cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6320811
title: Macromolecule distributions input file for the OCEANFILMS parameterization

description: This dataset provides the inputs required for the OCEANFILMS parameterization of sea spray organic matter emissions, as it has been implemented in the Energy Exascale Earth System Model version 1 (E3SMv1; Burrows et al., 2014; 2022). The file was generated as described in Burrows et al. (2014). Briefly, we used the Parallel Ocean Program (POP; Maltrud et al., 1998) to simulate the general circulation and its biogeochemical elemental cycling (BEC) routines (Moore et al., 2004) to simulate marine biogeochemistry. Both are components of the Community Earth System Model (CESM; http://www2.cesm.ucar.edu, Hurrell et al., 2013). Calculations were performed using the CESM 1.0 beta release 11. The macromolecular distributions contained in these files were calculated based on various fields from these CESM simulations. 1. <strong>Lipids</strong> were calculated on the basis of the POP-simulated phytoplankton and zooplankton concentrations (Burrows et al., 2014; Eq. 11). 2. <strong>Polysaccharides</strong> were assumed to have a concentration identical to POP-simulated semilabile dissolved organic carbon (SDOC; Burrows et al., 2014; Eq. 12). 3. <strong>Proteins</strong> were assumed to have a concentration equal to one-third of POP-simulated SDOC (Burrows et al., 2014; Eq. 13). 4. A <strong>processed</strong> DOC group was estimated as a residual term from these surface pools (Burrows et al., 2014; Eq. 14, and surrounding text). This field has negligible impacts on the results of the OCEANFILMS parameterization, but has been retained here for clarity. 5. A <strong>humic</strong> compound group was estimated by assuming a fixed concentration of humic substances below the mixed layer, and estimating the effects of mixing this humic matter into the ocean mixed layer (Burrows et al., 2014; Eq. 17). As with the processed DOC group, this field's impact on the resulting predictions of the OCEANFILMS parameterization is negligible, but it has been retained here for clarity. All fields have the units µM C. The dataset is also available form the E3SM inputdata repository (last access 17 March 2022): https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mam/marine_BGC/monthly_macromolecules_0.1deg_bilinear_latlon_year01_merge_date.nc
DOI: 10.25345/c51g0hz69
title: MassIVE MSV000089258 - MCC_interactome_centrosome_Tomaz_Dunn
title: This dataset consists of 6 raw MS files and associated peak lists and result files, acquired on an Orbitrap classic or Orbitrap Velos mass spectrometer operated in Data Dependent Acquisition mode. Samples were generated by Bernard Liu, formerly of the Pawson lab. MassIVE report was performed by Anne-Claude Gingras. The files are associated with a manuscript submitted for publication by Lucian Tomaz et al. that describes the relocalization of Mutated in Colorectal Cancer (MCC) during intestinal cell differentiation. Dr. Ray Dunn is the corresponding author of the manuscript (ray.dunn@ntu.edu.sg); Anne-Claude Gingras or Bernard Liu (Bernard.a.liu@gmail.com) should be contacted for questions on this submission (gingras@lunenfeld.ca). This submission is associated with 3 Supplementary Files (in addition to this README file) Table 1 describes the composition of this dataset Table 2 lists all the peptide identification evidence (as per iProphet) Table 3 lists the SAINTexpress interactions Internal reference from the Gingras lab ProHits implementation: Project: P17, Export version: N/A SAINT Task ID: 5987
DOI: 10.6084/m9.figshare.19585810.v2
title: variable_catalog

description: See README
DOI: 10.25345/c5wp9tb1s
title: MassIVE Reanalysis RMSV000000645.1 - CPTAC MSV000082875/ S017 CPTAC, TCGA Colorectal Cancer Proteome Study Comparison and Reference Samples (CompRef), annotation file only
title: Annotation file for CPTAC MSV000082875/ S017 CPTAC, TCGA Colorectal Cancer Proteome Study Comparison and Reference Samples (CompRef)
DOI: 10.6073/pasta/95b1aeab15d98f73775feccf7e40bdd8
title: Identifying the drivers and responses of abrupt changes across spatial and temporal scales in ecology: a review

