all miRNA modules and module membership (MM) values for each miRNA in dataset: modules constructed in the High intramuscular fat (IMF) group (Table S15), modules constructed in the Low IMF group (Table S16). (XLSX 260 kb)
DOI: 10.6084/m9.figshare.5867139.v1
title: Additional file 12: Tables S15 and S16. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

description: Full list of all miRNA modules and module membership (MM) values for each miRNA in dataset: modules constructed in the High intramuscular fat (IMF) group (Table S15), modules constructed in the Low IMF group (Table S16). (XLSX 260 kb)
DOI: 10.6084/m9.figshare.5867118
title: Additional file 11: Tables S13 and S14. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

description: Full list of all mRNA modules and module membership (MM) values for each gene in dataset: modules constructed in the High intramuscular fat (IMF) group (Table S13), modules constructed in the Low IMF group (Table S14). (XLSX 18066 kb)
DOI: 10.6084/m9.figshare.5867118.v1
title: Additional file 11: Tables S13 and S14. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

description: Full list of all mRNA modules and module membership (MM) values for each gene in dataset: modules constructed in the High intramuscular fat (IMF) group (Table S13), modules constructed in the Low IMF group (Table S14). (XLSX 18066 kb)
DOI: 10.6084/m9.figshare.5867109
title: Additional file 1: of A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production

description: The following supplementary files are part of this publication. (ZIP 77Â kb)
DOI: 10.6084/m9.figshare.5867109.v1
title: Additional file 1: of A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production

description: The following supplementary files are part of this publication. (ZIP 77Â kb)
DOI: 10.6084/m9.figshare.5867094
title: Additional file 10: Table S12. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

description: Gene ontology (GO) enrichment analysis by Cytoscape of genes highly correlated with top PIF and RIF genes and miRNAs. The table contains gene symbol and ENSEMBL of each top gene, gene ontology term ID, p-value and adjusted p-value of GO enrichments, the description of each GO term and the genes present in each enriched biological process. (XLSX 76 kb)
DOI: 10.6084/m9.figshare.5867094.v1
title: Additional file 10: Table S12. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

description: Gene ontology (GO) enrichment analysis by Cytoscape of genes highly correlated with top PIF and RIF genes and miRNAs. The table contains gene symbol and ENSEMBL of each top gene, gene ontology term ID, p-value and adjusted p-value of GO enrichments, the description of each GO term and the genes present in each enriched biological process. (XLSX 76 kb)
DOI: 10.6084/m9.figshare.5867031
title: wimu-master_1.zip

description: new bkp
DOI: 10.6084/m9.figshare.5867031.v1
title: wimu-master_1.zip

description: new bkp
DOI: 10.6084/m9.figshare.5866971
title: Fipy Benchmark 3

description: Simulation of a dendrite for phase field benchmark 3 https://pages.nist.gov/pfhub/benchmarks/benchmark3.ipynb/<br>
DOI: 10.6084/m9.figshare.5866950
title: Chlamydial Ortholog Mappings

description: A reciprocal best pair derived mapping of orthologous genes between 4 chlamydial model organisms.Chlamydia trachomatis 434/buChlamydia trachomatis D/UW-3/CX<br>Chlamydia muridarum Nigg.Chlamydia pneumonia CWL029<br>
DOI: 10.6084/m9.figshare.5866950.v1
title: Chlamydial Ortholog Mappings

description: A reciprocal best pair derived mapping of orthologous genes between 4 chlamydial model organisms.Chlamydia trachomatis 434/buChlamydia trachomatis D/UW-3/CX<br>Chlamydia muridarum Nigg.Chlamydia pneumonia CWL029<br>
DOI: 10.6084/m9.figshare.5866926
title: Data and Song Files for "Global song divergence in barn swallows (Hirundo rustica): exploring the roles of genetic, geographic, and climatic distance in sympatry and allopatry"

