cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8237094
title: Engineered poplar for bioproduction of the triterpene squalene

description: Building sustainable platforms to produce biofuels and specialty chemicals has become an increasingly important strategy to supplement and replace fossil fuels and petrochemical-derived products. Terpenoids are the most diverse class of natural products which have many commercial roles as specialty chemicals. Poplar is a fast growing, biomass dense bioenergy crop with many species known to produce large amounts of the hemiterpene isoprene, suggesting an inherent capacity to produce large amounts of other terpenes. Here we aimed to engineer poplar with optimized pathways to produce squalene, a triterpene commonly used in cosmetic oils, a potential biofuel candidate, and the precursor to the further diversified classes of triterpenoids and sterols. The squalene production pathways were either re-targeted from the cytosol to plastids or co-produced with lipid droplets in the cytosol. Squalene and lipid droplet co-production appeared to be toxic, which we hypothesize to be due to disruption of adventitious root formation, suggesting a need for tissue specific production. Plastidial squalene production enabled up to 0.63 mg/g fresh weight in leaf tissue, which also resulted in reductions in isoprene emission and photosynthesis. These results were also studied through a technoeconomic analysis, providing further insight into developing poplar as a production host.
description: This work was supported by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409. We would also like to acknowledge partial support from the Department of Biochemistry and Molecular Biology startup funding and support from AgBioResearch (MICL02454).
DOI: 10.5281/zenodo.8237095
title: Engineered poplar for bioproduction of the triterpene squalene

description: Building sustainable platforms to produce biofuels and specialty chemicals has become an increasingly important strategy to supplement and replace fossil fuels and petrochemical-derived products. Terpenoids are the most diverse class of natural products which have many commercial roles as specialty chemicals. Poplar is a fast growing, biomass dense bioenergy crop with many species known to produce large amounts of the hemiterpene isoprene, suggesting an inherent capacity to produce large amounts of other terpenes. Here we aimed to engineer poplar with optimized pathways to produce squalene, a triterpene commonly used in cosmetic oils, a potential biofuel candidate, and the precursor to the further diversified classes of triterpenoids and sterols. The squalene production pathways were either re-targeted from the cytosol to plastids or co-produced with lipid droplets in the cytosol. Squalene and lipid droplet co-production appeared to be toxic, which we hypothesize to be due to disruption of adventitious root formation, suggesting a need for tissue specific production. Plastidial squalene production enabled up to 0.63 mg/g fresh weight in leaf tissue, which also resulted in reductions in isoprene emission and photosynthesis. These results were also studied through a technoeconomic analysis, providing further insight into developing poplar as a production host.
description: This work was supported by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409. We would also like to acknowledge partial support from the Department of Biochemistry and Molecular Biology startup funding and support from AgBioResearch (MICL02454).
DOI: 10.5281/zenodo.10397616
title: Data for: Assessing hydrology, biogeochemistry and organic micropollutants in an urban stream-aquifer system: an interdisciplinary dataset

description: Accompanying data for data article "Assessing hydrology, biogeochemistry and organic micropollutants in an urban stream-aquifer system: a comprehensive dataset" of Popp et al., JGR:Biogeosciences.

In this repository, all data described in Table 1 of the manuscript can be found, except for the data already published by Popp et al., 2020, ES&T, doi: 10.1021/acs.est.9b05393. These data can be freely accessed in ERIC (Eawag Research Data Institutional Collection): doi.org/10.25678/0001JD. 

Data are structured the following way:1_logger-data: time series of logger data (water temperature, water levels, electrical conductivity and pH [the latter only for the stream]) obtained at the stream Chriesbach and piezometers P1 and P4;2_tracer-data: time series of nutrients, ions, and other tracer data obtained at the stream Chriesbach, the piezometers (P1, P4, P5) and the regional groundwater well (reg-gw);  3_micropollutant_data: time series of organic micropolluntants obtained at the stream Chriesbach, P1, P4, P5 and the regional groundwater well (reg-gw);4_R-script: R script used for statistical analysis and to create the plots shown in the manuscript.

