cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19686453.v2
title: RNA-seq Titration Results used in plotting for "Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously"

description: This data accompanies the manuscript "Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously" by Foltz, Taroni, and Greene. Please refer to our github page. <br> The file contains all data necessary to recreate the main and supplementary figures in our manuscript. <br> Abstract: Large compendia of gene expression data have proven valuable for the discovery of novel biological relationships. Historically, the majority of available RNA assays were run on microarray, while RNA-seq is now the platform of choice for many new experiments. The data structure and distributions between the platforms differ, making it challenging to combine them directly. Here we perform supervised and unsupervised machine learning evaluations to assess which existing normalization methods are best suited for combining microarray and RNA-seq data. We find that quantile and Training Distribution Matching normalization allow for supervised and unsupervised model training on microarray and RNA-seq data simultaneously. Nonparanormal normalization and z-scores are also appropriate for some applications, including pathway analysis with Pathway-Level Information Extractor (PLIER). We demonstrate that it is possible to perform effective cross-platform normalization using existing methods to combine microarray and RNA-seq data for machine learning applications.
DOI: 10.25573/data.21719933.v1
title: Long-term monitoring of social insects in a tropical rainforest

description: Number of individuals collected each year (2009-2021) on Barro Colorado Island, Panama, for each species (n=252 spp.) recruiting from 7 assemblages of social insects: <br> Bess beetles: Passalidae Termite workers and soldiers: Isoptera Termite alates: Isoptera Sweat bees: Halictidae Orchid bees: Euglossini Ant workers: Formicidae Army ant alates: Dorylinae <br>
DOI: 10.25573/data.21719933
title: Long-term monitoring of social insects in a tropical rainforest

description: Number of individuals collected each year (2009-2021) on Barro Colorado Island, Panama, for each species (n=252 spp.) recruiting from 7 assemblages of social insects: <br> Bess beetles: Passalidae Termite workers and soldiers: Isoptera Termite alates: Isoptera Sweat bees: Halictidae Orchid bees: Euglossini Ant workers: Formicidae Army ant alates: Dorylinae <br>
DOI: 10.5517/ccdc.csd.cc2c87nk
title: CCDC 2182668: Experimental Crystal Structure Determination

description: Related Article: Jin-Lin Wan, Jing-Mei Huang|2022|Org.Lett.|24|8914|doi:10.1021/acs.orglett.2c03774
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.5718535
title: Inflammation and cell-to-cell communication, two related aspects in frailty

description: The database includes the raw data of the article “Inflammation and cell-to-cell communication, two related aspects in frailty”. Aim of the work was to investigate inflammation and altered intercellular communication, both mechanisms involved in the biology of frailty, to ultimately identify if extracellular vesicles (EVs), specifically large EVs (lEVs) could play a role in the immune function in frail subjects. The database contains data obtained by means the following evaluations: i) Cobas 6000 automated analysis for the detection of c-reactive protein (CRP) plasma levels; ii) Meso Scale Discovery analysis for detection of cytokines (IL-1β, IL-6, TNFα, IFNγ and IL-13) plasma levels; iii) Nano Tracking Assay analysis for the detection of size and concentration of lEVs; iv) flow cytometry analysis for the detection of immunological markers (TLR2, TLR4, CD40 and CD120B) and senescence markers (CD221 and IL-6R) on lEVs. We found that CRP plasma levels increases in Fr subjects, thus suggesting a role of CRP as a possible biomarker in subjects experiencing symptoms of frailty. Moreover, we observed an increase in IL-1β, IL-6 and TNFα plasma levels in frail subjects. All these evidences point the robust involvement of inflammaging in frailty and suggest the role of circulating cytokines in the identification of frailty. We also focused on the role of lEVs and pro-inflammatory and pro-senescent hallmarks in frailty. We reported that lEVs size and concentration is not affected by frailty, howeverTLR2, TLR4 , CD40 and CD120b (TNF Receptor II) are significantly more expressed in lEVs of frail subjects respect to nFr. These results are indicative of a first and clear involvement of lEVs in the activation of pro-inflammatory pathways in frailty. Finally, in frail individuals we reported a significant increase in lEVs positive to markers of senescence: the IGF1receptor (CD221) and the IL6 receptor (IL6R). These evidences suggest IGF1 as a new potential biomarker of frailty, although new studies are needed. Moreover, positivity for the IL6R and the concomitant increase in circulating IL6 suggest a possible crucial role of lEVs in the delivery of cytokines through extracellular release and absorption. In conclusion, lEVs may contribute to the creation of a pro-inflammatory and pro-senescent microenvironment that acts as one of the major contributors to frailty.
description: Funding: Cariplo Foundation (Italy); EuroNanoMed III JTC 2018; Ministry of Health (Italy)
DOI: 10.5281/zenodo.5718534
title: Inflammation and cell-to-cell communication, two related aspects in frailty