description: All song files and measurements associated with MR Wilkins, et al. (2018) "Global song divergence in barn swallows (Hirundo rustica): exploring the roles of genetic, geographic, and climatic distance in sympatry and allopatry." Biological Journal of the Linnean Society.<br>Song Recording Descriptions:We present 1700 recordings from 19 sites across 6 countries, encompassing 5 of 6 currently described barn swallow subspecies: rustica, erythrogaster, gutturalis, tytleri, and transitiva. We include the downsampled and filtered song files used for analysis in Avisoft. Some of these files have been edited slightly to erase loud sounds in the recordings which threw off measures of peak frequency (see methods). The original, unfiltered 48kHz recordings are also included in a separate ZIP archive.<br>Data File Descriptions:1) Raw Song Measures_Wilkins et al_BJLS_2018.csv: Song measurements for each song file. Blanks are due to absence of a particular note (e.g. P-note) or inability to measure for a particular song (e.g. due to overlap with another bird).<br><br>2) Individual Mean Song Measures_Wilkins et al_BJLS_2018.csv: Average song measures for each individual.<br>Abbreviations: W.L=Warble LengthR.L=Rattle LengthPF.W= Peak Frequency of the WarblePF.R= Peak Frequency of the RattlePF.CR= Peak Frequency of the Central RattleW.WE= Warble Weiner EntropyCR.FB= Central Rattle Frequency BandwidthR.Tempo= Rattle TempoZcount= count of omega syllablesZprop= proportion of omega syllables<br>See main text for description of how these were measured.<br><br><br>
DOI: 10.17608/k6.auckland.5866902
title: An ISCC-NBS Colour List for ‘roloc’

description: This report describes the development of a colour list and colour metric for the ‘roloc’ package that is based on the ISCC-NBS System of Color Designation.
DOI: 10.17608/k6.auckland.5866902.v1
title: An ISCC-NBS Colour List for ‘roloc’

description: This report describes the development of a colour list and colour metric for the ‘roloc’ package that is based on the ISCC-NBS System of Color Designation.
DOI: 10.6084/m9.figshare.5866899
title: Kinematic Data Description by column

description: Excel file and image explaining the inertial motion data (from Xsens) records structure. Every column found in the inertial motion data records can be identified through this descriptor and matched on the submitted anatomical illustration.
DOI: 10.6084/m9.figshare.5866899.v1
title: Kinematic Data Description by column

description: Excel file and image explaining the inertial motion data (from Xsens) records structure. Every column found in the inertial motion data records can be identified through this descriptor and matched on the submitted anatomical illustration.
DOI: 10.6084/m9.figshare.5866785
title: Hur gör du din forskning allmänt tillgänglig (open access)? Gratis och lagligt.

description: Den har infographic visar hur man uppnår 100% open access, gratis och lagligt.<br><br>Svensk översättning av "How to make your research open access? For free and legally" (Matthias & Tennant 2017).<br>Original by Lisa and Jon (CC BY 4.0), Swedish translations by Lachlan Fetterplace. <br><br>Reference:Matthias, Lisa; Tennant, Jon (2017): How to make your research open access? For free and legally.. figshare.)<br><br>
DOI: 10.6084/m9.figshare.5866785.v1
title: Hur gör du din forskning allmänt tillgänglig (open access)?

description: Den har infographic visar hur man uppnår 100% open access, gratis och lagligt.<br><br>Svensk översättning av "How to make your research open access? For free and legally" (Matthias & Tennant 2017).<br>Original by Lisa and Jon (CC BY 4.0), Swedish translations by Lachlan Fetterplace. <br><br>Reference:Matthias, Lisa; Tennant, Jon (2017): How to make your research open access? For free and legally.. figshare.)<br><br>
DOI: 10.6084/m9.figshare.5864115
title: wimu-master.zip

description: BKP wimu github Feb 7 2018
DOI: 10.6084/m9.figshare.5864115.v1
title: wimu-master.zip

description: BKP wimu github Feb 7 2018
DOI: 10.6084/m9.figshare.5864070
title: DNA methylation reprogramming of human cancer cells by expression of a plant 5-methylcytosine DNA glycosylase