description: Recently, the theoretical basis for understanding abrupt changes in ecosystems relative to regime shifts has emerged (Ratajczak et al. 2018). Abrupt changes are defined as, “substantial changes in the mean or variability of a system that occur in a short period of time relative to typical rates of change” (Ratajczak et al. 2018). Despite a driver-response framework to guide the environmental conditions under which abrupt changes are likely to occur coupled with many examples of unexpected changes from long-term ecological research, our theoretical basis of understanding of abrupt changes doesn’t include long-term scales, variability in drivers and responses, changes in the magnitude or direction of drivers, or the interactions among multiple drivers across spatiotemporal scales (sensu Ratajczak et al. 2018). Further, a critical review of the literature is lacking and essential to further understanding how common abrupt changes are detected and reported, as well as patterns and scales of drivers and responses of abrupt change in ecosystems. To address this knowledge gap, we searched the existing ecological literature for evidence and commonalities of abrupt change across ecosystems to identify commonalities and differences of abrupt change drivers and responses across terrestrial, freshwater, and marine ecosystems. We specifically asked the following questions: (1) How common are abrupt changes reported in the ecological literature? (2) How do driver and response temporal and spatial scales of abrupt changes compare and vary across terrestrial, freshwater, and marine ecosystem types? (3) Is there relative congruence between the temporal and spatial scale of drivers and responses? (3) What are common types of drivers and responses to abrupt changes, and how do they vary across ecosystem types? (4) What terms are most associated with drivers and responses of abrupt changes among ecosystem types?
DOI: 10.25345/c5rx93h7d
title: MassIVE Reanalysis RMSV000000646.1 - CPTAC MSV000084233/ S018 CPTAC, TCGA Breast Cancer Proteome Study Comparison and Reference Samples (CompRef), annotation file only
title: Annotation file for CPTAC MSV000084233/ S018 CPTAC, TCGA Breast Cancer Proteome Study Comparison and Reference Samples (CompRef)
DOI: 10.6073/pasta/6dc3b214627046f2a068061b50e581b9
title: Marcell Experimental Forest 30-minute resolution meteorological data, 2006 - ongoing

description: This data publication contains 30-minute meteorological data collected from 2006 - ongoing at the Marcell Experimental Forest (MEF) in Itasca County, Minnesota, which is operated and maintained by the USDA Forest Service, Northern Research Station. Air temperature, relative humidity, wind speed and direction, photosynthetic photon flux density, soil temperature, and soil volumetric water content were measured at three meteorological monitoring stations. One station is in an upland clearing, one is under an upland forest canopy, and the third is in a peatland.
DOI: 10.25345/c5n58cq3k
title: MassIVE Reanalysis RMSV000000647.1 - CPTAC MSV000083043/ S015 CPTAC, TCGA Cancer Proteome Study of Breast Tissue, annotation file only
title: Annotation file for CPTAC MSV000083043/ S015 CPTAC, TCGA Cancer Proteome Study of Breast Tissue
DOI: 10.25345/c5hd7nw9t
title: MassIVE Reanalysis RMSV000000648.1 - CPTAC MSV000079852 S016/ S019 CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue / Global Proteome Analysis of Normal Colon Epithelium Samples, annotation file only
title: Annotation file for CPTAC MSV000079852 S016/ S019 CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue / Global Proteome Analysis of Normal Colon Epithelium Samples
DOI: 10.6084/m9.figshare.19601935
title: model-14-04-22:57

description: This description is a placeholder
DOI: 10.6084/m9.figshare.19601935.v1
title: model-14-04-22:57

description: This description is a placeholder
DOI: 10.6084/m9.figshare.13169212
title: Use of mobile phone among patients with HIV/AIDS in a low-middle income setting: a descriptive exploratory study

