cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6121382.v1
title: Mass spectrometry data of Xenacoelomorph neuropeptides

description: Mass spectrometric data of peptide extracts from three Xenacoelomorpha species Convolutriloba macropyga (Cmac R1), Hofstenia miamia (Hmia R2), Isodiametra pulchra (Ipul R3). Data includes scores and spectra of identified peptides.
DOI: 10.6084/m9.figshare.6121379
title: Cluster analysis of secretin type neuropeptide GPCR

description: Cluster analysis of secretin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. Programm: CLANS 2<br>
DOI: 10.6084/m9.figshare.6121379.v1
title: Cluster analysis of secretin type neuropeptide GPCR

description: Cluster analysis of secretin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. Programm: CLANS 2<br>
DOI: 10.6084/m9.figshare.6121376
title: Cluster analysis of rhodopsin type neuropeptide GPCRs

description: Cluster analysis of rhodopsin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. Programm: CLANS 2
DOI: 10.6084/m9.figshare.6121373
title: Phylogenetic analysis of secretin type neuropeptide GPCRs using RAxML.

description: Phylogenetic analysis of aligned secretin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia. Programm: RAxML v.8.2.9, amino acid substitution model: LG
DOI: 10.6084/m9.figshare.6121364
title: Phylogenetic analysis of secretin type neuropeptide GPCRs using FastTree.

description: Phylogenetic analysis of aligned secretin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia. Programm: FastTree v.2.1, amino acid substitution model: LG
DOI: 10.6084/m9.figshare.6121349
title: Phylogenetic analysis of rhodopsin type neuropeptide GPCRs using RAxML

description: Phylogenetic analysis of aligned rhodopsin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. Programm: RAxML v.8.2.9, amino acid substitution model: LG
DOI: 10.6084/m9.figshare.6121349.v1
title: Phylogenetic analysis of rhodopsin type neuropeptide GPCRs using RAxML

description: Phylogenetic analysis of aligned rhodopsin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. Programm: RAxML v.8.2.9, amino acid substitution model: LG
DOI: 10.6084/m9.figshare.6121340
title: Phylogenetic analysis of rhodopsin type neuropeptide GPCRs using FastTree

description: Phylogenetic analysis of aligned rhodopsin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. Programm: FastTree v.2.1, amino acid substitution model: LG
DOI: 10.6084/m9.figshare.6121337
title: Number code of secretin type neuropeptide GPCR alignment

description: Key to identify the numbered sequences that were used in the alignment of secretin type neuropeptide GPCRs.
DOI: 10.6084/m9.figshare.6121340.v1
title: Phylogenetic analysis of rhodopsin type neuropeptide GPCRs using FastTree

description: Phylogenetic analysis of aligned rhodopsin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. Programm: FastTree v.2.1, amino acid substitution model: LG
DOI: 10.6084/m9.figshare.6121337.v1
title: Number code of secretin type neuropeptide GPCR alignment

description: Key to identify the numbered sequences that were used in the alignment of secretin type neuropeptide GPCRs.
DOI: 10.6084/m9.figshare.6121331
title: Number code of rhodopsin type neuropeptide GPCR alignment

description: Key to identify the numbered sequences that were used in the alignment of rhodopsin type neuropeptide GPCRs.
DOI: 10.6084/m9.figshare.6121331.v1
title: Number code of rhodopsin type neuropeptide GPCR alignment

description: Key to identify the numbered sequences that were used in the alignment of rhodopsin type neuropeptide GPCRs.
DOI: 10.6084/m9.figshare.6121328
title: Alignment of secretin type neuropeptide GPCRs

description: Alignment of secretin type neuropeptide GPCRs belonging to Xenacoelomorpha, Deuterostomia, Protostomia. 516 sequences, 453 amino acid position.
DOI: 10.6084/m9.figshare.6121322
title: Data Set: Web of Science Data

description: Bibliographic citation data for articles citing the inaugural Berman et al. (2000) reference (with permission from Clarivate Analytics)
DOI: 10.6084/m9.figshare.6121322.v1
title: Data Set: Web of Science Data

description: Bibliographic citation data for articles citing the inaugural Berman et al. (2000) reference (with permission from Clarivate Analytics)
DOI: 10.6084/m9.figshare.6121316
title: THERPA: A small molecule database related to prion protein regulation and prion diseases progression