description: Patterns of DNA methylation, an important epigenetic modification involved in gene silencing and development, are disrupted in cancer cells. Understanding the functional significance of aberrant methylation in tumors remains challenging, due in part to the lack of suitable tools to actively modify methylation patterns. DNA demethylation caused by mammalian DNA methyltransferase inhibitors is transient and replication-dependent, whereas that induced by TET enzymes involves oxidized 5mC derivatives that perform poorly understood regulatory functions. Unlike animals, plants possess enzymes that directly excise unoxidized 5mC from DNA, allowing restoration of unmethylated C through base excision repair. Here, we show that expression of <i>Arabidopsis</i> 5mC DNA glycosylase DEMETER (DME) in colon cancer cells demethylates and reactivates hypermethylated silenced loci. Interestingly, DME expression causes genome-wide changes that include both DNA methylation losses and gains, and partially restores the methylation pattern observed in normal tissue. Furthermore, such methylome reprogramming is accompanied by altered cell cycle responses and increased sensibility to anti-tumor drugs, decreased ability to form colonospheres, and tumor growth impairment <i>in vivo</i>. Our study shows that it is possible to reprogram a human cancer DNA methylome by expression of a plant DNA demethylase.
DOI: 10.6084/m9.figshare.5864070.v1
title: DNA methylation reprogramming of human cancer cells by expression of a plant 5-methylcytosine DNA glycosylase

description: Patterns of DNA methylation, an important epigenetic modification involved in gene silencing and development, are disrupted in cancer cells. Understanding the functional significance of aberrant methylation in tumors remains challenging, due in part to the lack of suitable tools to actively modify methylation patterns. DNA demethylation caused by mammalian DNA methyltransferase inhibitors is transient and replication-dependent, whereas that induced by TET enzymes involves oxidized 5mC derivatives that perform poorly understood regulatory functions. Unlike animals, plants possess enzymes that directly excise unoxidized 5mC from DNA, allowing restoration of unmethylated C through base excision repair. Here, we show that expression of <i>Arabidopsis</i> 5mC DNA glycosylase DEMETER (DME) in colon cancer cells demethylates and reactivates hypermethylated silenced loci. Interestingly, DME expression causes genome-wide changes that include both DNA methylation losses and gains, and partially restores the methylation pattern observed in normal tissue. Furthermore, such methylome reprogramming is accompanied by altered cell cycle responses and increased sensibility to anti-tumor drugs, decreased ability to form colonospheres, and tumor growth impairment <i>in vivo</i>. Our study shows that it is possible to reprogram a human cancer DNA methylome by expression of a plant DNA demethylase.
DOI: 10.6084/m9.figshare.5864061
title: Low <i>HOX</i> gene expression in <i>PML-RARα-</i>positive leukemia results from suppressed histone demethylation

description: Homeobox (<i>HOX</i>) genes are frequently dysregulated in leukemia. Previous studies have shown that aberrant <i>HOX</i> gene expression accompanies leukemogenesis and affects disease progression and leukemia patient survival. Patients with acute myeloid leukemia (AML) bearing <i>PML-RARα</i> fusion gene have distinct HOX gene signature in comparison to other subtypes of AML patients, although the mechanism of transcription regulation is not completely understood. We previously found an association between the mRNA levels of <i>HOX</i> genes and those of the histone demethylases <i>JMJD3</i> and <i>UTX</i> in <i>PML-RARα</i>- positive leukemia patients. Here, we demonstrate that the release of the PML-RARα-mediated block in <i>PML-RARα</i>-positive myeloid leukemia cells increased both <i>JMJD3</i> and <i>HOX</i> gene expression, while inhibition of JMJD3 using the specific inhibitor GSK-J4 reversed the effect. This effect was driven specifically through PML-RARα fusion protein since expression changes did not occur in cells with mutated <i>RARα</i> and was independent of differentiation<i>.</i> We confirmed that gene expression levels were inversely correlated with alterations in H3K27me3 histone marks localized at <i>HOX</i> gene promoters. Furthermore, data from chromatin immunoprecipitation followed by sequencing broaden a list of clustered <i>HOX</i> genes regulated by JMJD3 in <i>PML-RARα</i>-positive leukemic cells. Interestingly, the combination of GSK-J4 and all-trans retinoic acid (ATRA) significantly increased <i>PML-RARα</i>-positive cell apoptosis compared with ATRA treatment alone. This effect was also observed in ATRA-resistant NB4 clones, which may provide a new therapeutic opportunity for patients with acute promyelocytic leukemia (APL) resistant to current treatment. The results of our study reveal the mechanism of <i>HOX</i> gene expression regulation and contribute to our understanding of APL pathogenesis.
DOI: 10.6084/m9.figshare.5864061.v1
title: Low <i>HOX</i> gene expression in <i>PML-RARα-</i>positive leukemia results from suppressed histone demethylation

