cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5909998
title: Data and code from: Ecosystem functional response across precipitation extremes in a sagebrush steppe

description: <b>usses_water: Experimental Test of Climate Change Impacts on Grassland ANPP</b><br>Research project data and code for an analysis of drought and irrigation experiment at US Sheep Experiment State (USSES) near Dubois, ID.Goal is to quantify the impact of a 50% increase/decrease of precipitation on:<br>* ANPP through time* Relationship of ANPP to soil moisture* Species composition<br><b>Running the code</b><br><br>To fully run this code you will need R and a number of R packages.Running `00_source_usses_water_scripts` in the `code/` directory will run all necessary scripts to complete the analysis.The code will also stop and send errors letting you know what R packages need to be installed.Once all packages are installed, the code should run all the way through.<br>You must source the script from RStudio, rather than from command line, because we use some Rstudio-specific commands to set working directories.<br><b>Citation information</b><br>This work has been accepted for publication in PeerJ (https://peerj.com/).It is currently in press, so for now please cite as<br>Tredennick, A.T., A.R. Kleinhesselink, J.B. Taylor, and P.B. Adler. (In press). Ecosystem functional response across precipitation extremes in a sagebrush steppe. <i>PeerJ</i>.<br>The preprint can be found at: https://www.biorxiv.org/content/early/2018/01/24/195594.<br>Additionally, please cite the Figshare fileset if reusing data or code as:<br>Tredennick, A.T., A.R. Kleinhesselink, J.B. Taylor, and P.B. Adler. Data and code from: Ecosystem functional response across precipitation extremes in a sagebrush steppe. Figshare. 10.6084/m9.figshare.5909998 <br>
DOI: 10.6084/m9.figshare.5909962
title: Data

description: The raw data, of mass loss, is obtained using a precision weighing scale (Sartorius GPA5202). Some of the data is in analyzed form. Top surface temperature data is measured using an IR camera (FLUKE Ti400).<br>
DOI: 10.6084/m9.figshare.5909962.v1
title: Data

description: The raw data, of mass loss, is obtained using a precision weighing scale (Sartorius GPA5202). Some of the data is in analyzed form. Top surface temperature data is measured using an IR camera (FLUKE Ti400).<br>
DOI: 10.6084/m9.figshare.5909959
title: The exoribonuclease Xrn1 is a post-transcriptional negative regulator of autophagy

description: Macroautophagy/autophagy is a conserved catabolic process that promotes survival during stress. Autophagic dysfunction is associated with pathologies such as cancer and neurodegenerative diseases. Thus, autophagy must be strictly modulated at multiple levels (transcriptional, post-transcriptional, translational and post-translational) to prevent deregulation. Relatively little is known about the post-transcriptional control of autophagy. Here we report that the exoribonuclease Xrn1/XRN1 functions as a negative autophagy factor in the yeast <i>Saccharomyces cerevisiae</i> and in mammalian cells. In yeast, chromosomal deletion of <i>XRN1</i> enhances autophagy and the frequency of autophagosome formation. Loss of Xrn1 results in the upregulation of autophagy-related (<i>ATG</i>) transcripts under nutrient-replete conditions, and this effect is dependent on the ribonuclease activity of Xrn1. Xrn1 expression is regulated by the yeast transcription factor Ash1 in rich conditions. In mammalian cells, siRNA depletion of XRN1 enhances autophagy and the replication of 2 picornaviruses. This work provides insight into the role of the RNA decay factor Xrn1/XRN1 as a post-transcriptional regulator of autophagy.
DOI: 10.6084/m9.figshare.5909959.v2
title: The exoribonuclease Xrn1 is a post-transcriptional negative regulator of autophagy