description: Prion diseases are fatal neurodegenerative disorders that affect humans and animals. Although various small molecules have been evaluated for application in the treatment of prion diseases, none have been shown to be efficacious. Expanding our knowledge of these molecules is important for understanding of the complex mechanisms of prion diseases. To improve access to the scattered information on small molecules related to prion diseases, we built a database of therapeutic molecules associated with prion diseases (THERPA, therpa.pythonanywhere.com). THERPA includes 119 small molecules and their 283 relationships with prion diseases. THERPA is an interactive visual database and useful for improving search efficiency which can help researchers identify intrinsic small molecules that can be used for developing therapeutics for prion diseases.
DOI: 10.6084/m9.figshare.6121316.v2
title: THERPA: A small molecule database related to prion protein regulation and prion diseases progression

description: Prion diseases are fatal neurodegenerative disorders that affect humans and animals. Although various small molecules have been evaluated for application in the treatment of prion diseases, none have been shown to be efficacious. Expanding our knowledge of these molecules is important for understanding of the complex mechanisms of prion diseases. To improve access to the scattered information on small molecules related to prion diseases, we built a database of therapeutic molecules associated with prion diseases (THERPA, therpa.pythonanywhere.com). THERPA includes 119 small molecules and their 283 relationships with prion diseases. THERPA is an interactive visual database and useful for improving search efficiency which can help researchers identify intrinsic small molecules that can be used for developing therapeutics for prion diseases.
DOI: 10.6084/m9.figshare.6121316.v1
title: THERPA: a small molecule database related to prion protein regulation and prion disease progression

description: Prion diseases are fatal neurodegenerative disorders that affect humans and animals. Although various small molecules have been evaluated for application in the treatment of prion diseases, none have been shown to be efficacious. Expanding our knowledge of these molecules is important for understanding of the complex mechanisms of prion diseases. To improve access to the scattered information on small molecules related to prion diseases, we built a database of therapeutic molecules associated with prion diseases (THERPA, therpa.pythonanywhere.com). THERPA includes 119 small molecules and their 283 relationships with prion diseases. THERPA is an interactive visual database and useful for improving search efficiency which can help researchers identify intrinsic small molecules that can be used for developing therapeutics for prion diseases.
DOI: 10.6084/m9.figshare.6121310
title: Simple discrimination of sub-cycling cells by propidium iodide flow cytometric assay in Jurkat cell samples with extensive DNA fragmentation

description: Human leukemia Jurkat T cells were analyzed for apoptosis and cell cycle by flow cytometry, using the Annexin V/propidium iodide (PI) standard assay, and a simple PI staining in Triton X-100/digitonin-enriched PI/RNase buffer, respectively. Cells treated with doxorubicin or menadione displayed a very strong correlation between the apoptotic cell fraction measured by the Annexin V/PI assay, and the weight of a secondary cell population that emerged on the forward scatter (FS)/PI plot, as well as on the side scatter (SS)/PI and FL1/PI plots generated from parallel cell cycle recordings. In both cases, the Pearson correlation coefficients were &gt;0.99. In cell cycle determinations, PI fluorescence was detected on FL3 (620/30 nm), and control samples exhibited the expected linear dependence of FL3 on FL1 (525/40 nm) signals. However, increasing doses of doxorubicin or menadione generated a growing subpopulation of cells displaying a definite right-shift on the FS/FL3, SS/FL3 and FL1/FL3 plots, as well as decreased PI fluorescence, indicative of ongoing fragmentation and loss of nuclear DNA. By gating on these events, the resulting fraction of presumably sub-cycling cells (i.e. cells with cleaved DNA, counting sub-G<sub>0</sub>/G<sub>1</sub>, sub-S and sub-G<sub>2</sub>/M cells altogether) was closely similar to the apoptotic rate assessed by Annexin V/PI labeling. Taken together, these findings suggest a possible way to recognize the entire population of cells undergoing apoptotic DNA cleavage and simultaneously determine the cell cycle distribution of non-apoptotic cells in PI-labeled cell samples with various degrees of DNA fragmentation, using a simple and reproducible multiparametric analysis of flow cytometric recordings.
DOI: 10.6084/m9.figshare.6121310.v1
title: Simple discrimination of sub-cycling cells by propidium iodide flow cytometric assay in Jurkat cell samples with extensive DNA fragmentation

