cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1295208
title: Functional analysis of free fatty acid receptor GPR120 in human eosinophils: implications in metabolic homeostasis

description: Recent evidence has shown that eosinophils play an important role in metabolic homeostasis through Th2 cytokine production. GPR120 (FFA4) is a G protein-coupled receptor (GPCR) for long-chain fatty acids that functions as a regulator of physiological energy metabolism. In the present study, we aimed to investigate whether human eosinophils express GPR120 and, if present, whether it possesses a functional capacity on eosinophils. Eosinophils isolated from peripheral venous blood expressed GPR120 at both the mRNA and protein levels. Stimulation with a synthetic GPR120 agonist, GW9508, induced rapid down-regulation of cell surface expression of GPR120, suggesting ligand-dependent receptor internalization. Although GPR120 activation did not induce eosinophil chemotactic response and degranulation, we found that GW9508 inhibited eosinophil spontaneous apoptosis and Fas receptor expression. The anti-apoptotic effect was attenuated by phosphoinositide 3-kinase (PI3K) inhibitors and was associated with inhibition of caspase-3 activity. Eosinophil response investigated using ELISpot assay indicated that stimulation with a GPR120 agonist induced IL-4 secretion. These findings demonstrate the novel functional properties of fatty acid sensor GPR120 on human eosinophils and indicate the previously unrecognized link between nutrient metabolism and the immune system.
DOI: 10.6084/m9.figshare.1295208.v1
title: Functional analysis of free fatty acid receptor GPR120 in human eosinophils: implications in metabolic homeostasis

description: Recent evidence has shown that eosinophils play an important role in metabolic homeostasis through Th2 cytokine production. GPR120 (FFA4) is a G protein-coupled receptor (GPCR) for long-chain fatty acids that functions as a regulator of physiological energy metabolism. In the present study, we aimed to investigate whether human eosinophils express GPR120 and, if present, whether it possesses a functional capacity on eosinophils. Eosinophils isolated from peripheral venous blood expressed GPR120 at both the mRNA and protein levels. Stimulation with a synthetic GPR120 agonist, GW9508, induced rapid down-regulation of cell surface expression of GPR120, suggesting ligand-dependent receptor internalization. Although GPR120 activation did not induce eosinophil chemotactic response and degranulation, we found that GW9508 inhibited eosinophil spontaneous apoptosis and Fas receptor expression. The anti-apoptotic effect was attenuated by phosphoinositide 3-kinase (PI3K) inhibitors and was associated with inhibition of caspase-3 activity. Eosinophil response investigated using ELISpot assay indicated that stimulation with a GPR120 agonist induced IL-4 secretion. These findings demonstrate the novel functional properties of fatty acid sensor GPR120 on human eosinophils and indicate the previously unrecognized link between nutrient metabolism and the immune system.
DOI: 10.6084/m9.figshare.1295198.v1
title: Supplementary Information for "Organization and distribution of glomeruli in the bowhead whale olfactory bulb"

description: A STL-formatted image of the 3D bowhead whale olfactory bulb
DOI: 10.6084/m9.figshare.1294995
title: Subjective well-being for online college professors

description: A generic qualitative research study was completed to see how happy highly successful online educators are in the jobs that they are doing.
DOI: 10.6084/m9.figshare.1294983
title: Breast cancer data from TCGA for machine learning exercise

description: I accessed the data used in this publication (https://tcga-data.nci.nih.gov/docs/publications/brca_2012/) and parsed the clinical data to determine which patients were HER2 positive. I then extracted gene-expression data for these patients and created a matrix that indicates expression levels for all genes with no missing values. The first row indicates HER2 status (1 = positive, -1 = negative)
DOI: 10.6084/m9.figshare.1294995.v1
title: Subjective well-being for online college professors

description: A generic qualitative research study was completed to see how happy highly successful online educators are in the jobs that they are doing.
DOI: 10.6084/m9.figshare.1295197.v1
title: Supplementary Data S1

description: A STL-formatted image of the 3D bowhead whale olfactory bulb
DOI: 10.6084/m9.figshare.1294980
title: Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas

description: Chordomas are an aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1–4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2’-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8,819 loci (2.9%) that were significantly differentially methylated (&gt;0.2 average β-value difference) between chordomas and nucleus pulposus samples (adjusted <i>P &lt;</i> 0.05). Among these, 5,868 probes (66.5%) were hypomethylated, compared to 2,951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2,951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.
DOI: 10.6084/m9.figshare.1294983.v1
title: Breast cancer data from TCGA for machine learning exercise