description: The use of mobile phone and factors influencing usage have least been explored in spite of its relevance in mHealth adoption. We conducted a descriptive exploratory study to evaluate the use of mobile phone alarm application, text messaging and voice call among HIV positive clients. We randomly selected 362 respondents who were 18–65 years and receive care from two health facilities in Accra, Ghana. Questionnaires were administered and data analysed to describe and predict mobile phone use. SPSS version 20 was used to process data for analysis. Findings revealed respondent (<i>n</i> = 338, 93%) did not share their mobile phones. Voice call was predominantly used (<i>n</i> = 227, 63%) while text messaging and mobile alarm functions were sparingly used. Majority (<i>n</i> = 285, 78.9%) did not use the mobile phone application to support adherence. Age and employment predicted the use of mobile phone alarm (OR ± 1.56, <i>p</i> &lt; 0.05), test messaging (OR ± 1.48, <i>p</i> &lt; 0.05) and voice calls (OR ± 1.25, <i>p</i> &lt; 0.05). We observed that younger age and employment influence the use of mobile phones. Voice calls are more acceptable because it is simple and easy to use. Knowledge and persuasion are fundamental to mobile phone literacy skills development and should be integrated in mHealth interventions.
DOI: 10.6084/m9.figshare.13169212.v1
title: Use of mobile phone among patients with HIV/AIDS in a low-middle income setting: a descriptive exploratory study

description: The use of mobile phone and factors influencing usage have least been explored in spite of its relevance in mHealth adoption. We conducted a descriptive exploratory study to evaluate the use of mobile phone alarm application, text messaging and voice call among HIV positive clients. We randomly selected 362 respondents who were 18–65 years and receive care from two health facilities in Accra, Ghana. Questionnaires were administered and data analysed to describe and predict mobile phone use. SPSS version 20 was used to process data for analysis. Findings revealed respondent (<i>n</i> = 338, 93%) did not share their mobile phones. Voice call was predominantly used (<i>n</i> = 227, 63%) while text messaging and mobile alarm functions were sparingly used. Majority (<i>n</i> = 285, 78.9%) did not use the mobile phone application to support adherence. Age and employment predicted the use of mobile phone alarm (OR ± 1.56, <i>p</i> &lt; 0.05), test messaging (OR ± 1.48, <i>p</i> &lt; 0.05) and voice calls (OR ± 1.25, <i>p</i> &lt; 0.05). We observed that younger age and employment influence the use of mobile phones. Voice calls are more acceptable because it is simple and easy to use. Knowledge and persuasion are fundamental to mobile phone literacy skills development and should be integrated in mHealth interventions.
DOI: 10.25919/4w6z-0a31
title: Experimental Data: Impact of Wearing on Filtration Performance of Electrostatic Filter Face Masks

description: Original data used in manuscript entitled “Impact of Wearing on Filtration Performance of Electrostatic Filter Face Masks” of the International Journal of Environmental Research and Public Health IJERPH to underpin findings on how wearing of respirator masks that contained electrostatically enhanced wool-polypropylene media affected performance in terms of filtration, breathing resistance, physical properties and dust loading as well as some general considerations concerning leakage.
DOI: 10.25345/c5cn6z353
title: MassIVE Reanalysis RMSV000000649.1 - CPTAC MSV000084236/ S021 CPTAC, TCGA Ovarian Cancer Proteome Study Comparison and Reference Samples (CompRef), annotation file only
title: Annotation file for CPTAC MSV000084236/ S021 CPTAC, TCGA Ovarian Cancer Proteome Study Comparison and Reference Samples (CompRef)
DOI: 10.25345/c5804xp52
title: MassIVE Reanalysis RMSV000000650.1 - CPTAC MSV000084252/ S020 CPTAC, TCGA Cancer Proteome Study of Ovarian Tissue, annotation file only
title: Annotation file for CPTAC MSV000084252/ S020 CPTAC, TCGA Cancer Proteome Study of Ovarian Tissue
DOI: 10.6084/m9.figshare.19601953.v1
title: Species checklists of mammal, bird and amphibian in the Himalaya Mountains.docx

description: The lowest and highest elevations known for each species are used to delineate its elevational limits. We assume that species potentially exist between their elevational limits. For species that have a single elevational distribution record (resulting in an elevational range of zero) as well as those with elevational ranges less than 200 m, we adjusted their elevation ranges to 200 m. We verified all data for accuracy by experts within the region and any dubious outlying records were removed. Elevational limits were given for 1,488 species, including 314 mammals, 1027 birds, and 147 amphibians in the Himalayas.
DOI: 10.6084/m9.figshare.12805640
title: Marine mineral-catalyzed NO and N2O formation on the anoxic early Earth