description: Human leukemia Jurkat T cells were analyzed for apoptosis and cell cycle by flow cytometry, using the Annexin V/propidium iodide (PI) standard assay, and a simple PI staining in Triton X-100/digitonin-enriched PI/RNase buffer, respectively. Cells treated with doxorubicin or menadione displayed a very strong correlation between the apoptotic cell fraction measured by the Annexin V/PI assay, and the weight of a secondary cell population that emerged on the forward scatter (FS)/PI plot, as well as on the side scatter (SS)/PI and FL1/PI plots generated from parallel cell cycle recordings. In both cases, the Pearson correlation coefficients were &gt;0.99. In cell cycle determinations, PI fluorescence was detected on FL3 (620/30 nm), and control samples exhibited the expected linear dependence of FL3 on FL1 (525/40 nm) signals. However, increasing doses of doxorubicin or menadione generated a growing subpopulation of cells displaying a definite right-shift on the FS/FL3, SS/FL3 and FL1/FL3 plots, as well as decreased PI fluorescence, indicative of ongoing fragmentation and loss of nuclear DNA. By gating on these events, the resulting fraction of presumably sub-cycling cells (i.e. cells with cleaved DNA, counting sub-G<sub>0</sub>/G<sub>1</sub>, sub-S and sub-G<sub>2</sub>/M cells altogether) was closely similar to the apoptotic rate assessed by Annexin V/PI labeling. Taken together, these findings suggest a possible way to recognize the entire population of cells undergoing apoptotic DNA cleavage and simultaneously determine the cell cycle distribution of non-apoptotic cells in PI-labeled cell samples with various degrees of DNA fragmentation, using a simple and reproducible multiparametric analysis of flow cytometric recordings.
DOI: 10.6084/m9.figshare.6121298
title: Alignment of rhodopsin type neuropeptide GPCRs

description: Alignment of rhodopsin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. 1591 sequences, 271 amino acid position.
DOI: 10.6084/m9.figshare.6121298.v1
title: Alignment of rhodopsin type neuropeptide GPCRs

description: Alignment of rhodopsin type neuropeptide GPCRs, belonging to Xenacoelomorpha, Deuterostomia, Protostomia, Cnidaria. 1591 sequences, 271 amino acid position.
DOI: 10.6084/m9.figshare.6121280
title: Supplementary Material for: Downregulation and Aberrant Localization of Forkhead Box J1 in Allergic Nasal Mucosa

description: <b><i>Background:</i></b> Forkhead box J1 (FOXJ1) plays pivotal roles in motile cilia formation. However, it remains unclear whether abnormal expression or localization of FOXJ1 in nasal mucosa tissues is associated with allergic rhinitis (AR), in which impaired mucociliary clearance is implicated. <b><i>Objective:</i></b> We sought to investigate the expression and localization of FOXJ1 in inferior turbinate from patients with AR and controls. <b><i>Methods:</i></b> We assayed mRNA levels of FOXJ1, DNAI1, DNALI1, and DNAH9 by using whole-genome expression array and quantitative real-time polymerase chain reaction. We elucidated the localization of FOXJ1 by using immunofluorescence assays in paraffin sections and primary single cells. Four patterns of FOXJ1 localization (normal, N; intermediate, I; mislocalization, M; absence, A) were defined. We developed a semiquantitative scoring system to elucidate their localization in 5 areas per paraffin section, with individual sections being assigned a score between 0 and 2. <b><i>Results:</i></b> The mRNA levels of FOXJ1, DNAI1, DNALI1, and DNAH9 were significantly reduced in patients with AR compared with controls (all <i>p</i> &lt; 0.05). The median (1st and 3rd quartile) of the FOXJ1 score was 0.4 (0.0 and 0.85) in patients with AR, and 0.2 (0.0 and 0.4) in controls (<i>p</i> &lt; 0.05). For primary cytospin samples, the mean percentages of FOXJ1 localization patterns N, I, M, and A were 46.7, 10.0, 30.0, and 26.7% in patients with AR, and 82.5, 5.0, 5.0, and 7.5% in controls, respectively (<i>p</i> &lt; 0.05). <b><i>Conclusion:</i></b> Downregulation and aberrant localization of FOXJ1 may be crucial characteristics of the allergic nasal mucosa.
DOI: 10.6084/m9.figshare.6121280.v1
title: Supplementary Material for: Downregulation and Aberrant Localization of Forkhead Box J1 in Allergic Nasal Mucosa