description: Macroautophagy/autophagy is a conserved catabolic process that promotes survival during stress. Autophagic dysfunction is associated with pathologies such as cancer and neurodegenerative diseases. Thus, autophagy must be strictly modulated at multiple levels (transcriptional, post-transcriptional, translational and post-translational) to prevent deregulation. Relatively little is known about the post-transcriptional control of autophagy. Here we report that the exoribonuclease Xrn1/XRN1 functions as a negative autophagy factor in the yeast <i>Saccharomyces cerevisiae</i> and in mammalian cells. In yeast, chromosomal deletion of <i>XRN1</i> enhances autophagy and the frequency of autophagosome formation. Loss of Xrn1 results in the upregulation of autophagy-related (<i>ATG</i>) transcripts under nutrient-replete conditions, and this effect is dependent on the ribonuclease activity of Xrn1. Xrn1 expression is regulated by the yeast transcription factor Ash1 in rich conditions. In mammalian cells, siRNA depletion of XRN1 enhances autophagy and the replication of 2 picornaviruses. This work provides insight into the role of the RNA decay factor Xrn1/XRN1 as a post-transcriptional regulator of autophagy.
DOI: 10.6084/m9.figshare.5909959.v1
title: The Exoribonuclease Xrn1 Is a Post-Transcriptional Negative Regulator of Autophagy

description: Macroautophagy/autophagy is a conserved catabolic process that promotes survival during stress. Autophagic dysfunction is associated with pathologies such as cancer and neurodegenerative diseases. Thus, autophagy must be strictly modulated at multiple levels (transcriptional, post-transcriptional, translational and post-translational) to prevent deregulation. Relatively little is known about the post-transcriptional control of autophagy. Here we report that the exoribonuclease Xrn1/XRN1 functions as a negative autophagy factor in the yeast <i>Saccharomyces cerevisiae</i> and in mammalian cells. In yeast, chromosomal deletion of <i>XRN1</i> enhances autophagy and the frequency of autophagosome formation. Loss of Xrn1 results in the upregulation of autophagy-related (<i>ATG</i>) transcripts under nutrient-replete conditions, and this effect is dependent on the ribonuclease activity of Xrn1. Xrn1 expression is regulated by the yeast transcription factor Ash1 in rich conditions. In mammalian cells, siRNA depletion of XRN1 enhances autophagy and the replication of 2 picornaviruses. This work provides insight into the role of the RNA decay factor Xrn1/XRN1 as a post-transcriptional regulator of autophagy.
DOI: 10.6084/m9.figshare.5909956
title: Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta

description: DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the <i>CUB and Sushi Multiple Domains 1</i> (<i>CSMD1</i>) gene on chromosome 8. The sex-specific differential methylation pattern observed in this region was validated in additional placentas using in-solution target capture. In a new RNA-seq data set from 64 female and 67 male placentas, <i>CSMD1</i> mRNA was 1.8-fold higher in male than in female placentas (<i>P</i> value = 8.5 × 10<sup>−7</sup>, Mann-Whitney test). Exon-level quantification of <i>CSMD1</i> mRNA from these 131 placentas suggested a likely placenta-specific <i>CSMD1</i> isoform not detected in the 21 somatic tissues analyzed. We show that the gene body of an autosomal gene, <i>CSMD1</i>, is differentially methylated in a sex- and placental-specific manner, displaying sex-specific differences in placental transcript abundance.
DOI: 10.6084/m9.figshare.5909956.v2
title: Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta

description: DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the <i>CUB and Sushi Multiple Domains 1</i> (<i>CSMD1</i>) gene on chromosome 8. The sex-specific differential methylation pattern observed in this region was validated in additional placentas using in-solution target capture. In a new RNA-seq data set from 64 female and 67 male placentas, <i>CSMD1</i> mRNA was 1.8-fold higher in male than in female placentas (<i>P</i> value = 8.5 × 10<sup>−7</sup>, Mann-Whitney test). Exon-level quantification of <i>CSMD1</i> mRNA from these 131 placentas suggested a likely placenta-specific <i>CSMD1</i> isoform not detected in the 21 somatic tissues analyzed. We show that the gene body of an autosomal gene, <i>CSMD1</i>, is differentially methylated in a sex- and placental-specific manner, displaying sex-specific differences in placental transcript abundance.
DOI: 10.6084/m9.figshare.5909956.v1
title: Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta

description: DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the <i>CUB and Sushi Multiple Domains 1</i> (<i>CSMD1</i>) gene on chromosome 8. The sex-specific differential methylation pattern observed in this region was validated in additional placentas using in-solution target capture. In a new RNA-seq data set from 64 female and 67 male placentas, <i>CSMD1</i> mRNA was 1.8-fold higher in male than in female placentas (<i>P</i> value = 8.5 × 10<sup>−7</sup>, Mann-Whitney test). Exon-level quantification of <i>CSMD1</i> mRNA from these 131 placentas suggested a likely placenta-specific <i>CSMD1</i> isoform not detected in the 21 somatic tissues analyzed. We show that the gene body of an autosomal gene, <i>CSMD1</i>, is differentially methylated in a sex- and placental-specific manner, displaying sex-specific differences in placental transcript abundance.
DOI: 10.6084/m9.figshare.5909929
title: present-day temperature profiles

description: North and South present-day temperature profiles of suitable models (Figure 11) (in kelvins). Corresponding radius are given in the files "radius" (in kilometers).<br>Files with BestModel correspond to the best model described in section 4.1. Files with Min and Max correspond to the extremum temperatures observed among suitable models.
DOI: 10.6084/m9.figshare.5909929.v1
title: present-day temperature profiles

description: North and South present-day temperature profiles of suitable models (Figure 11) (in kelvins). Corresponding radius are given in the files "radius" (in kilometers).<br>Files with BestModel correspond to the best model described in section 4.1. Files with Min and Max correspond to the extremum temperatures observed among suitable models.
DOI: 10.6084/m9.figshare.5909917
title: Elastic thickness evolution

description: North and South elastic thickness evolution (in meters) for the models that suitably fit the four constraints (elastic thickness evolution constraints and present-day volcanism in the Southern hemisphere).<br>Elastic thickness of the best model described in section 4.1 is given in files with 'BestModel'. Min and Max correspond to the extremum values observed among suitable models (Figure 5, shaded areas)<br>files with 1014 correspond to the elastic thickness evolution when considering a strain rate representative of the time scale of polar cap deposition : Figure 5bfiles with 1017 correspond to the elastic thickness evolution when considering a strain rate representative of the time scale of mantle convection : Figure 5a<br>data files give the estimations of martian elastic thicknesses made by previous studies, which are compiled in Figure 2b. Each line represent one estimation and gives in order: the elastic thickness estimation, the range (minimum and maximum values), the age of this elastic thickness, the range of this age (maximaum and minimum).
DOI: 10.6084/m9.figshare.5909917.v1
title: Elastic thickness evolution

description: North and South elastic thickness evolution (in meters) for the models that suitably fit the four constraints (elastic thickness evolution constraints and present-day volcanism in the Southern hemisphere).<br>Elastic thickness of the best model described in section 4.1 is given in files with 'BestModel'. Min and Max correspond to the extremum values observed among suitable models (Figure 5, shaded areas)<br>files with 1014 correspond to the elastic thickness evolution when considering a strain rate representative of the time scale of polar cap deposition : Figure 5bfiles with 1017 correspond to the elastic thickness evolution when considering a strain rate representative of the time scale of mantle convection : Figure 5a<br>data files give the estimations of martian elastic thicknesses made by previous studies, which are compiled in Figure 2b. Each line represent one estimation and gives in order: the elastic thickness estimation, the range (minimum and maximum values), the age of this elastic thickness, the range of this age (maximaum and minimum).
DOI: 10.6084/m9.figshare.5909914
title: UCM Monte carlo results - dry crust, dry mantle rheology

description: Rheology = dry mantle and dry crust, diffusion creep<br>Monte Carlo results for UCM simulations (Figure 10a). <br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.
DOI: 10.6084/m9.figshare.5909914.v1
title: UCM Monte carlo results - dry crust, dry mantle rheology

description: Rheology = dry mantle and dry crust, diffusion creep<br>Monte Carlo results for UCM simulations (Figure 10a). <br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.
DOI: 10.6084/m9.figshare.5909908
title: NUCM Monte Carlo results - dry crust and dry mantle rheology

description: Monte Carlo results for NUCM simulations (Figure 10b)Rheology = dry mantle and dry crust, diffusion creep<br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.
DOI: 10.6084/m9.figshare.5909908.v1
title: NUCM Monte Carlo results - dry crust and dry mantle rheology

description: Monte Carlo results for NUCM simulations (Figure 10b)Rheology = dry mantle and dry crust, diffusion creep<br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.
DOI: 10.6084/m9.figshare.5909875
title: NUCM2 Monte Carlo results - wet crust and dry mantle rheology

description: Monte Carlo results for NUCM2 simulations (Figure 9b)Rheology = dry mantle and wet crust, diffusion creep<br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.<br>The percentage of radioelement contained in the Northern and Southern crusts are given in files "RadioelementContents".
DOI: 10.6084/m9.figshare.5909857
title: UCM Monte Carlo results - wet crust and dry mantle rheology

description: Monte Carlo results for UCM simulations (Figures 6a-b-c-d, 7a and 9a). Rheology = dry mantle and wet crust, diffusion creep<br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.<br>The percentage of radioelement contained in the Northern and Southern crusts are given in files "RadioelementContents".<br>
DOI: 10.6084/m9.figshare.5909857.v1
title: UCM Monte Carlo results - wet crust and dry mantle rheology

description: Monte Carlo results for UCM simulations (Figures 6a-b-c-d, 7a and 9a). Rheology = dry mantle and wet crust, diffusion creep<br><b>Files:</b>Each line of the files (scores, thickness, enrichment factor and crustal radioelement content) corresponds to a model with given crustal parameters (crustal thickness in meters and enrichment factor) and the results obtained for this model.<br>Gaussian scores for the three constraints on elastic thickness are given in the files "score". To compute scores between 0 and 1, these scores have to be divided by the maximum of the corresponding gaussian (given in "Gaussian_maximum.csv": in order for the Noachian, the Southern polar cap and the Northern polar cap)<br>The file "MeltFormation" gives the difference in meters between the depth of the stagnant lid and the depth of melt formation in the Southern hemisphere. Models with present-day formation in the South are those where this difference is lower than 100 km.<br>The percentage of radioelement contained in the Northern and Southern crusts are given in files "RadioelementContents".<br>
DOI: 10.6084/m9.figshare.5909836
title: Model Validation for Quantitative X-Ray Measurements

description: Soft–X-ray (SXR) brightness measurements contain information on a number of physics parameters in fusion plasmas; however, it is nearly impossible to extract the information without modeling. A validated forward model is therefore necessary for the accurate interpretation of SXR measurements and will be critical in the burning plasma era, where medium- and high-Z impurities are ever present. The Atomic Data and Analysis Structure (ADAS) database is a powerful interpretive tool that is extensively used to model and predict atomic spectra, level populations, and ionization balance for fusion plasmas. These predictions are in good agreement with experimental measurements. However, continuum radiation in the X-ray range, while also modeled in ADAS, has not been rigorously verified or tested against experimental data. We therefore performed a systematic comparison of ADAS to a simplified model called PFM. PFM only calculates continuum radiation but shows good agreement with experimental data when only continuum radiation is present. ADAS and the simplified model agree to within 1% to 2% indicating that ADAS is calculating continuum radiation correctly. We have also begun a validation of SXR brightness calculations from ADAS. The SXR brightness measurements modeled by ADAS agree well with experimental measurements from an extreme where the signal is dominated by line radiation continuously through another extreme where the signal is dominated by continuum emission. While this validation work is preliminary, it strongly suggests that ADAS accurately models the physics that lead to SXR radiation.