description: Homeobox (<i>HOX</i>) genes are frequently dysregulated in leukemia. Previous studies have shown that aberrant <i>HOX</i> gene expression accompanies leukemogenesis and affects disease progression and leukemia patient survival. Patients with acute myeloid leukemia (AML) bearing <i>PML-RARα</i> fusion gene have distinct HOX gene signature in comparison to other subtypes of AML patients, although the mechanism of transcription regulation is not completely understood. We previously found an association between the mRNA levels of <i>HOX</i> genes and those of the histone demethylases <i>JMJD3</i> and <i>UTX</i> in <i>PML-RARα</i>- positive leukemia patients. Here, we demonstrate that the release of the PML-RARα-mediated block in <i>PML-RARα</i>-positive myeloid leukemia cells increased both <i>JMJD3</i> and <i>HOX</i> gene expression, while inhibition of JMJD3 using the specific inhibitor GSK-J4 reversed the effect. This effect was driven specifically through PML-RARα fusion protein since expression changes did not occur in cells with mutated <i>RARα</i> and was independent of differentiation<i>.</i> We confirmed that gene expression levels were inversely correlated with alterations in H3K27me3 histone marks localized at <i>HOX</i> gene promoters. Furthermore, data from chromatin immunoprecipitation followed by sequencing broaden a list of clustered <i>HOX</i> genes regulated by JMJD3 in <i>PML-RARα</i>-positive leukemic cells. Interestingly, the combination of GSK-J4 and all-trans retinoic acid (ATRA) significantly increased <i>PML-RARα</i>-positive cell apoptosis compared with ATRA treatment alone. This effect was also observed in ATRA-resistant NB4 clones, which may provide a new therapeutic opportunity for patients with acute promyelocytic leukemia (APL) resistant to current treatment. The results of our study reveal the mechanism of <i>HOX</i> gene expression regulation and contribute to our understanding of APL pathogenesis.
DOI: 10.6084/m9.figshare.5864058
title: Predation on artificial and natural nests in the lowland rainforest of Papua New Guinea

description: <b>Capsule:</b> Although survival of nests was similar between forest fragments and continuous forest, the range of predators differed. Artificial nests provide an under-estimate of nest predation by snakes. <b>Aims:</b> To estimate the natural nest predation rate in continuous primary forest, compare it with predation rates in forest fragments. To assess the reliability of nest survival rates determined by the use of artificial nests with clay eggs and identify the main nest predators. <b>Methods:</b> We observed survival of natural nests during the incubation period in continuous primary forest in Papua New Guinea. Some nests were monitored with infrared cameras. We also used artificial nests deployed with clay eggs to identify predators. <b>Results:</b> There was a predation rate of 50% for natural nests and snakes were major predators of nest contents. Clutch daily survival rates (DSRs) differed among nest types. The DSR of artificial nests (0.977) was not significantly different to that of natural cup nests (0.969). Survival rates of artificial nests were similar in forest fragments and continuous forest. Forest fragments had, however, a higher proportion of avian predators than continuous forest. <b>Conclusion:</b> Although, we observed similar survival rates in artificial and natural nests, the composition of nest predators was different between natural and artificial nests. Artificial nests were not suitable for estimating the real predation caused by reptiles. Nevertheless, we find that participation of avian nest predators can be estimated correctly with the use of artificial nests.
DOI: 10.6084/m9.figshare.5863965
title: PubMed Phrases