description: <b><i>Background:</i></b> Forkhead box J1 (FOXJ1) plays pivotal roles in motile cilia formation. However, it remains unclear whether abnormal expression or localization of FOXJ1 in nasal mucosa tissues is associated with allergic rhinitis (AR), in which impaired mucociliary clearance is implicated. <b><i>Objective:</i></b> We sought to investigate the expression and localization of FOXJ1 in inferior turbinate from patients with AR and controls. <b><i>Methods:</i></b> We assayed mRNA levels of FOXJ1, DNAI1, DNALI1, and DNAH9 by using whole-genome expression array and quantitative real-time polymerase chain reaction. We elucidated the localization of FOXJ1 by using immunofluorescence assays in paraffin sections and primary single cells. Four patterns of FOXJ1 localization (normal, N; intermediate, I; mislocalization, M; absence, A) were defined. We developed a semiquantitative scoring system to elucidate their localization in 5 areas per paraffin section, with individual sections being assigned a score between 0 and 2. <b><i>Results:</i></b> The mRNA levels of FOXJ1, DNAI1, DNALI1, and DNAH9 were significantly reduced in patients with AR compared with controls (all <i>p</i> &lt; 0.05). The median (1st and 3rd quartile) of the FOXJ1 score was 0.4 (0.0 and 0.85) in patients with AR, and 0.2 (0.0 and 0.4) in controls (<i>p</i> &lt; 0.05). For primary cytospin samples, the mean percentages of FOXJ1 localization patterns N, I, M, and A were 46.7, 10.0, 30.0, and 26.7% in patients with AR, and 82.5, 5.0, 5.0, and 7.5% in controls, respectively (<i>p</i> &lt; 0.05). <b><i>Conclusion:</i></b> Downregulation and aberrant localization of FOXJ1 may be crucial characteristics of the allergic nasal mucosa.
DOI: 10.6084/m9.figshare.6121277
title: Facies analysis, stratigraphy and marine vertebrate assemblage of the lower Miocene Chilcatay Formation at Ullujaya (Pisco basin, Peru)

description: This paper is the first integrated account of the sedimentology, stratigraphy, and vertebrate paleontology for the marine strata of the Chilcatay Formation exposed at Ullujaya, Pisco basin (southern Peru). An allostratigraphic framework for the investigated strata was established using geological mapping (1:4000 scale) and conventional sedimentary facies analysis and resulted in recognition of two unconformity-bounded allomembers (designated Ct1 and Ct2 in ascending order). The chronostratigraphic framework is well constrained by integration of micropaleontological data and isotope geochronology and indicates deposition during the early Miocene. The marine vertebrate fossil assemblage is largely dominated by cetaceans (odontocetes), whereas isolated teeth and spines indicate a well-diversified elasmobranch assemblage. Our field surveys, conducted to evaluate the paleontological sensitivity of the investigated strata, indicate that vertebrate remains only came from a rather restricted stratigraphic interval of the Ct1 allomember and reveal the high potential for these sediments to yield abundant and scientifically significant fossil assemblages.
DOI: 10.6084/m9.figshare.6121277.v1
title: Facies analysis, stratigraphy and marine vertebrate assemblage of the lower Miocene Chilcatay Formation at Ullujaya (Pisco basin, Peru)

description: This paper is the first integrated account of the sedimentology, stratigraphy, and vertebrate paleontology for the marine strata of the Chilcatay Formation exposed at Ullujaya, Pisco basin (southern Peru). An allostratigraphic framework for the investigated strata was established using geological mapping (1:4000 scale) and conventional sedimentary facies analysis and resulted in recognition of two unconformity-bounded allomembers (designated Ct1 and Ct2 in ascending order). The chronostratigraphic framework is well constrained by integration of micropaleontological data and isotope geochronology and indicates deposition during the early Miocene. The marine vertebrate fossil assemblage is largely dominated by cetaceans (odontocetes), whereas isolated teeth and spines indicate a well-diversified elasmobranch assemblage. Our field surveys, conducted to evaluate the paleontological sensitivity of the investigated strata, indicate that vertebrate remains only came from a rather restricted stratigraphic interval of the Ct1 allomember and reveal the high potential for these sediments to yield abundant and scientifically significant fossil assemblages.
DOI: 10.6084/m9.figshare.6121274
title: Olympic history: longitudinal data scraped from www.sports-reference.com