description: I accessed the data used in this publication (https://tcga-data.nci.nih.gov/docs/publications/brca_2012/) and parsed the clinical data to determine which patients were HER2 positive. I then extracted gene-expression data for these patients and created a matrix that indicates expression levels for all genes with no missing values.
DOI: 10.6084/m9.figshare.1294980.v1
title: Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas

description: Chordomas are aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1%-4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2’-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8819 loci (2.9%) that were significantly differentially methylated (&gt;0.2 average β-value difference) between chordomas and nucleus pulposus samples (adjusted <i>P</i> &lt; 0.05). Among these, 5868 probes (66.5%) were hypomethylated, compared to 2951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.
DOI: 10.6084/m9.figshare.1294983.v2
title: Breast cancer data from TCGA for machine learning exercise

description: I accessed the data used in this publication (https://tcga-data.nci.nih.gov/docs/publications/brca_2012/) and parsed the clinical data to determine which patients were HER2 positive. I then extracted gene-expression data for these patients and created a matrix that indicates expression levels for all genes with no missing values. The first row indicates HER2 status (1 = positive, -1 = negative)
DOI: 10.6084/m9.figshare.1294980.v2
title: Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas

description: Chordomas are an aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1–4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2’-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8,819 loci (2.9%) that were significantly differentially methylated (&gt;0.2 average β-value difference) between chordomas and nucleus pulposus samples (adjusted <i>P &lt;</i> 0.05). Among these, 5,868 probes (66.5%) were hypomethylated, compared to 2,951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2,951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.
DOI: 10.6084/m9.figshare.1294980.v4
title: Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas

description: Chordomas are an aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1–4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2’-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8,819 loci (2.9%) that were significantly differentially methylated (&gt;0.2 average β-value difference) between chordomas and nucleus pulposus samples (adjusted <i>P &lt;</i> 0.05). Among these, 5,868 probes (66.5%) were hypomethylated, compared to 2,951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2,951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.
DOI: 10.6084/m9.figshare.1294980.v3
title: Genome-wide DNA methylation profiling of recurrent and non-recurrent chordomas

description: Chordomas are an aggressive rare type of malignant bone tumors arising from the remnant of the notochord. Chordomas occur mainly in vertebral bones and account for 1–4% of malignant bone tumors. Management and treatment of chordomas are difficult as they are resistant to conventional chemotherapy; therefore, they are mainly treated with surgery and radiation therapy. In this study, we performed DNA methylation profiling of 26 chordomas and normal nucleus pulposus samples plus UCH-1 chordoma cell line using the Illumina Infinium HumanMethylation450 BeadChips. Combined bisulfite restriction analysis and bisulfite sequencing was used to confirm the methylation data. Gene expression was analyzed using RT-PCR before and after 5-aza-2’-deoxycytidine (5-azaDC) treatment of chordoma cell lines. Analysis of the HumanMethylation450 BeadChip data led to the identification of 8,819 loci (2.9%) that were significantly differentially methylated (&gt;0.2 average β-value difference) between chordomas and nucleus pulposus samples (adjusted <i>P &lt;</i> 0.05). Among these, 5,868 probes (66.5%) were hypomethylated, compared to 2,951 (33.5%) loci that were hypermethylated in chordomas compared to controls. From the 2,951 differentially hypermethylated probes, 33.3% were localized in the promoter region (982 probes) and, among these, 104 probes showed cancer-specific hypermethylation. Ingenuity Pathway Analysis indicates that the cancer-specific differentially methylated loci are involved in various networks including cancer disease, nervous system development and function, cell death and survival, cellular growth, cellular development, and proliferation. Furthermore, we identified a subset of probes that were differentially methylated between recurrent and non-recurrent chordomas. BeadChip methylation data was confirmed for these genes and gene expression was shown to be upregulated in methylated chordoma cell lines after treatment with 5-azaDC. Understanding epigenetic changes in chordomas may provide insights into chordoma tumorigenesis and development of epigenetic biomarkers.
DOI: 10.6084/m9.figshare.1294965
title: Causes and Periods of Earth Electricity

description: Causes and periods of Earth electricity. GIC are geomagnetically induced currents, TID are traveling ionospheric disturbances, and EM is an abbreviation for the term electromagnetic. These data are published as Table 1 in: Helman, D. S. (2014). Earth electricity: a review of mechanisms which cause telluric currents in the lithosphere. Annals of Geophysics, 56(5), G0564.
DOI: 10.6084/m9.figshare.1294973
title: Magnitude, Duration and Transmission Frequency of Earth Electricity, Arranged by Magnitude