description: While microbial denitrification is the major pathway converting fixed nitrogen species into gases in extant oceans, it has been unclear how such transformations occurred within the early nitrogen cycle of the Archean. Here we report that in a Fe2+-rich (ferruginous) marine environment, Fe minerals could have catalyzed abiotic denitrification reactions leading to the formation of nitric oxide (NO) and nitrous oxide (N2O) at rates comparable to those measured in modern oxygen minimum zones. We experimentally simulated anoxic surface-catalyzed reduction of nitrite and nitrate via green rust and magnetite. Nitrate did not exhibit reactivity in the presence of either mineral or aqueous Fe2+, however, both minerals induced rapid nitrite reduction to NO and N2O. While N2O escaped into the atmosphere (63% of nitrite-nitrogen, with green rust as catalyst), NO remained associated with precipitates (7%). Using diffusion and photochemical modeling, we determine that marine N2O emissions would have sustained 0.8-6 ppb of atmospheric N2O without a protective ozone layer. Simultaneously, sinking of green rust particles constituted an effective shuttle for mineral-associated NO to reach benthic ocean layers. Seawater NO and N2O were either available as energy sources for early microbial metabolisms (~100 to 300 kcal e–1) or acted as cell toxins. Our findings add critical detail to the as yet incompletely documented Archean nitrogen cycle, implying a globally distributed process driven by chemical kinetics similar to those of modern enzymatically mediated conversions.
DOI: 10.6084/m9.figshare.12805640.v2
title: Marine mineral-catalyzed NO and N2O formation on the anoxic early Earth

description: While microbial denitrification is the major pathway converting fixed nitrogen species into gases in extant oceans, it has been unclear how such transformations occurred within the early nitrogen cycle of the Archean. Here we report that in a Fe2+-rich (ferruginous) marine environment, Fe minerals could have catalyzed abiotic denitrification reactions leading to the formation of nitric oxide (NO) and nitrous oxide (N2O) at rates comparable to those measured in modern oxygen minimum zones. We experimentally simulated anoxic surface-catalyzed reduction of nitrite and nitrate via green rust and magnetite. Nitrate did not exhibit reactivity in the presence of either mineral or aqueous Fe2+, however, both minerals induced rapid nitrite reduction to NO and N2O. While N2O escaped into the atmosphere (63% of nitrite-nitrogen, with green rust as catalyst), NO remained associated with precipitates (7%). Using diffusion and photochemical modeling, we determine that marine N2O emissions would have sustained 0.8-6 ppb of atmospheric N2O without a protective ozone layer. Simultaneously, sinking of green rust particles constituted an effective shuttle for mineral-associated NO to reach benthic ocean layers. Seawater NO and N2O were either available as energy sources for early microbial metabolisms (~100 to 300 kcal e–1) or acted as cell toxins. Our findings add critical detail to the as yet incompletely documented Archean nitrogen cycle, implying a globally distributed process driven by chemical kinetics similar to those of modern enzymatically mediated conversions.
DOI: 10.6084/m9.figshare.12805640.v1
title: Marine mineral-catalyzed NO and N2O formation on the anoxic early Earth

description: Microbial metabolisms were limited by available terminal electron acceptors in the anoxic environment of the early Archean. However, iron mineral phases in Fe2+-rich (ferruginous) oceans could have catalyzed reactions with abiotically fixed nitrogen leading to the formation of nitrous oxide (N2O), a potentially favorable terminal electron acceptor. We experimentally simulated anoxic surface-catalyzed reduction of nitrite and nitrate via green rust and magnetite. Besides N2O, we detected and quantified the formation of substantial amounts of nitric oxide (NO). While N2O escaped into the gas phase (63% of nitrite-nitrogen, with green rust as catalyst), NO remained associated with precipitates (7% of nitrite-nitrogen). Using diffusion and photochemical modeling, we show that marine N2O emissions could have sustained atmospheric N2O pools of 1-7 ppb. Although this concentration was insufficient to cause significant warming, the seawater enriched in N2O and NO could have critically affected early benthic life by providing the opportunity to conserve energy.<br>
DOI: 10.6084/m9.figshare.19601953.v3
title: Elevational range of mammals, birds, and amphibians in the Himalayas