description: The database includes the raw data of the article “Inflammation and cell-to-cell communication, two related aspects in frailty”. Aim of the work was to investigate inflammation and altered intercellular communication, both mechanisms involved in the biology of frailty, to ultimately identify if extracellular vesicles (EVs), specifically large EVs (lEVs) could play a role in the immune function in frail subjects. The database contains data obtained by means the following evaluations: i) Cobas 6000 automated analysis for the detection of c-reactive protein (CRP) plasma levels; ii) Meso Scale Discovery analysis for detection of cytokines (IL-1β, IL-6, TNFα, IFNγ and IL-13) plasma levels; iii) Nano Tracking Assay analysis for the detection of size and concentration of lEVs; iv) flow cytometry analysis for the detection of immunological markers (TLR2, TLR4, CD40 and CD120B) and senescence markers (CD221 and IL-6R) on lEVs. We found that CRP plasma levels increases in Fr subjects, thus suggesting a role of CRP as a possible biomarker in subjects experiencing symptoms of frailty. Moreover, we observed an increase in IL-1β, IL-6 and TNFα plasma levels in frail subjects. All these evidences point the robust involvement of inflammaging in frailty and suggest the role of circulating cytokines in the identification of frailty. We also focused on the role of lEVs and pro-inflammatory and pro-senescent hallmarks in frailty. We reported that lEVs size and concentration is not affected by frailty, howeverTLR2, TLR4 , CD40 and CD120b (TNF Receptor II) are significantly more expressed in lEVs of frail subjects respect to nFr. These results are indicative of a first and clear involvement of lEVs in the activation of pro-inflammatory pathways in frailty. Finally, in frail individuals we reported a significant increase in lEVs positive to markers of senescence: the IGF1receptor (CD221) and the IL6 receptor (IL6R). These evidences suggest IGF1 as a new potential biomarker of frailty, although new studies are needed. Moreover, positivity for the IL6R and the concomitant increase in circulating IL6 suggest a possible crucial role of lEVs in the delivery of cytokines through extracellular release and absorption. In conclusion, lEVs may contribute to the creation of a pro-inflammatory and pro-senescent microenvironment that acts as one of the major contributors to frailty.
description: Funding: Cariplo Foundation (Italy); EuroNanoMed III JTC 2018; Ministry of Health (Italy)
DOI: 10.5281/zenodo.7434758
title: Clausal Causal Markers in the Languages of Europe: A Database

description: The present typological database accumulates clausal causal markers in the languages of Europe. Clausal causal markers are used in polypredicative constructions (cf. <em>I fell down, because the floor was slippery</em>). The database contains more than 100 markers from Russian, Ukrainian, Belarusian, Polish, Czech, Slovak, Serbian, Bulgarian, Macedonian, Latvian, Lithuanian, German, English, Dutch, Danish, Swedish, Norwegian, Portuguese, Spanish, French, Italian, Catalan, Modern Greek, Albanian, Estonian, Finnish, Hungarian, Basque, Chuvash, and Georgian (currently 30 languages in total). The data were collected from grammars and language corpora and via elicitation. The typological parameters taken into consideration are: 1) semantic varieties of causal meanings: direct causal meaning (<em>I fell down, because the floor was slippery</em>); motive (<em>As it is your birthday today, I have bought you a present</em>); inferential (<em>Peter is at home, because he is not at work</em>); illocutionary-imperative (<em>Wrap it up with your packing, or (= because) you'll be late for your train</em>); illocutionary-question<em> </em>(<em>How much are the cucumbers, because I want to take a couple of kilos?</em>); logic (<em>It is a triangle, because it has three angles</em>); 2) assessment (positive vs. negative); 3) reality of the cause; 4) stylistic features; 5) morphosyntactic features (position of the marker within the clause, preposition vs. postposition of the causal clause; occurrence in emphatic constructions and under negation, etc.) 6) diachronic information and polysemy patterns. Further updates and expansion of the database are possible. The database was created at the Institute for Linguistic Studies, RAS with support from the Russian Science Foundation grant # 18-18-00472 “Causal Constructions in World Languages (Semantics and Typology)”.
DOI: 10.5281/zenodo.7434757
title: Clausal Causal Markers in the Languages of Europe: A Database

