cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5716363.v1
title: Acclimation curve data from Gradual plasticity alters population dynamics in variable environments: thermal acclimation in the green alga <i>Chlamydomonas reinhartdii</i>

description: Environmental variability is ubiquitous, but its effects on populations are not fully understood or predictable. Recent attention has focused on how rapid evolution can impact ecological dynamics via adaptive trait change. However, the impact of trait change arising from plastic responses has received less attention, and is often assumed to optimize performance and unfold on a separate, faster timescale than ecological dynamics. Challenging these assumptions, we propose that gradual plasticity is important for ecological dynamics, and present a study of the plastic responses of the freshwater green algae <i>Chlamydomonas reinhardtii</i> as it acclimates to temperature changes. First, we show that <i>C. reinhardtii</i>'s gradual acclimation responses can both enhance and suppress its performance after a perturbation, depending on its prior thermal history. Second, we demonstrate that where conventional approaches fail to predict the population dynamics of <i>C. reinhardtii</i> exposed to temperature fluctuations, a new model of gradual acclimation succeeds. Finally, using high-resolution data, we show that phytoplankton in lake ecosystems can experience thermal variation sufficient to make acclimation relevant. These results challenge prevailing assumptions about plasticity's interactions with ecological dynamics. Amidst the current emphasis on rapid evolution, it is critical that we also develop predictive methods accounting for plasticity.
DOI: 10.6084/m9.figshare.5716357
title: Fluctuating temperature experiment data from Gradual plasticity alters population dynamics in variable environments: thermal acclimation in the green alga <i>Chlamydomonas reinhartdii</i>

description: Environmental variability is ubiquitous, but its effects on populations are not fully understood or predictable. Recent attention has focused on how rapid evolution can impact ecological dynamics via adaptive trait change. However, the impact of trait change arising from plastic responses has received less attention, and is often assumed to optimize performance and unfold on a separate, faster timescale than ecological dynamics. Challenging these assumptions, we propose that gradual plasticity is important for ecological dynamics, and present a study of the plastic responses of the freshwater green algae <i>Chlamydomonas reinhardtii</i> as it acclimates to temperature changes. First, we show that <i>C. reinhardtii</i>'s gradual acclimation responses can both enhance and suppress its performance after a perturbation, depending on its prior thermal history. Second, we demonstrate that where conventional approaches fail to predict the population dynamics of <i>C. reinhardtii</i> exposed to temperature fluctuations, a new model of gradual acclimation succeeds. Finally, using high-resolution data, we show that phytoplankton in lake ecosystems can experience thermal variation sufficient to make acclimation relevant. These results challenge prevailing assumptions about plasticity's interactions with ecological dynamics. Amidst the current emphasis on rapid evolution, it is critical that we also develop predictive methods accounting for plasticity.
DOI: 10.6084/m9.figshare.5716357.v1
title: Fluctuating temperature experiment data from Gradual plasticity alters population dynamics in variable environments: thermal acclimation in the green alga <i>Chlamydomonas reinhartdii</i>

description: Environmental variability is ubiquitous, but its effects on populations are not fully understood or predictable. Recent attention has focused on how rapid evolution can impact ecological dynamics via adaptive trait change. However, the impact of trait change arising from plastic responses has received less attention, and is often assumed to optimize performance and unfold on a separate, faster timescale than ecological dynamics. Challenging these assumptions, we propose that gradual plasticity is important for ecological dynamics, and present a study of the plastic responses of the freshwater green algae <i>Chlamydomonas reinhardtii</i> as it acclimates to temperature changes. First, we show that <i>C. reinhardtii</i>'s gradual acclimation responses can both enhance and suppress its performance after a perturbation, depending on its prior thermal history. Second, we demonstrate that where conventional approaches fail to predict the population dynamics of <i>C. reinhardtii</i> exposed to temperature fluctuations, a new model of gradual acclimation succeeds. Finally, using high-resolution data, we show that phytoplankton in lake ecosystems can experience thermal variation sufficient to make acclimation relevant. These results challenge prevailing assumptions about plasticity's interactions with ecological dynamics. Amidst the current emphasis on rapid evolution, it is critical that we also develop predictive methods accounting for plasticity.
DOI: 10.6084/m9.figshare.5716354
title: Single isolate data from Gradual plasticity alters population dynamics in variable environments: thermal acclimation in the green alga <i>Chlamydomonas reinhartdii</i>

description: Environmental variability is ubiquitous, but its effects on populations are not fully understood or predictable. Recent attention has focused on how rapid evolution can impact ecological dynamics via adaptive trait change. However, the impact of trait change arising from plastic responses has received less attention, and is often assumed to optimize performance and unfold on a separate, faster timescale than ecological dynamics. Challenging these assumptions, we propose that gradual plasticity is important for ecological dynamics, and present a study of the plastic responses of the freshwater green algae <i>Chlamydomonas reinhardtii</i> as it acclimates to temperature changes. First, we show that <i>C. reinhardtii</i>'s gradual acclimation responses can both enhance and suppress its performance after a perturbation, depending on its prior thermal history. Second, we demonstrate that where conventional approaches fail to predict the population dynamics of <i>C. reinhardtii</i> exposed to temperature fluctuations, a new model of gradual acclimation succeeds. Finally, using high-resolution data, we show that phytoplankton in lake ecosystems can experience thermal variation sufficient to make acclimation relevant. These results challenge prevailing assumptions about plasticity's interactions with ecological dynamics. Amidst the current emphasis on rapid evolution, it is critical that we also develop predictive methods accounting for plasticity.
DOI: 10.6084/m9.figshare.5716351
title: Metadata summary from Gradual plasticity alters population dynamics in variable environments: thermal acclimation in the green alga <i>Chlamydomonas reinhartdii</i>

description: Summary of the contents and associated metadata for the 3 subsequent data files provided along with our manuscript.
DOI: 10.6084/m9.figshare.5716351.v1
title: Metadata summary from Gradual plasticity alters population dynamics in variable environments: thermal acclimation in the green alga <i>Chlamydomonas reinhartdii</i>

description: Summary of the contents and associated metadata for the 3 subsequent data files provided along with our manuscript.
DOI: 10.6084/m9.figshare.5716294
title: Genotype data of the six SNPs from Prediction of cholesterol ratios within a Korean population

description: Genotype data of 6 SNPs which were used in the present study.
DOI: 10.6084/m9.figshare.5716294.v1
title: Genotype data of the six SNPs from Prediction of cholesterol ratios within a Korean population

description: Genotype data of 6 SNPs which were used in the present study.
DOI: 10.6084/m9.figshare.5716282
title: R code from Limited support for the X-linked grandmother hypothesis in pre-industrial Finland

description: R code used for analyses
DOI: 10.6084/m9.figshare.5716282.v1
title: R code from Limited support for the X-linked grandmother hypothesis in pre-industrial Finland

description: R code used for analyses
DOI: 10.6084/m9.figshare.5716270
title: 60-90S Monthly Pressure Reconstruction

description: Monthly pressure anomaly reconstruction 60-90S performed by a kriging interpolation of 19 long-term Antarctic station observations. The data is from January 1957 - December 2016 by month, using the 80km x 80km Cartesian grid centered over the South Pole. Use the file 'wrf_latlon_80km.nc' for the lat-lon grid for plotting. Please address questions to Dr. Ryan Fogt at Ohio University, fogtr@ohio.edu.
DOI: 10.6084/m9.figshare.5716270.v1
title: 60-90S Monthly Pressure Reconstruction

description: Monthly pressure anomaly reconstruction 60-90S performed by a kriging interpolation of 19 long-term Antarctic station observations. The data is from January 1957 - December 2016 by month, using the 80km x 80km Cartesian grid centered over the South Pole. Use the file 'wrf_latlon_80km.nc' for the lat-lon grid for plotting. Please address questions to Dr. Ryan Fogt at Ohio University, fogtr@ohio.edu.
DOI: 10.6084/m9.figshare.5716150
title: Supplementary Material for: Diversity in Antagonistic Interactions between Commensal Oral Streptococci and Streptococcus mutans

description: Arginine metabolism via the arginine deiminase system (ADS) of oral bacteria generates ammonia, which can increase the pH of oral biofilms and decrease the risk for dental caries. Antagonistic interactions between ADS-positive and cariogenic bacteria in oral biofilms may be an important ecological determinant of caries. This study investigated the antagonistic potential and mechanisms of clinical isolates of arginolytic streptococci on and by <i>Streptococcus mutans </i>UA159, a well-characterized cariogenic human isolate. Low-passage isolates of <i>Streptococcus gordonii</i>, <i>Streptococcus sanguinis</i>, <i>Streptococcus parasanguinis, Streptococcus australis</i>, and <i>Streptococcus cristatus</i> inhibited the growth of <i>S. mutans </i>to various degrees when they were inoculated on growth media first or simultaneously with <i>S. mutans</i>. The antagonistic effects of arginolytic strains against <i>S. mutans </i>and the production of H<sub>2</sub>O<sub>2</sub> by these strains were enhanced during growth in a less-rich medium or when galactose was substituted for glucose as the primary carbohydrate source. Pyruvate oxidase was the dominant pathway for H<sub>2</sub>O<sub>2</sub> production by arginolytic strains, but lactate oxidase activity was also detected in some strains of <i>S. gordonii</i> and<i> S. cristatus. </i>UA159 inhibited the growth of all tested arginolytic strains when inoculated first, especially in aerobic conditions. However, the antagonistic effects of <i>S. mutans </i>on certain strains of <i>S. gordonii</i> and<i> S. australis</i> were not observed during anaerobic growth in the presence of arginine. Thus, arginolytic commensal streptococci may have a synergistically positive impact on the ecology of oral biofilms by moderating biofilm pH while antagonizing the growth and virulence of caries pathogens.
DOI: 10.6084/m9.figshare.5716099
title: Supplementary Material for: Th17 Inhibitors in Active Psoriatic Arthritis: A Systematic Review and Meta-Analysis of Randomized Controlled Clinical Trials

description: <b><i>Background:</i></b> Several biologics targeting the Th17 pathway have been developed for the treatment of psoriatic arthritis (PsA), a disabling disease with moderate response and an increased incidence of serious infections to first-line biologics (TNF-α antagonists). Th17 inhibitors could replace TNF-α antagonists as first-line biologic agents. We determined the overall treatment effect of Th17 pathway inhibitors compared to placebo or active control on American College of Rheumatology (ACR) 20 response at week 12 (primary objective), risk of infections, discontinuation of treatment due to adverse events, and serious adverse events during the placebo-controlled period (12-24 weeks) in adults with active PsA in published randomized controlled trials. <b><i>Methods:</i></b> The SCOPUS database was searched. The Cochrane risk of bias tool was used for assessing quality. The pooled relative risk (RR) was derived from random effects models. <b><i>Results:</i></b> Seven randomized controlled trials were included which randomized 1,718 patients to Th17 inhibitors and 840 to placebo. Patients treated with Th17 inhibitors had an RR of 2.04 (95% CI: 1.79-2.33; <i>p</i> &lt; 0.001) for achieving an ACR20 response at week 12 (I<sup>2</sup> = 0%; <i>p</i> = 0.89) compared to placebo-treated patients. There was no evidence of publication bias. The result was consistent for study phase and outcome (ACR50/70), mechanism of action and TNF-α naivety. RR of infections was 1.06 (0.91-1.23), that of candida infections was 3.35 (0.75-14.95), that of serious adverse events was 0.82 (0.42-1.59) and that of discontinuation of treatment was 0.54 (0.31-0.93) among treated versus placebo subjects. No incident cases of tuberculosis were reported. <b><i>Conclusion:</i></b> In patients with active PsA, biologics targeting the Th17 axis produce a clinically significant improvement in joint disease activity with acceptable safety and tolerability for short-term treatment compared to placebo.
DOI: 10.6084/m9.figshare.5716033
title: recount.rpkm.RData

description: This is the output of a pipeline that trains a Pathway-Level Information ExtractoR (PLIER) model on recount2 data (RPKM). See: https://github.com/greenelab/rheum-plier-data/tree/978c37938383ff7adcadacfcbc35931ce5e62b17<br><br>It was run in a Docker container. See the Github repository for more information. <br><br>Below, we include information about the scripts used to generate each item using the relative path from the repo top directory.<br><br>It contains:<br>* The rse-gene files downloaded from the recount bioconductor package (recount_experiments_rse-gene.tar.gz, output of recount2/1-get_all_recount_dataset.R)<br>* The RPKM normalized recount data (recount_rpkm.RDS, output of recount2/2-prep_recount_for_plier.R)<br>* The recount data processed for use with PLIER, the pathway data prepped for use with PLIER, and the k parameter for use with PLIER (recount_data_prep_PLIER.RDS, output of recount2/2-prep_recount_for_plier.R)<br>* The PLIER model itself (recount_PLIER_model.RDS, output of recount2/3-run_recount_plier.R)<br><br>If you use any of this 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><br>And the PLIER preprint, if you use the PLIER model:<br><br>Mao W, Harmann B, Sealfon SC, Zaslavsky E, and Chikina M (2017). "Pathway-Level Information ExtractoR (PLIER) for gene expression data." bioRxiv. doi: 10.1101/116061<br><br><br>
DOI: 10.6084/m9.figshare.5716033.v1
title: recount.rpkm.RData

description: recount2 (https://jhubiostatistics.shinyapps.io/recount/) samples gene expression, normalized by rpkm (Reads Per Kilobase Million).<br><br><br>
DOI: 10.6084/m9.figshare.5716033.v2
title: recount.rpkm.RData

description: This is the output of a pipeline that trains a Pathway-Level Information ExtractoR (PLIER) model on recount2 data (RPKM). See: https://github.com/greenelab/rheum-plier-data/tree/978c37938383ff7adcadacfcbc35931ce5e62b17<br><br>It was run in a Docker container. See the Github repository for more information. <br><br>Below, we include information about the scripts used to generate each item using the relative path from the repo top directory.<br><br>It contains:<br>* The rse-gene files downloaded from the recount bioconductor package (recount_experiments_rse-gene.tar.gz, output of recount2/1-get_all_recount_dataset.R)<br>* The RPKM normalized recount data (recount_rpkm.RDS, output of recount2/2-prep_recount_for_plier.R)<br>* The recount data processed for use with PLIER, the pathway data prepped for use with PLIER, and the k parameter for use with PLIER (recount_data_prep_PLIER.RDS, output of recount2/2-prep_recount_for_plier.R)<br>* The PLIER model itself (recount_PLIER_model.RDS, output of recount2/3-run_recount_plier.R)<br><br>If you use any of this 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><br>And the PLIER preprint, if you use the PLIER model:<br><br>Mao W, Harmann B, Sealfon SC, Zaslavsky E, and Chikina M (2017). "Pathway-Level Information ExtractoR (PLIER) for gene expression data." bioRxiv. doi: 10.1101/116061<br><br><br>
DOI: 10.6084/m9.figshare.5715976
title: Supplementary Material for: Racial/Ethnic Differences in Barriers to Kidney Transplant Evaluation among Hemodialysis Patients

description: <b><i>Background:</i></b> Only a small percentage of dialysis patients receive a transplant and this is particularly the case for racial/ethnic minorities. Our objective was to identify barriers to initial transplant evaluation in our dialysis centers.<b><i> Methods:</i></b> We conducted a survey of adult hemodialysis patients from 4 dialysis units in the Denver Metro area in 2016. Participants completed an 11-item survey with demographic information and questions regarding time on dialysis, if a provider ever spoke to them about transplant, and whether they had been evaluated for a transplant. Reasons for not having an evaluation were explored. Descriptive statistics, chi-square analyses, and multivariate analyses were used to examine the responses.<b><i> Results:</i></b> A total of 167 patients completed the survey (response rate 63.9%). The majority of participants were male and were Hispanic (49%) or Non-Hispanic black (31.7%). Of these, 140 patients (84.0%) reported discussing kidney transplantation with their doctor but only 53% reported having a transplant evaluation. After adjustment for age, gender, and time on dialysis, significantly fewer blacks reported having an evaluation than Non-Hispanic whites or Hispanics (43.4 vs. 57.7% [whites] and 59.7% [Hispanics], <i>p</i> = 0.03). The most frequent responses of the patients who had not been evaluated were the following: not referred by their provider (46%), did not know how to proceed (43.4%), or did not understand the benefits (39.5%) or transplant process (38.2%). Compared to Non-Hispanic whites, blacks and Hispanics reported less understanding of the benefits and process of transplant. <b><i>Conclusion:</i></b> Timely referral by providers and improved kidney transplantation education may reduce disparities in access to kidney transplantation.
DOI: 10.6084/m9.figshare.5715976.v1
title: Supplementary Material for: Racial/Ethnic Differences in Barriers to Kidney Transplant Evaluation among Hemodialysis Patients

description: <b><i>Background:</i></b> Only a small percentage of dialysis patients receive a transplant and this is particularly the case for racial/ethnic minorities. Our objective was to identify barriers to initial transplant evaluation in our dialysis centers.<b><i> Methods:</i></b> We conducted a survey of adult hemodialysis patients from 4 dialysis units in the Denver Metro area in 2016. Participants completed an 11-item survey with demographic information and questions regarding time on dialysis, if a provider ever spoke to them about transplant, and whether they had been evaluated for a transplant. Reasons for not having an evaluation were explored. Descriptive statistics, chi-square analyses, and multivariate analyses were used to examine the responses.<b><i> Results:</i></b> A total of 167 patients completed the survey (response rate 63.9%). The majority of participants were male and were Hispanic (49%) or Non-Hispanic black (31.7%). Of these, 140 patients (84.0%) reported discussing kidney transplantation with their doctor but only 53% reported having a transplant evaluation. After adjustment for age, gender, and time on dialysis, significantly fewer blacks reported having an evaluation than Non-Hispanic whites or Hispanics (43.4 vs. 57.7% [whites] and 59.7% [Hispanics], <i>p</i> = 0.03). The most frequent responses of the patients who had not been evaluated were the following: not referred by their provider (46%), did not know how to proceed (43.4%), or did not understand the benefits (39.5%) or transplant process (38.2%). Compared to Non-Hispanic whites, blacks and Hispanics reported less understanding of the benefits and process of transplant. <b><i>Conclusion:</i></b> Timely referral by providers and improved kidney transplantation education may reduce disparities in access to kidney transplantation.
DOI: 10.6084/m9.figshare.5715880
title: TISSUES datasets

description: Tissue expression datasets available in the TISSUES 2.0. database (including non-confident gene-tissue associations)
DOI: 10.6084/m9.figshare.5715880.v1
title: TISSUES datasets

description: Tissue expression datasets available in the TISSUES 2.0. database (including non-confident gene-tissue associations)
DOI: 10.6084/m9.figshare.5715847
title: Supplementary Material for: Rosiglitazone Inhibits Angiotensin II-Induced Proliferation of Glomerular Mesangial Cells via the Gαq/Plcβ4/TRPC Signaling Pathway

description: <b><i>Background/Aims:</i></b> Mesangial cell proliferation and extracellular matrix accumulation (ECM) deposition play an important role in the pathogenesis of glomerulosclerosis. TRPC and PPAR-γ can regulate cell proliferation. Angiotensin II (AngII) can induce mesangial cell proliferation and affect TRPC expression. However, the mechanism has not been fully elucidated. This study was designed to investigate the role of TRPC and the effect of rosiglitazone (RSG) in the proliferation of rat glomerular mesangial cells (HBZY-1) that were stimulated by AngII and the underlying mechanisms. <b><i>Methods:</i></b> Immunofluorescence staining and qRT-PCR were performed to examine the expression levels of TRPCs in HBZY-1. Gene expression levels of TRPC, PPAR-γ, RGS4 (regulators of G protein signaling), the GPCR/Gαq/PLCβ4/TRPC signaling pathway and major downstream molecules (PCNA, SKP2, P21 and P27) were detected by qRT-PCR and western blotting. Additionally, changes in intracellular Ca<sup>2+</sup> levels were determined through Fluo-4 Ca<sup>2+</sup> imaging, and the cell cycle was analyzed by flow cytometry. <b><i>Results:</i></b> Our results found that TRPC1 and 6 were at higher expression levels in HBZY-1 cells. Following AngII stimulation, there were increased levels of TRPC1 and 6, Ca<sup>2+</sup> entry, PCNA and SKP2, decreased expression levels of P21 and P27 and a reduced G<sub>0</sub>/G<sub>1</sub> percentage. Silencing TRPC1 and 6 by siRNAs led to decrease in Ca<sup>2+</sup> influx, G<sub>0</sub>/G<sub>1</sub> cell cycle arrest and cell proliferation. Notably, PPAR-γ activation by RSG upregulated RGS4 expression, which can interact with the Gαq family to inhibit the Gαq-mediated signaling cascade. The results were similar to silencing TRPC1 and 6 by siRNAs. <b><i>Conclusion:</i></b> All these results indicate that RSG could inhibit HBZY-1 cell proliferation via the Gαq/PLCβ4/TRPC signaling pathway.
DOI: 10.6084/m9.figshare.5715814
title: Snapshots_hypoxantine

description: Snapshots of hypoxanthine in 100 water molecules
DOI: 10.6084/m9.figshare.5715814.v1
title: Snapshots_hypoxantine

description: Snapshots of hypoxanthine in 100 water molecules
DOI: 10.6084/m9.figshare.5715790
title: snapshots_cytosine.tar.gz

description: Snapshots of cytosine including 100 water molecules
DOI: 10.6084/m9.figshare.5715790.v2
title: snapshots_cytosine.tar.gz

description: Snapshots of cytosine including 100 water molecules
DOI: 10.6084/m9.figshare.5715787
title: Molten Salt Fast Reactor – Defining a Priority List

description: The results of the calculations using extraction and addition approaches for different number of histories per batch. There is also the python script which has been used to run the calculations using OpenMC code.