description: The lowest and highest elevations known for each species are used to delineate its elevational limits. We assume that species potentially exist between their elevational limits. For species that have a single elevational distribution record (resulting in an elevational range of zero) as well as those with elevational ranges less than 200 m, we adjusted their elevation ranges to 200 m. We verified all data for accuracy by experts within the region and any dubious outlying records were removed. Elevational limits were given for 1,488 species, including 314 mammals, 1027 birds, and 147 amphibians in the Himalayas.
DOI: 10.6084/m9.figshare.19601953
title: Elevational range of mammals, birds, and amphibians in the Himalayas

description: The lowest and highest elevations known for each species are used to delineate its elevational limits. We assume that species potentially exist between their elevational limits. For species that have a single elevational distribution record (resulting in an elevational range of zero) as well as those with elevational ranges less than 200 m, we adjusted their elevation ranges to 200 m. We verified all data for accuracy by experts within the region and any dubious outlying records were removed. Elevational limits were given for 1,488 species, including 314 mammals, 1027 birds, and 147 amphibians in the Himalayas.
DOI: 10.6084/m9.figshare.19601953.v2
title: Elevational range of mammals, birds, and amphibians in the Himalayas

description: The lowest and highest elevations known for each species are used to delineate its elevational limits. We assume that species potentially exist between their elevational limits. For species that have a single elevational distribution record (resulting in an elevational range of zero) as well as those with elevational ranges less than 200 m, we adjusted their elevation ranges to 200 m. We verified all data for accuracy by experts within the region and any dubious outlying records were removed. Elevational limits were given for 1,488 species, including 314 mammals, 1027 birds, and 147 amphibians in the Himalayas.
DOI: 10.6084/m9.figshare.19601944.v1
title: Raw data

description: We collected the data from 2004 to 2018 to test the effect of grazing exclusion and the duration on stability.
DOI: 10.17632/7w3fwx7y2y.1
title: IMAGINE trial data 

description: Data from IMAGINE feasibility randomised controlled trial. 56 adolescents who were randomised to imagery-based cognitive therapy or nondirective supportive therapy. Main outcomes are feasibility, acceptability and and safety data. Secondary outcomes are clinical data including measures of depression, anxiety  and   memory specificity. Please see protocol paper for full methodology and list of measures.
DOI: 10.17632/yhyf2cs7s8.1
title: Supplementary tables for "Cutaneous T-cell lymphoma following dupilumab use: A systematic review"

description: In this systematic review, we aimed to evaluate reported cases of CTLC following dupilumab use and identify characteristics, histologic findings, and timeline of CTCL development. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was performed using PubMed and Embase databases (Figure 1). Key search terms were: “mycosis fungoides and dupilumab”,  “cutaneous T cell lymphoma and dupilumab”, “sezary and dupilumab”. Additional relevant studies were identified using the reference lists from the included articles. Studies reporting at least one patient who developed CTCL, such as mycosis fungoides (MF) or sezary syndrome (SS), after dupilumab treatment for an initial diagnosis other than CTCL, or studies demonstrating exacerbation of CTCL with dupilumab were included. Letters from the editor and cases reporting clinical improvement of MF or SS after dupilumab therapy were excluded. Two reviewers (A.P. and A.E.) independently assessed the articles. Data extracted included: study type, patient demographics, preliminary diagnosis, initial treatment, duration of dupilumab treatment, clinical signs and symptoms, sites involved, body surface area involved, TNM classification/tumor stage, pre- and post-dupilumab histopathologic features, time to biopsy after dupilumab, immunohistochemical phenotype, TCR gene rearrangement, final diagnosis, treatment, and clinical outcome.
DOI: 10.17632/7vbp983x44.2
title: Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20. Vieira-Vieira et al Figure S5A

description: RNA-binding proteins (RBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in RBPs have been identified, little is known about how these modifications regulate RBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular RBPs pulled down with polyadenylated mRNAs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of RBPs. Almost 200 phosphorylation events increased or decreased pull-down efficiency compared to the unmodified RBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytoplasmic RNP granules and alternative splicing. Together, we show that qRIC in conjunction with phosphoproteomics is a scalable method to identify functional posttranslational modification sites in RBPs.