description: The present typological database accumulates clausal causal markers in the languages of Europe. Clausal causal markers are used in polypredicative constructions (cf. <em>I fell down, because the floor was slippery</em>). The database contains more than 100 markers from Russian, Ukrainian, Belarusian, Polish, Czech, Slovak, Serbian, Bulgarian, Macedonian, Latvian, Lithuanian, German, English, Dutch, Danish, Swedish, Norwegian, Portuguese, Spanish, French, Italian, Catalan, Modern Greek, Albanian, Estonian, Finnish, Hungarian, Basque, Chuvash, and Georgian (currently 30 languages in total). The data were collected from grammars and language corpora and via elicitation. The typological parameters taken into consideration are: 1) semantic varieties of causal meanings: direct causal meaning (<em>I fell down, because the floor was slippery</em>); motive (<em>As it is your birthday today, I have bought you a present</em>); inferential (<em>Peter is at home, because he is not at work</em>); illocutionary-imperative (<em>Wrap it up with your packing, or (= because) you'll be late for your train</em>); illocutionary-question<em> </em>(<em>How much are the cucumbers, because I want to take a couple of kilos?</em>); logic (<em>It is a triangle, because it has three angles</em>); 2) assessment (positive vs. negative); 3) reality of the cause; 4) stylistic features; 5) morphosyntactic features (position of the marker within the clause, preposition vs. postposition of the causal clause; occurrence in emphatic constructions and under negation, etc.) 6) diachronic information and polysemy patterns. Further updates and expansion of the database are possible. The database was created at the Institute for Linguistic Studies, RAS with support from the Russian Science Foundation grant # 18-18-00472 “Causal Constructions in World Languages (Semantics and Typology)”.
DOI: 10.15482/usda.adc/1528344
title: Data from: Implied climate warming contributions of enteric methane emissions are dependent on the estimate source and accounting methodology

description: This dataset was used in the generation of the manuscript titled: Implied climate warming contributions of enteric methane emissions are dependent on the estimate source and accounting methodology (DOI: 10.15232/aas.2022-02344). The objectives of this manuscript were to (1) demonstrate the differences in enteric methane emission estimates between 2 reporting entities (FAO and EPA) and to (2) demonstrate how the implied contribution to climate warming caused by enteric methane is dependent on accounting methodologies. The accounting methodologies explored were the conventional global warming potential (GWP) based on a 100-year time horizon (GWP100) or the newer GWP*. The GWP* methodology was developed because GWP100 fails to capture the short atmospheric lifespan of CH4, which is only 12-years (EPA, 2021a). The equations to calculate GWP100 (Equation 1; IPCC, 2013) and GWP* (Equation 2; Smith et al., 2021) are:
CH4, Mt CO2 equivalence = 28 × CH4(t) [Equation 1];
CH4, Mt CO2-we = (4.53 × CH4(t) – 4.25 × CH4(t–20)) × 28 [Equation 2].
Where CH4(t) is the CH4 emitted in million metric tons (Mt) at year t and CH4(t-20) is the amount of CH4 emitted in Mt 20-years prior.
Data was obtained from publicly available sources — the USDA-NASS biannual reports on cow and calf inventory in January and June (USDA-NASS, 2022), the EPA website (EPA, 2021b), and FAO from the FAOSTAT website (FAO, 2022). The data provided herein is an excel spreadsheet (.xlsx format) and contains 5 different sheets. Sheet titled "Descriptions" describe what each column names contain for the data-containing sheets.
References:
EPA (US Environmental Protection Agency). 2021a. Inventory of US Greenhouse Gas Emissions and Sinks 1990–2019. US Environmental Protection Agency.
EPA (US Environmental Protection Agency). 2021b. Inventory of US Greenhouse Gas Emissions and Sinks: 1990–2019. Accessed May 18, 2022. https://www.epa.gov/ghgemissions/inventory-us-greenhouse-gas-emissions-a....
FAO (Food and Agriculture Organization). 2022. FAOSTAT Emissions Totals. Accessed: May 18, 2022. https://www.fao.org/faostat/en/#data/GT.
IPCC (Intergovernmental Panel on Climate Change). 2013. Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. T. F. Stocker, D. Qin, G. K. Plattner, M. Tignor, S. K. Allen, J. Boschung, A. Nauels, Y. Xia, V. Bex, and P. M. Midgley, ed. Cambridge University Press.
NASS (National Agricultural Statistics Service). 2022. Cattle NASS. Accessed May 18, 2022. https://usda.library.cornell.edu/concern/publications/h702q636h?locale=en.
Smith, M. A., M. Cain, and M. R. Allen. 2021. Further improvement of warming-equivalent emissions calculation. npj Clim. Atmos. Sci. 4:1–3. https://doi.org/10.1038/s41612-021-00169-8.
DOI: 10.6084/m9.figshare.21711599
title: The acute phase response in bats (Carollia perspicillata) varies with time and dose of the immune challenge