Units, estimated uncertainties or other measures of uncertainty such as limits of quantification are provided in the respective files. Each subfolder contains its own readme file with relevant metadata. 

Coordinates (WGS84):        Location    Latitude    LongitudeStream logger monitoring    47.404613    8.6113Stream sampling    47.404459    8.607777Piezometer 1 (P1)    47.4044    8.6080Piezometer 4 (P4)    47.4044    8.6078Piezometer 5 (P5)    47.404392    8.607619Regional groundwater    47.40501    8.60822
DOI: 10.5281/zenodo.10397617
title: Data for: Assessing hydrology, biogeochemistry and organic micropollutants in an urban stream-aquifer system: an interdisciplinary dataset

description: Accompanying data for data article "Assessing hydrology, biogeochemistry and organic micropollutants in an urban stream-aquifer system: a comprehensive dataset" of Popp et al., JGR:Biogeosciences.

In this repository, all data described in Table 1 of the manuscript can be found, except for the data already published by Popp et al., 2020, ES&T, doi: 10.1021/acs.est.9b05393. These data can be freely accessed in ERIC (Eawag Research Data Institutional Collection): doi.org/10.25678/0001JD. 

Data are structured the following way:1_logger-data: time series of logger data (water temperature, water levels, electrical conductivity and pH [the latter only for the stream]) obtained at the stream Chriesbach and piezometers P1 and P4;2_tracer-data: time series of nutrients, ions, and other tracer data obtained at the stream Chriesbach, the piezometers (P1, P4, P5) and the regional groundwater well (reg-gw);  3_micropollutant_data: time series of organic micropolluntants obtained at the stream Chriesbach, P1, P4, P5 and the regional groundwater well (reg-gw);4_R-script: R script used for statistical analysis and to create the plots shown in the manuscript.

Units, estimated uncertainties or other measures of uncertainty such as limits of quantification are provided in the respective files. Each subfolder contains its own readme file with relevant metadata. 

Coordinates (WGS84):        Location    Latitude    LongitudeStream logger monitoring    47.404613    8.6113Stream sampling    47.404459    8.607777Piezometer 1 (P1)    47.4044    8.6080Piezometer 4 (P4)    47.4044    8.6078Piezometer 5 (P5)    47.404392    8.607619Regional groundwater    47.40501    8.60822
DOI: 10.25377/sussex.20655072
title: Reanimating and rematriating WRAP (with staff and students at Manchester Metropolitan University): Documentation of the second of two reanimating data workshops with students at Manchester Metropolitan University: missing stories and our many selves

description: In 2019-2020 the ESRC funded 'Reanimating data: experiments with people, places and archives'. Part of the project involved staging a series of reanimations using data from interviews with young women from Manchester, conducted thirty years previously as part of the Women, Risk and AIDS Project (WRAP 1988-1990). Each reanimation involved a collaboration between young women, educators and researchers and used creative methods to explore the WRAP data and bring it to life in new ways.   
<br>
This zip file containins materials relating to the second of two sessions carried out with students at Manchester Metropolitan University. Participants were Youth and Childhood Studies undergraduate students, predominantly young women living in the Greater Manchester area. They took part in two creative activities to explore the WRAP archive and their own stories about womanhood and sexuality. First they drew their 'many selves' and then considered how their many selves shaped their practice as child/youth professionals and later their relationship to the WRAP data. Each image captures different aspects of the students' identities that were important to them. 
<br>
Secondarily students engaged with some of the WRAP data (interviews MIS09, USD06, BT14, AMB18, EDD184, EDD135, ABC09) by cutting out data extracts, working with them and placing them in a pinata that would be opened for others to read. They selected stories that they thought needed to be heard by current and future generations. They also wrote and added their own stories, reflections and mind-maps to the mini pinata archive.   
<br>
The file contains:  

 images of students depictions of their 'many selves', created in the session. 
 images of the 'stories' that students created for the mini pinata archive. This includes extracts of WRAP data. 
 reflective notes by one of the faciltators describing and reflecting on the session activities and student engagement and responses.
DOI: 10.25377/sussex.20655072.v1
title: Reanimating and rematriating WRAP (with staff and students at Manchester Metropolitan University): Documentation of the second of two reanimating data workshops with students at Manchester Metropolitan University: missing stories and our many selves

description: In 2019-2020 the ESRC funded 'Reanimating data: experiments with people, places and archives'. Part of the project involved staging a series of reanimations using data from interviews with young women from Manchester, conducted thirty years previously as part of the Women, Risk and AIDS Project (WRAP 1988-1990). Each reanimation involved a collaboration between young women, educators and researchers and used creative methods to explore the WRAP data and bring it to life in new ways.   
<br>
This zip file containins materials relating to the second of two sessions carried out with students at Manchester Metropolitan University. Participants were Youth and Childhood Studies undergraduate students, predominantly young women living in the Greater Manchester area. They took part in two creative activities to explore the WRAP archive and their own stories about womanhood and sexuality. First they drew their 'many selves' and then considered how their many selves shaped their practice as child/youth professionals and later their relationship to the WRAP data. Each image captures different aspects of the students' identities that were important to them. 
<br>
Secondarily students engaged with some of the WRAP data (interviews MIS09, USD06, BT14, AMB18, EDD184, EDD135, ABC09) by cutting out data extracts, working with them and placing them in a pinata that would be opened for others to read. They selected stories that they thought needed to be heard by current and future generations. They also wrote and added their own stories, reflections and mind-maps to the mini pinata archive.   
<br>
The file contains:  

 images of students depictions of their 'many selves', created in the session. 
 images of the 'stories' that students created for the mini pinata archive. This includes extracts of WRAP data. 
 reflective notes by one of the faciltators describing and reflecting on the session activities and student engagement and responses.
DOI: 10.25377/sussex.21028276
title: Reanimating and rematriating WRAP (with staff and students at Manchester Metropolitan University): Documentation of a thematic analysis teaching session using data from the Women, Risk and AIDS Project (WRAP)

description: In 2019-2020 the ESRC funded 'Reanimating data: experiments with people, places and archives'. Part of the project involved staging a series of reanimations using data from interviews with young women from Manchester, conducted thirty years previously as part of the Women, Risk and AIDS Project (WRAP 1988-1990). Each reanimation involved a collaboration between young women, educators and researchers and used creative methods to explore the WRAP data and bring it to life in new ways.    
<br>
As part of the project the team supported two members of staff at Manchester Metropolitan University (Charlotte Bagnall and Claire Fox) to use two WRAP interviews (NMC12 and MAG12) to teach thematic analysis methods to their students. Charlotte and Claire analysed the data ahead of the session and identified two key themes: gendered double standard and basic or limited sex education. These themes were further explored by students. 
<br>
The zip file contains:   * A blog by Charlotte Bagnall explaining how they worked with the data an delivered the session.  * Written discussion of the gendered double standard theme by Charlotte Bagnall and Dr. Claire Fox. * Written discussion of the basic / limited sex education theme by first year student Angel Mellor-Davis. * Coding table for the gendered double standard theme.
DOI: 10.25377/sussex.21028276.v1
title: Reanimating and rematriating WRAP (with staff and students at Manchester Metropolitan University): Documentation of a thematic analysis teaching session using data from the Women, Risk and AIDS Project (WRAP)

description: In 2019-2020 the ESRC funded 'Reanimating data: experiments with people, places and archives'. Part of the project involved staging a series of reanimations using data from interviews with young women from Manchester, conducted thirty years previously as part of the Women, Risk and AIDS Project (WRAP 1988-1990). Each reanimation involved a collaboration between young women, educators and researchers and used creative methods to explore the WRAP data and bring it to life in new ways.    
<br>
As part of the project the team supported two members of staff at Manchester Metropolitan University (Charlotte Bagnall and Claire Fox) to use two WRAP interviews (NMC12 and MAG12) to teach thematic analysis methods to their students. Charlotte and Claire analysed the data ahead of the session and identified two key themes: gendered double standard and basic or limited sex education. These themes were further explored by students. 
<br>
The zip file contains:   * A blog by Charlotte Bagnall explaining how they worked with the data an delivered the session.  * Written discussion of the gendered double standard theme by Charlotte Bagnall and Dr. Claire Fox. * Written discussion of the basic / limited sex education theme by first year student Angel Mellor-Davis. * Coding table for the gendered double standard theme.
DOI: 10.25377/sussex.21027940
title: Reanimating and rematriating WRAP (with staff and students at Manchester Metropolitan University): Documentation of a group discussion with adult researchers at Manchester Metropolitan University using data from the Women, Risk and AIDS Project (WRAP)

description: In 2019-2020 the ESRC funded 'Reanimating data: experiments with people, places and archives'. Part of the project involved staging a series of reanimations using data from interviews with young women from Manchester, conducted thirty years previously as part of the Women, Risk and AIDS Project (WRAP 1988-1990). Each reanimation involved a collaboration between young women, educators and researchers and used creative methods to explore the WRAP data and bring it to life in new ways.     
<br>
In this group discussion four adult researchers try out and reflect on two reanimation methods. The first involves cutting out questions from the WRAP data that stand out to participants and then reasking these questions to each other in a group. The second method involves cutting out stories or moments from the data that participants think should be heard. Participants then revoice these moments in pairs. In their discussion the group reflect on both methods and discuss the Reanimating Data Project more widely. This is a long wide ranging discussion and the data has been edited and organised according to the two methods. 
<br>
The records contains:    * Transcription and audio recording of method 1 - reasking * Transcription and audio recording of method 2 - save and revoice <br>
DOI: 10.25377/sussex.21027940.v1
title: Reanimating and rematriating WRAP (with staff and students at Manchester Metropolitan University): Documentation of a group discussion with adult researchers at Manchester Metropolitan University using data from the Women, Risk and AIDS Project (WRAP)

description: In 2019-2020 the ESRC funded 'Reanimating data: experiments with people, places and archives'. Part of the project involved staging a series of reanimations using data from interviews with young women from Manchester, conducted thirty years previously as part of the Women, Risk and AIDS Project (WRAP 1988-1990). Each reanimation involved a collaboration between young women, educators and researchers and used creative methods to explore the WRAP data and bring it to life in new ways.     
<br>
In this group discussion four adult researchers try out and reflect on two reanimation methods. The first involves cutting out questions from the WRAP data that stand out to participants and then reasking these questions to each other in a group. The second method involves cutting out stories or moments from the data that participants think should be heard. Participants then revoice these moments in pairs. In their discussion the group reflect on both methods and discuss the Reanimating Data Project more widely. This is a long wide ranging discussion and the data has been edited and organised according to the two methods. 
<br>
The records contains:    * Transcription and audio recording of method 1 - reasking * Transcription and audio recording of method 2 - save and revoice <br>
DOI: 10.6073/pasta/e784fc01dee775af2e92929c06b78338
title: Local water year for HU4 hydrological areas across the conterminous U.S.

description: This dataset was generated as part of a project that quantifies how natural lakes (NLs) and reservoirs (RSVRs) across the conterminous U.S. (CONUS) with different levels of hydrologic connectivity respond to drought and how natural and human factors operating at multiple spatial scales affect lake responses.Traditionally, the effects of precipitation on aquatic systems have been analyzed based on a calendar year (i.e., January-December), which cannot capture the asynchrony between precipitation and its impacts. To better quantify the contribution of precipitation to surface runoff, take into account the regional variation in water flow patterns, and fully understand ecosystems’ responses to droughts, a timeframe that takes into account both timing and lag effects should be considered. Wasko et al. (2020) proposed a more local-focused definition of the water year (i.e., local water year, LWY) where the LWY of each site is defined as the 12-month-period starting from the month with the lowest local streamflow. However, data from Wasko et al. (2020) did not cover all the HU4 (4-digit Hydrologic Unit) hydrological areas across the conterminous U.S. (CONUS). Using their definition and data, we employed a spatial interpolation method to estimate the LWY for all the HU4 hydrological areas across the CONUS.
DOI: 10.5281/zenodo.10256844
title: Data supplement for paper on Gnuastro's zero point measurement script

description: Data supplements to the paper titled "Gnuastro: Estimating the Zero Point Magnitude in Astronomical Imaging", published in Research Notes of the American Astronomical Society (RNAAS) journal (arXiv:2312.04263). This paper introduces a recently added program to GNU Astronomy Utilities (Gnuastro). This repository contains all the necessary inputs and output data (listed below). This paper is written in Maneage and its source is available in Codeberg. For more information on how to reproduce this paper, see the README.md and README-hacking.md. The version string e31dd15 (which is imprinted on some file names and hard-coded in others), represents the Git commit used for this publication. The source of this project is also archived in SoftwareHeritage.

A brief description of the contents in this repository:



paper-e31dd15.pdf: The complete PDF of the paper.

sdss-dr12-catalog.fits: SDSS DR12 catalog which overlaps with input image, to find the zero point magnitude with reference catalog (in this paper SDSS catalog is reference catalog).

gaia-dr3-overlap-ra-dec.fits: Gaia catalog to use for finding stars in images.

6-arcsec-zp-with-ref-img.txt: Output data files that are used in the demonstration the pink filled circles in left panel of plot in the paper.

2-arcsec-zp-with-ref-img.txt: Output data files that are used in the demonstration the blue filled circles in left panel of plot in the paper.

6-arcsec-zp-with-ref-cat.txt: Output data files that are used in the demonstration the purple filled circles in right panel of plot in the paper.

2-arcsec-zp-with-ref-cat.txt: Output data files that are used in the demonstration the yellow filled circles in right panel of plot in the paper. 


For any issues or questions on this project, please contact Sepideh Eskandarlou (corresponding author in PDF).
DOI: 10.5281/zenodo.10256845
title: Data supplement for paper on Gnuastro's zero point measurement script

description: Data supplements to the paper titled "Gnuastro: Estimating the Zero Point Magnitude in Astronomical Imaging", published in Research Notes of the American Astronomical Society (RNAAS) journal (arXiv:2312.04263). This paper introduces a recently added program to GNU Astronomy Utilities (Gnuastro). This repository contains all the necessary inputs and output data (listed below). This paper is written in Maneage and its source is available in Codeberg. For more information on how to reproduce this paper, see the README.md and README-hacking.md. The version string e31dd15 (which is imprinted on some file names and hard-coded in others), represents the Git commit used for this publication. The source of this project is also archived in SoftwareHeritage.

A brief description of the contents in this repository:



paper-e31dd15.pdf: The complete PDF of the paper.

sdss-dr12-catalog.fits: SDSS DR12 catalog which overlaps with input image, to find the zero point magnitude with reference catalog (in this paper SDSS catalog is reference catalog).

gaia-dr3-overlap-ra-dec.fits: Gaia catalog to use for finding stars in images.

6-arcsec-zp-with-ref-img.txt: Output data files that are used in the demonstration the pink filled circles in left panel of plot in the paper.

2-arcsec-zp-with-ref-img.txt: Output data files that are used in the demonstration the blue filled circles in left panel of plot in the paper.

6-arcsec-zp-with-ref-cat.txt: Output data files that are used in the demonstration the purple filled circles in right panel of plot in the paper.

2-arcsec-zp-with-ref-cat.txt: Output data files that are used in the demonstration the yellow filled circles in right panel of plot in the paper. 


For any issues or questions on this project, please contact Sepideh Eskandarlou (corresponding author in PDF).