description: Magnitude, duration and transmission frequency of Earth electricity, arranged by magnitude. GIC are geomagnetically induced currents, TID are traveling ionospheric disturbances and e- is electrons. This is published as Table 2 in: Helman, D. S. (2014). Earth electricity: a review of mechanisms which cause telluric currents in the lithosphere. Annals of Geophysics, 56(5), G0564.
DOI: 10.6084/m9.figshare.1294965.v1
title: Causes and Periods of Earth Electricity

description: Causes and periods of Earth electricity. GIC are geomagnetically induced currents, TID are traveling ionospheric disturbances, and EM is an abbreviation for the term electromagnetic. These data are published as Table 1 in: Helman, D. S. (2014). Earth electricity: a review of mechanisms which cause telluric currents in the lithosphere. Annals of Geophysics, 56(5), G0564.
DOI: 10.6084/m9.figshare.1294973.v1
title: Magnitude, Duration and Transmission Frequency of Earth Electricity, Arranged by Magnitude

description: Magnitude, duration and transmission frequency of Earth electricity, arranged by magnitude. GIC are geomagnetically induced currents, TID are traveling ionospheric disturbances and e- is electrons. This is published as Table 2 in: Helman, D. S. (2014). Earth electricity: a review of mechanisms which cause telluric currents in the lithosphere. Annals of Geophysics, 56(5), G0564.
DOI: 10.6084/m9.figshare.1294961
title: Fossil musk turtles (Kinosternidae, <i>Sternotherus</i>) from the late Miocene–early Pliocene (Hemphillian) of Tennessee and Florida

description: ABSTRACTThe oldest fossil musk turtles, genus <i>Sternotherus</i>, are reported from the Hemphillian of eastern Tennessee and central Florida. <i>Sternotherus palaeodorus</i>, n. sp., is known from five partial shells discovered at the late Miocene–early Pliocene (7–4.5 Ma; late Hemphillian) Gray Fossil Site in Washington County, Tennessee. <i>Sternotherus palaeodorus</i> possesses an enlarged intergular scute, wide first vertebral scute that overlaps peripheral set 1, posteriorly extensive hypoplastron to peripheral 7 contact, and a posteriorly situated inguinal musk duct pore (characteristics more typically seen in <i>Kinosternon</i>). A cladistic analysis recovered <i>S. palaeodorus</i> within crown group <i>Sternotherus</i> in the strict consensus and on the stem of <i>Sternotherus</i> in the majority rule consensus. <i>Sternotherus bonevalleyensis</i>, n. sp., from the Palmetto Fauna (5.5–5 Ma; late Hemphillian) of central Florida was perhaps contemporaneous with <i>S. palaeodorus</i> and is known only from isolated shell fragments. It is morphologically most similar to the <i>Sternotherus minor</i> complex and <i>Sternotherus depressus</i>. Subsequent Blancan fossils from the Suwannee River of Florida represent aff. <i>S. minor peltifer</i>. Additionally, a fragmentary left hyoplastron of cf. <i>Sternotherus</i> from Haile 19A, Alachua County, Florida, could be the oldest record for the genus (ca. 9–8.5 Ma; early Hemphillian). These accounts reveal that <i>Sternotherus</i> was diverse and moderately well distributed geographically by its first known fossil occurrences and support previous hypotheses that the <i>Sternotherus minor</i> complex evolved in the Gulf coastal plain and dispersed throughout that region since at least the latest Miocene–earliest Pliocene. http://zoobank.org/urn:lsid:zoobank.org:pub:A1B8586C-0FCB-4B5E-B0B3-BD2D55B1ADC8SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1294963
title: A reevaluation of <i>Pliophoca etrusca</i> (Pinnipedia, Phocidae) from the Pliocene of Italy: phylogenetic and biogeographic implications

description: ABSTRACTThe holotype of <i>Pliophoca etrusca,</i> a partial skeleton from the late Pliocene (Piacenzian) of central Italy, is redescribed. Referred material from the Pliocene of Italy, France, and Spain is compared with the holotype and reassigned to <i>Pliophoca</i> cf. <i>P. etrusca</i>. New dental and postcranial material from the late Pliocene and Pleistocene of Italy is referred to Monachini indeterminate. Purported referred material from Pliocene deposits in the eastern North Atlantic (Lee Creek Mine, North Carolina) likely represents several new monachine taxa rather than <i>Pliophoca etrusca</i>. Using the largest novel data set to date, including extant and fossil monachines and comprising morphological and molecular data, we inferred phylogenetic relationships among monachine phocids. Results of morphological and combined analyses revealed that <i>Pliophoca etrusca</i> is most closely related to the Mediterranean monk seal, <i>Monachus monachus,</i> although this result is not strongly supported. Based on our phylogenetic framework, the origin of Monachini occurred during the early–middle Miocene, centered in either the Tethys Sea or the West Atlantic.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP