cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6982991
title: Study data.xlsx

description: A top-down approach was adopted for the identification, measurement, and valuation of the direct costs of CKD and ESKD, based on administrative data obtained from the SIA/SUS and SIH/SUS. These systems serve as a registry of all procedures reimbursed by the Brazilian Ministry of Health to health facilities (hospitals, clinics, and laboratories), public or private, that provide services to the Unified Health System. Direct costs were defined as those of outpatient (SIA/SUS) and inpatient (SIH/SUS) procedures, such as doctor’s appointments, laboratory tests, medications, hospital admissions, treatment of complications, renal replacement therapy, and renal transplantation. Non-medical direct costs (patient transport, caregiver payment), indirect costs (absenteeism, presenteeism, and early death), and intangible costs (loss of ability to work, loss of quality of life, among others) were disregarded. For analysis, direct costs were stratified by variable (sex, race/skin color, and age) and combined with International Classification of Diseases (ICD-10) codes for CKD (N18, N18.8, N18.9) and ESKD (N18.0). The variables sex, race/skin color, and age were divided into the following categories: a) sex – female and male; b) age – 18 to 29 years, 30 to 59 years, 60 to 64 years, 65 to 74 years, and &gt;75 years; c) race/skin color – yellow (Asian), white, red (Native Brazilian), mix-race (<i>pardo</i>), black, and not reported. Specifically for the race/skin color variable, data reallocation was required, as 24% of database entries belonged to the “not reported” category. Data reallocation was performed by calculating the percent share of the categories “yellow”, “white”, “red”, “mix-race”, “black” in relation to total cost, disregarding costs for the “not reported” category; then, costs for the “not reported” category were redistributed based on the percent share calculated in the previous step. Nominal values ​​for the 2010-2016 period were used, without any adjustment for inflation.
DOI: 10.6084/m9.figshare.6983006.v1
title: Saudi tweets dataset

description: This dataset was used in the paper entitled "Issues of Dialectal Saudi Twitter Corpus" that will be published by the International Arab Journal of Information Technology.<br>
DOI: 10.6084/m9.figshare.6983006.v2
title: Saudi tweets dataset

description: This dataset was used in the paper entitled "Issues of Dialectal Saudi Twitter Corpus" that will be published by the International Arab Journal of Information Technology.<br>
DOI: 10.7284/119575
title: GNSS (Global Navigation Satellite System) data collected during research cruise PE15-24 using a Trimble SPS351 instrument system onboard the platform RV Pelican
DOI: 10.6084/m9.figshare.6982919
title: MultiPLIER Fileset

description: This is the code and data from the MultiPLIER project v0.2.0 (https://github.com/greenelab/multi-plier/tree/v0.2.0). Please see the GitHub repository for more information, including code licensing information.<br>Please see https://github.com/greenelab/rheum-plier-data for more information about individual datasets and citations and cite the original publications as appropriate.<br>If you use any PLIER models, please be sure to cite:<br>Mao W, Harmann B, Sealfon SC, Zaslavsky E, Chikina M. Pathway-Level Information ExtractoR (PLIER) for gene expression data. <i>bioRxiv</i>. 2017. DOI: 10.1101/116061<br>If you use any recount2 data or models trained on these data, please be sure to cite:<br><br>Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B and Leek JT (2017). "Reproducible RNA-seq analysis using recount2." Nature Biotechnology. doi: 10.1038/nbt.3838<br>All recount2 data is CC-BY, recount2 authors.<br>
DOI: 10.6084/m9.figshare.6982919.v1
title: MultiPLIER Fileset

description: This is the code and data from the MultiPLIER project v0.1.0 (https://github.com/greenelab/multi-plier/tree/v0.1.0). Please see the GitHub repository for more information, including code licensing information.<br>Please see https://github.com/greenelab/rheum-plier-data for more information about individual datasets and citations and cite the original publications as appropriate.<br>If you use any PLIER models, please be sure to cite:<br>Mao W, Harmann B, Sealfon SC, Zaslavsky E, Chikina M. Pathway-Level Information ExtractoR (PLIER) for gene expression data. <i>bioRxiv</i>. 2017. DOI: 10.1101/116061
DOI: 10.7284/101431
title: Multiplexed data collected during research cruise PS0912 using a MLML UDAS instrument system onboard the platform RV Point Sur
DOI: 10.7284/101427
title: Multiplexed data collected during research cruise PS0915 using a MLML UDAS instrument system onboard the platform RV Point Sur
DOI: 10.7284/109883
title: Multiplexed data collected during research cruise PS1229 using a Hawaii UHDAS instrument system onboard the platform RV Point Sur
DOI: 10.6084/m9.figshare.6982454
title: Responses of the chloroplast glyoxalase system to high CO<sub>2</sub> concentrations

description: Sugar metabolism pathways such as photosynthesis produce dicarbonyls, e.g. methylglyoxal (MG), which can cause cellular damage. The glyoxalase (GLX) system comprises two enzymes GLX1 and GLX2, and detoxifies MG; however, this system is poorly understood in the chloroplast, compared with the cytosol. In the present study, we determined GLX1 and GLX2 activities in spinach chloroplasts, which constituted 40% and 10%, respectively, of the total leaf glyoxalase activity. In <i>Arabidopsis thaliana</i>, five GFP-fusion GLXs were present in the chloroplasts. Under high CO<sub>2</sub> concentrations, where increased photosynthesis promotes the MG production, GLX1 and GLX2 activities in <i>A. thaliana</i> increased and the expression of <i>AtGLX1-2</i> and <i>AtGLX2-5</i> was enhanced. On the basis of these findings and the phylogeny of GLX in oxygenic phototrophs, we propose that the GLX system scavenges MG produced in chloroplasts during photosynthesis. The glyoxalase system scavenges methylglyoxal produced in chloroplasts during photosynthesis.
DOI: 10.6084/m9.figshare.6982454.v1
title: Responses of the chloroplast glyoxalase system to high CO<sub>2</sub> concentrations

description: Sugar metabolism pathways such as photosynthesis produce dicarbonyls, e.g. methylglyoxal (MG), which can cause cellular damage. The glyoxalase (GLX) system comprises two enzymes GLX1 and GLX2, and detoxifies MG; however, this system is poorly understood in the chloroplast, compared with the cytosol. In the present study, we determined GLX1 and GLX2 activities in spinach chloroplasts, which constituted 40% and 10%, respectively, of the total leaf glyoxalase activity. In <i>Arabidopsis thaliana</i>, five GFP-fusion GLXs were present in the chloroplasts. Under high CO<sub>2</sub> concentrations, where increased photosynthesis promotes the MG production, GLX1 and GLX2 activities in <i>A. thaliana</i> increased and the expression of <i>AtGLX1-2</i> and <i>AtGLX2-5</i> was enhanced. On the basis of these findings and the phylogeny of GLX in oxygenic phototrophs, we propose that the GLX system scavenges MG produced in chloroplasts during photosynthesis. The glyoxalase system scavenges methylglyoxal produced in chloroplasts during photosynthesis.
DOI: 10.6084/m9.figshare.6982298
title: Application of sensitivity analysis to incomplete longitudinal CD4 count data

description: In this paper, we investigate the effect of tuberculosis pericarditis (TBP) treatment on CD4 count changes over time and draw inferences in the presence of missing data. We accounted for missing data and conducted sensitivity analyses to assess whether inferences under missing at random (MAR) assumption are sensitive to not missing at random (NMAR) assumptions using the selection model (SeM) framework. We conducted sensitivity analysis using the local influence approach and stress-testing analysis. Our analyses showed that the inferences from the MAR are robust to the NMAR assumption and influential subjects do not overturn the study conclusions about treatment effects and the dropout mechanism. Therefore, the missing CD4 count measurements are likely to be MAR. The results also revealed that TBP treatment does not interact with HIV/AIDS treatment and that TBP treatment has no significant effect on CD4 count changes over time. Although the methods considered were applied to data in the IMPI trial setting, the methods can also be applied to clinical trials with similar settings.
DOI: 10.6084/m9.figshare.6982298.v1
title: Application of sensitivity analysis to incomplete longitudinal CD4 count data

description: In this paper, we investigate the effect of tuberculosis pericarditis (TBP) treatment on CD4 count changes over time and draw inferences in the presence of missing data. We accounted for missing data and conducted sensitivity analyses to assess whether inferences under missing at random (MAR) assumption are sensitive to not missing at random (NMAR) assumptions using the selection model (SeM) framework. We conducted sensitivity analysis using the local influence approach and stress-testing analysis. Our analyses showed that the inferences from the MAR are robust to the NMAR assumption and influential subjects do not overturn the study conclusions about treatment effects and the dropout mechanism. Therefore, the missing CD4 count measurements are likely to be MAR. The results also revealed that TBP treatment does not interact with HIV/AIDS treatment and that TBP treatment has no significant effect on CD4 count changes over time. Although the methods considered were applied to data in the IMPI trial setting, the methods can also be applied to clinical trials with similar settings.
DOI: 10.7284/113186
title: Multiplexed data collected during research cruise PS1306 using a MLML UDAS instrument system onboard the platform RV Point Sur
DOI: 10.6084/m9.figshare.6982274
title: MOESM6 of JARID2 and the PRC2 complex regulate skeletal muscle differentiation through regulation of canonical Wnt signaling

description: Additional file 6: File S1 . TCGA data analysis used in study.
DOI: 10.6084/m9.figshare.6982274.v1
title: MOESM6 of JARID2 and the PRC2 complex regulate skeletal muscle differentiation through regulation of canonical Wnt signaling

description: Additional file 6: File S1 . TCGA data analysis used in study.
DOI: 10.6084/m9.figshare.6982256
title: Additional file 1: of Clinical impact of endocapillary proliferation according to the Oxford classification among adults with Henoch-Schönlein purpura nephritis: a multicenter retrospective cohort study

description: Data set of adult HSPN patients (39 females, 35 males, mean age 47.8 ± 17.4 years, and all Japanese). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6982256.v1
title: Additional file 1: of Clinical impact of endocapillary proliferation according to the Oxford classification among adults with Henoch-Schönlein purpura nephritis: a multicenter retrospective cohort study

description: Data set of adult HSPN patients (39 females, 35 males, mean age 47.8 ± 17.4 years, and all Japanese). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6982226
title: MOESM5 of Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors

description: Additional file 5. Zip file with all potential protein target structures protein data bank files.
DOI: 10.6084/m9.figshare.6982226.v1
title: MOESM5 of Predictive classification models and targets identification for betulin derivatives as Leishmania donovani inhibitors

description: Additional file 5. Zip file with all potential protein target structures protein data bank files.
DOI: 10.7284/121411
title: Fluorometer data collected during research cruise PS1416 using a Turner 10-AU instrument system onboard the platform RV Point Sur
DOI: 10.7284/121410
title: Singlebeam Echosounder data collected during research cruise PS1416 using a Knudsen 320B/R instrument system onboard the platform RV Point Sur
DOI: 10.6084/m9.figshare.6982157
title: Additional file 4: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Factors associated with Soil-transmitted helminths infections among the 562 preschool-age children that participated in the study in Hoima District. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6982157.v1
title: Additional file 4: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Factors associated with Soil-transmitted helminths infections among the 562 preschool-age children that participated in the study in Hoima District. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6982145
title: Additional file 1: of Pre-treatment with sumatriptan for cilostazol induced headache in healthy volunteers

description: Datasheet pre-treatment. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6982145.v1
title: Additional file 1: of Pre-treatment with sumatriptan for cilostazol induced headache in healthy volunteers

description: Datasheet pre-treatment. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6982142
title: Additional file 3: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Contains data used to draw conclusions. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.6982142.v1
title: Additional file 3: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Contains data used to draw conclusions. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.6982130
title: Additional file 2: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Contains data used to draw Fig. 1 (The Prevalence of STH), Fig. 2 (the distribution of STH and the intensity of STH among the 562 PSAC in Hoima district) & Fig. 3 (Intensity of STH infection among the 562 PSAC that participated in the study in Hoima District). (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6982130.v1
title: Additional file 2: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Contains data used to draw Fig. 1 (The Prevalence of STH), Fig. 2 (the distribution of STH and the intensity of STH among the 562 PSAC in Hoima district) & Fig. 3 (Intensity of STH infection among the 562 PSAC that participated in the study in Hoima District). (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6982124
title: Additional file 2: of Targeting the Tie2–αvβ3 integrin axis with bi-specific reagents for the inhibition of angiogenesis

description: Supporting data values. (XLSX 4536 kb)
DOI: 10.6084/m9.figshare.6982121
title: Additional file 1: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Prevalence of soil transmitted helminths infections among the 562 preschool-age children that participated in the study in Hoima. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6982121.v1
title: Additional file 1: of Prevalence, intensity and factors associated with soil-transmitted helminths infections among preschool-age children in Hoima district, rural western Uganda

description: Prevalence of soil transmitted helminths infections among the 562 preschool-age children that participated in the study in Hoima. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6982124.v1
title: Additional file 2: of Targeting the Tie2–αvβ3 integrin axis with bi-specific reagents for the inhibition of angiogenesis

description: Supporting data values. (XLSX 4536 kb)
DOI: 10.7284/121308
title: GNSS (Global Navigation Satellite System) data collected during research cruise TN332 using a C&C C-Nav 2000 instrument system onboard the platform RV Thomas G. Thompson
DOI: 10.6084/m9.figshare.6982079
title: MOESM2 of Dysregulation of the calcium handling protein, CCDC47, is associated with diabetic cardiomyopathy

description: Additional file 2: Table S1. List of Unique proteins associated with Calcium regulation and/or endoplasmic reticulum/sarcoplasmic reticulum (ER/SR).
DOI: 10.6084/m9.figshare.6982079.v1
title: MOESM2 of Dysregulation of the calcium handling protein, CCDC47, is associated with diabetic cardiomyopathy

description: Additional file 2: Table S1. List of Unique proteins associated with Calcium regulation and/or endoplasmic reticulum/sarcoplasmic reticulum (ER/SR).
DOI: 10.7284/106772
title: Multiplexed data collected during research cruise W1104B using a Hawaii UHDAS instrument system onboard the platform RV Wecoma
DOI: 10.7284/107065
title: GNSS (Global Navigation Satellite System) data collected during research cruise W1105B using a Garmin GPS-17HVS instrument system onboard the platform RV Wecoma
DOI: 10.7284/106958
title: Anemometer data collected during research cruise W1106A using a RM Young 05103 instrument system onboard the platform RV Wecoma
DOI: 10.6084/m9.figshare.6981842
title: Model output and meta-analysis data from INTERFACE paper

description: Model output and meta-analysis data from model-experiment comparison that came out of INTERFACE workshop. Includes output from five soil carbon models and a meta-analysis of warming and litter addition experiments.<br>Code is posted at: https://github.com/bsulman/INTERFACE-model-experiment-synthesis
DOI: 10.6084/m9.figshare.6981839
title: C-terminal psi blast tree

description: Files used to create phylogenetic tree to analyze the history of lineage specific ankyrin domain genes. Details on methodology given in forthcoming publication currently on biorxiv https://doi.org/10.1101/383968
DOI: 10.6084/m9.figshare.6981806
title: Physicochemical properties and oxidative potential of fine particles produced from coal combustion

description: The physical and chemical properties as well as the oxidative potential (OP) of water soluble components of coal combustion fine particles were examined. A laboratory-scale pulverized-coal burning system was used to produce coal combustion particles at different burning temperatures of 550 °C, 700 °C, 900 °C, and 1,100 °C. Few studies have reported the effects of burning temperature on both the chemistry and toxicity of coal combustion particles. The highest mass emission factor of particulate matter less than 2.5 µm (PM<sub>2.5</sub>) was found to be produced at 700 °C (3.51 g/kg), owing to strong elemental carbon (EC) emission and ash formation (ions and elements) resulting from the incomplete combustion of tar and char, and mineral fragmentation. The highest organic carbon in PM<sub>2.5</sub> was found at 550 °C. At a temperature higher than 700 °C, the fraction of carbonaceous species decreased while the fractions of ions and elements increased owing to ash formation. Sulfate was found to be the dominant ionic species, followed by sodium, calcium, and magnesium. The highest emission of elements (Al, As, Ba, Cd, Co, Cu, Fe, Mn, Ni, Pb, Sr, Ti, V, and Zn) and the highest fractions of Fe and Al were observed at 700 °C. Intrinsic OP activities obtained from dithiothreitol (DTT) and electron spin resonance (ESR) assays showed the highest values at 550 °C, suggesting that fine particles from low-temperature coal combustion had the highest reactive oxygen species generation capability (potentially toxic) among various tested burning temperatures. The results of principal component analysis suggested a correlation between OP-DTT activity and OC, EC, Cd, Co, V, and Zn, while OP-ESR activity was associated with chloride, nitrate, Ba, Pb, Sr, and Ti. © 2018 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.6981806.v1
title: Physicochemical properties and oxidative potential of fine particles produced from coal combustion