description: This file contains PubMed Phrases (all_dictionary.txt), PubMed Phrases with POS tags (all_dictionary.pos), PubMed Phrases grouped by substrings (all_dictionary.group), PubMed Phrases with PubMed IDs (all_dictionary.pmid), and PubMed Phrases with p-value/BM25 scores (all_dictionary.sco).
DOI: 10.6084/m9.figshare.5863965.v1
title: PubMed Phrases

description: This file contains PubMed Phrases (all_dictionary.txt), PubMed Phrases with POS tags (all_dictionary.pos), PubMed Phrases grouped by substrings (all_dictionary.group), PubMed Phrases with PubMed IDs (all_dictionary.pmid), and PubMed Phrases with p-value/BM25 scores (all_dictionary.sco).
DOI: 10.6084/m9.figshare.5863959
title: Correlation coefficients of scattering signals of rough and flat cracks

description: Data to generate Fig 5 in the paper,'Wave scattering from random rough surfaces in 3D: The role of dimensionality"
DOI: 10.6084/m9.figshare.5863959.v1
title: Correlation coefficients of scattering signals of rough and flat cracks

description: Data to generate Fig 5 in the paper,'Wave scattering from random rough surfaces in 3D: The role of dimensionality"
DOI: 10.6084/m9.figshare.5863911
title: Decoupling of the Occipitotemporal Cortex and the Brain’s Default-Mode Network in Dyslexia and a Role for the Cingulate Cortex in Good Readers: A Brain Imaging Study of Brazilian Children

description: The goal of the present study was to investigate intrinsic and reading-related brain function associated with dyslexia and typical readers in monolingual Brazilian children. Two fMRI studies were carried out: a resting-state and a word-reading study. The results show (a) underconnectivity between the occipitotemporal region (visual word form area) and the brain’s default-mode network in dyslexic readers and (b) more activation of the anterior cingulate cortex for typical readers relative to dyslexic readers. The findings provide evidence for brain connectivity and function differences in an underrepresented population in fMRI studies of dyslexia; the results suggest atypical intrinsic function, and differences in directed attention processes in dyslexia.
DOI: 10.6084/m9.figshare.5863911.v1
title: Decoupling of the Occipitotemporal Cortex and the Brain’s Default-Mode Network in Dyslexia and a Role for the Cingulate Cortex in Good Readers: A Brain Imaging Study of Brazilian Children

description: The goal of the present study was to investigate intrinsic and reading-related brain function associated with dyslexia and typical readers in monolingual Brazilian children. Two fMRI studies were carried out: a resting-state and a word-reading study. The results show (a) underconnectivity between the occipitotemporal region (visual word form area) and the brain’s default-mode network in dyslexic readers and (b) more activation of the anterior cingulate cortex for typical readers relative to dyslexic readers. The findings provide evidence for brain connectivity and function differences in an underrepresented population in fMRI studies of dyslexia; the results suggest atypical intrinsic function, and differences in directed attention processes in dyslexia.
DOI: 10.6084/m9.figshare.5863908
title: Embedded performance validity indicator for children: California Verbal Learning Test – Children’s Edition, forced choice

description: Performance validity testing in children undergoing neuropsychological testing is a growing research area. Accurate identification of performance validity is necessary to avoid invalid assessment conclusions. In the present research, a forced choice (FC) trial was created for the California Verbal Learning Test – Children’s Edition (CVLT-C), modeled after the established California Verbal Learning Test – Second Edition (CVLT-II) FC trial. Distractor words were taken directly from the CVLT-II FC Standard Form, with about half being concrete (n = 8) and half abstract (n = 7). The order of the items was organized similarly to the CVLT-II FC to ensure that items from within the same category were not sequential. The Test of Memory Malingering was administered for comparison, and three embedded measures that have previously been validated in adults were also calculated. The CVLT-C FC trial was administered to 40 children, aged 6–16 (M = 12.08, SD = 3.13). Average full scale IQ was 97.3 (SD = 12.41, range = 71–123). Ninety-three percent of examinees performed perfectly on the CVLT-C FC, suggesting high specificity, which is similar to findings for the CVLT-II FC normative group (90%). Results from other embedded measures are also presented.