description: The acute phase response (APR) is a core component of the innate immune response and represents the first line of immune defense used in response to infections. Although several studies with vertebrates reported fever, a decrease in food intake and body mass, and an increase in neutrophil/lymphocyte ratio and total white blood cell count after lipopolysaccharide (LPS) inoculation, there was great variability in the magnitude of these responses. Some of these differences might reflect, to some extent, differences in the time of endotoxin inoculation (during active or rest periods) and dose. Therefore, our study tested the interplay between LPS dose and time of injection on selected physiological (fever and increase in total white blood cell count and neutrophil/lymphocyte ratio) and behavioral (food intake) components of the APR using a Neotropical fruit-eating bat (<em>Carollia perspicillata</em>) as a model organism. We predicted that LPS would trigger a dose- and time-dependent response in APR components. APR components were assessed in rest and active periods after injection of three doses of LPS (5, 10 and 15 mg kg−1 LPS). The results indicate a more robust decrease in food intake at higher doses during the active period, while increased neutrophil/ lymphocyte ratio was more robust during the active period regardless of dose. Furthermore, the skin temperature increase lasted longer at higher doses regardless of the timing of injections. Our study offers important insights into the dependence of time as well as the LPS dosage effect in the APR of bats, and how they deal with the magnitude of infections at different times of day.
DOI: 10.6084/m9.figshare.21720272
title: Spotify songs

description: spotify songs data set
DOI: 10.5281/zenodo.5795375
title: Characterization of mitochondrial alterations in Aicardi-Goutières patients mutated in RNASEH2A and RNASEH2B Genes

description: The database includes the raw data of the article “Characterization of mitochondrial alterations in Aicardi-Goutières patients mutated in RNASEH2A and RNASEH2B genes”. Aim of the work was to investigate the role of mitochondria in AGS, both from a functional and a morphological point of view in lymphoblastoid cell lines (LCLs) derived from AGS patients mutated in the RNASEH2A and RNASEH2B genes, to ultimately establish the role of mitochondria in the pathogenesis of AGS. The database contains data obtained by means the following evaluations: i) flow cytometry analysis for the evaluation of the intermembrane mitochondrial potential (TMRE-Mitotracker) and for the quantification of produced ROS; ii) Seahorse Analysis for the evaluation of metabolic and energetic status of mutated LCLs; iii) RT-qPCR to determine the expression level of two glycolytic genes (PDK1 and LDHb) and quantify the mtDNA release into the cytoplasm; iiii) Western Blot analysis to quantify Oxphos system complexes protein level. Both mutant LCLs showed morphological and structural changes in mitochondria when compared to healthy controls, while RNASEH2A LCLs had the most loss of physiological membrane potential. Both mutant LCLs produced more ROS, but RNASEH2B LCLs produced substantially more. RNASEH2B LCLs had a considerably higher amount of cytoplasmic mtDNA. Mitochondrial damage was further confirmed by metabolic changes in both mutant cell lines. In particular RNASEH2A mutated LCLs showed higher ATP production rate and proton leak. These data were also confirmed by the expression level of two glycolytic genes that resulted enhanced in the RNASEH2A mutated cell line. Oxphos system complexes protein level did not show any significant differences. Our findings reveal for the first time the presence of mitochondrial abnormalities in AGS patients' LCLs, implying that these organelles play a critical role in AGS etiology.
description: Funding: NIH-funded grants (U01NS106845-01A1) and Ricerca Corrente 2017-2020 Ministry of Health (Italy)
DOI: 10.5281/zenodo.5795374
title: Characterization of mitochondrial alterations in Aicardi-Goutières patients mutated in RNASEH2A and RNASEH2B Genes