description: The physical and chemical properties as well as the oxidative potential (OP) of water soluble components of coal combustion fine particles were examined. A laboratory-scale pulverized-coal burning system was used to produce coal combustion particles at different burning temperatures of 550 °C, 700 °C, 900 °C, and 1,100 °C. Few studies have reported the effects of burning temperature on both the chemistry and toxicity of coal combustion particles. The highest mass emission factor of particulate matter less than 2.5 µm (PM<sub>2.5</sub>) was found to be produced at 700 °C (3.51 g/kg), owing to strong elemental carbon (EC) emission and ash formation (ions and elements) resulting from the incomplete combustion of tar and char, and mineral fragmentation. The highest organic carbon in PM<sub>2.5</sub> was found at 550 °C. At a temperature higher than 700 °C, the fraction of carbonaceous species decreased while the fractions of ions and elements increased owing to ash formation. Sulfate was found to be the dominant ionic species, followed by sodium, calcium, and magnesium. The highest emission of elements (Al, As, Ba, Cd, Co, Cu, Fe, Mn, Ni, Pb, Sr, Ti, V, and Zn) and the highest fractions of Fe and Al were observed at 700 °C. Intrinsic OP activities obtained from dithiothreitol (DTT) and electron spin resonance (ESR) assays showed the highest values at 550 °C, suggesting that fine particles from low-temperature coal combustion had the highest reactive oxygen species generation capability (potentially toxic) among various tested burning temperatures. The results of principal component analysis suggested a correlation between OP-DTT activity and OC, EC, Cd, Co, V, and Zn, while OP-ESR activity was associated with chloride, nitrate, Ba, Pb, Sr, and Ti. © 2018 American Association for Aerosol Research
DOI: 10.7284/106996
title: Meteorological Station data collected during research cruise W1109C using a Vaisala PTU301 instrument system onboard the platform RV Wecoma
DOI: 10.6084/m9.figshare.6981764
title: Polarization and Distribution of Tumor-Associated Macrophages and COX-2 Expression in Basal Cell Carcinoma of the Ocular Adnexae

description: <i>Purpose</i>: Basal cell carcinoma (BCC) is a locally invasive skin tumor which can be subdivided into a circumscribed nodular and an invasive fibrosing subtype. There is increasing evidence that macrophages play an important role in interacting between tumor cells and their microenvironment, thereby affecting not only the invasive potential but also the patients’ prognosis. Thus, we wanted to compare these two BCC variants with regard to tumor-related inflammation, COX-2 expression, distribution, and polarization of tumor-associated macrophages. <i>Material and Methods</i>: 30 BCCs (nodular: <i>n</i> = 15; fibrosing: <i>n</i> = 15) of the ocular adnexae were investigated by histopathology and immunohistochemistry. The grade of inflammation was evaluated on hematoxylin and eosin stains (score: 0–3). Immunohistochemical stains for CD68 (macrophages), Ki67 (proliferative activity), and COX-2 as well as immunofluorescence stains for CD68 and CD163 (to distinguish M1 and M2 macrophage subtypes) were performed. SPSS was used for statistical analysis. <i>Results</i>: Fibrosing BCCs were predominantly located on the lower lid, while nodular BCCs showed a broader distribution (<i>p</i> = 0.013). The fibrosing BCC subtype was associated with a higher degree of inflammation (<i>p</i> p = 0.012). COX-2-positive cells were predominantly located on the infiltrating edge of the tumor. Macrophage polarization was balanced regarding M1 and M2 macrophage subtypes. There was no difference in macrophage number (<i>p</i> = 0.389) or polarization (<i>p</i> = 0.161) between nodular and fibrosing BCC. <i>Conclusions</i>: The findings indicate that COX-2 represents a factor for invasion of BCC. Macrophage polarization did not play a major role for aggressive behavior. However, other inflammatory components than tumor-associated macrophages seem to be involved in tissue destruction and thereby an invading growth pattern since fibrosing BCC revealed a significantly more intense inflammatory reaction in the surrounding tissue.