description: Historical data on the modern Olympics from Athens 1896 to Rio 2016. The data was scraped from www.sports-reference.com in May 2018. <br><br>The file <b>athlete_events.csv</b> contains 271116 rows and 15 columns. Each row corresponds to an individual athlete competing in an individual Olympic event (athlete-events). The columns are:<br><br><b>1. ID</b> - Row numbers<b>2. Name </b>- Athlete's name<br><b>3. Sex</b> - M or F<b>4. Age</b> - Integer<b></b><i></i><sub></sub><sup></sup><br><b>5. Height</b> - In centimeters<b>6. Weight</b> - In kilograms<br><b>7. Team</b> - Team name<b>8. NOC</b> - National Olympic Committee 3-letter code<b>9. Games</b> - Year and season<br><b>10. Year</b> - Integer<br><b>11. Season</b> - Summer or Winter<b>12. City</b> - Host city<br><b>13. Sport</b> - Sport<br><b>14. Event</b> - Event<br><b>15. Medal </b>- Gold, Silver, Bronze, or NA<br><br>For more information:<br><br><b>About the sports-reference Olympic database:</b> http://olympstats.com/2016/08/21/the-olymadmen-and-olympstats-and-sports-reference/<br><br><b>About how I scraped the data:</b> https://rgriff23.github.io/2018/05/27/olympic-history-1-web-scraping.html<br><br><b>About how I wrangled the data:</b> <br>https://rgriff23.github.io/2018/05/28/olympic-history-2-data-wrangling-1.html<br>https://rgriff23.github.io/2018/05/28/olympic-history-3-data-wrangling-2.html<br><br><b>My GitHub repo for this project, including analyses using this data:<br></b>https://github.com/rgriff23/Olympic_history <br><b></b>
DOI: 10.6084/m9.figshare.6121100
title: Corrected supplementary files for Troupin D, Carmel Y (2018) Conservation planning under uncertainty in urban development and vegetation dynamics. PLOS ONE 13(4): e0195429. https://doi.org/10.1371/journal.pone.0195429

description: Supplementary files with correction of typological errors in titles and sheet names within the files.<br>
DOI: 10.6084/m9.figshare.6121100.v1
title: Supplementary files for Troupin D, Carmel Y (2018) Conservation planning under uncertainty in urban development and vegetation dynamics. PLOS ONE 13(4): e0195429. https://doi.org/10.1371/journal.pone.0195429

description: Supplementary files with correction of typos in titles/sheet names within the files<br>
DOI: 10.6084/m9.figshare.6121100.v3
title: Corrected supplementary files for Troupin D, Carmel Y (2018) Conservation planning under uncertainty in urban development and vegetation dynamics. PLOS ONE 13(4): e0195429. https://doi.org/10.1371/journal.pone.0195429

description: Supplementary files with correction of typological errors in titles and sheet names within the files.<br>
DOI: 10.6084/m9.figshare.6121100.v2
title: Supplementary files for Troupin D, Carmel Y (2018) Conservation planning under uncertainty in urban development and vegetation dynamics. PLOS ONE 13(4): e0195429. https://doi.org/10.1371/journal.pone.0195429

description: Supplementary files with correction of typological errors in titles and sheet names within the files.<br>
DOI: 10.6084/m9.figshare.6121022
title: Supplementary Material for: Exon Array Biomarkers for the Differential Diagnosis of Schizophrenia and Bipolar Disorder

description: This study developed potential blood-based biomarker tests for diagnosing and differentiating schizophrenia (SZ), bipolar disorder type I (BD), and normal control (NC) subjects using mRNA gene expression signatures. A total of 90 subjects (<i>n</i> = 30 each for the three groups of subjects) provided blood samples at two visits. The Affymetrix exon microarray was used to profile the expression of over 1.4 million probesets. We selected potential biomarker panels using the temporal stability of the probesets and also back-tested them at two different visits for each subject. The 18-gene biomarker panels, using logistic regression modeling, correctly differentiated the three groups of subjects with high accuracy across the two different clinical visits (83–88% accuracy). The results are also consistent with the actual data and the “leave-one-out” analyses, indicating that the models should be predictive when applied to independent data cohorts. Many of the SZ and BD subjects were taking antipsychotic and mood stabilizer medications at the time of blood draw, raising the possibility that these drugs could have affected some of the differential transcription signatures. Using an independent Illumina data set of gene expression data from antipsychotic medication-free SZ subjects, the 18-gene biomarker panels produced a receiver operating characteristic curve accuracy greater than 0.866 in patients that were less than 30 years of age and medication free. We confirmed select transcripts by quantitative PCR and the nCounter® System. The episodic nature of psychiatric disorders might lead to highly variable results depending on when blood is collected in relation to the severity of the disease/symptoms. We have found stable trait gene panel markers for lifelong psychiatric disorders that may have diagnostic utility in younger undiagnosed subjects where there is a critical unmet need. The study requires replication in subjects for ultimate proof of the utility of the differential diagnosis.