description: The database includes the raw data of the article “Characterization of mitochondrial alterations in Aicardi-Goutières patients mutated in RNASEH2A and RNASEH2B genes”. Aim of the work was to investigate the role of mitochondria in AGS, both from a functional and a morphological point of view in lymphoblastoid cell lines (LCLs) derived from AGS patients mutated in the RNASEH2A and RNASEH2B genes, to ultimately establish the role of mitochondria in the pathogenesis of AGS. The database contains data obtained by means the following evaluations: i) flow cytometry analysis for the evaluation of the intermembrane mitochondrial potential (TMRE-Mitotracker) and for the quantification of produced ROS; ii) Seahorse Analysis for the evaluation of metabolic and energetic status of mutated LCLs; iii) RT-qPCR to determine the expression level of two glycolytic genes (PDK1 and LDHb) and quantify the mtDNA release into the cytoplasm; iiii) Western Blot analysis to quantify Oxphos system complexes protein level. Both mutant LCLs showed morphological and structural changes in mitochondria when compared to healthy controls, while RNASEH2A LCLs had the most loss of physiological membrane potential. Both mutant LCLs produced more ROS, but RNASEH2B LCLs produced substantially more. RNASEH2B LCLs had a considerably higher amount of cytoplasmic mtDNA. Mitochondrial damage was further confirmed by metabolic changes in both mutant cell lines. In particular RNASEH2A mutated LCLs showed higher ATP production rate and proton leak. These data were also confirmed by the expression level of two glycolytic genes that resulted enhanced in the RNASEH2A mutated cell line. Oxphos system complexes protein level did not show any significant differences. Our findings reveal for the first time the presence of mitochondrial abnormalities in AGS patients' LCLs, implying that these organelles play a critical role in AGS etiology.
description: Funding: NIH-funded grants (U01NS106845-01A1) and Ricerca Corrente 2017-2020 Ministry of Health (Italy)
DOI: 10.3886/e176682v1
title: K-12 Civil Rights Complaints: Nationwide Data (1999-2019)

description: Through a Freedom of Information Act (FOIA) request, we sought information on all Office of Civil Rights (OCR) complaints filed against school districts between January 1st, 1999, and Dec 31st, 2019. In this dataset, we share the raw data received through the FOIA which includes the nature of the complaint, the associated civil rights law (including the specific section of the statute), the outcome of the complaint, the time for resolution, and the school district identifiers. A preliminary analysis of this data has been reported in a peer-reviewed publication "K-12 Civil Rights Complaints: A Nationwide Analysis" forthcoming in Educational Researcher.<b></b>
description: Collected by PIs through a Freedom of Information Act (FOIA) request to the Office of Civil Rights
DOI: 10.3886/e176682v2
title: K-12 Civil Rights Complaints: Nationwide Data (1999-2019)

description: Through a Freedom of Information Act (FOIA) request, we sought information on all Office for Civil Rights (OCR) complaints filed against school districts between January 1st, 1999, and Dec 31st, 2019. In this dataset, we share the raw data received through the FOIA which includes the nature of the complaint, the associated civil rights law (including the specific section of the statute), the outcome of the complaint, the time for resolution, and the school district identifiers. A preliminary analysis of this data has been reported in a peer-reviewed publication "K-12 Civil Rights Complaints: A Nationwide Analysis" forthcoming in Educational Researcher.<b></b>
description: Collected by PIs through a Freedom of Information Act (FOIA) request to the Office of Civil Rights
DOI: 10.6084/m9.figshare.21720227.v1
title: Table.docx

description: This table explained several product has been developed for diseases treatment