cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7611143
title: Portuguese measure of multiple environmental deprivation (PT-MEDIx)

description: PT-MEDIx was built at municipality level in four stages: (i) identify health-relevant environmental factors; (ii) acquire datasets about selected environmental factors and calculate municipality-level measures using Geographical Information Systems; (iii) test associations between selected environmental factors and mortality using negative binomial models, adjusting for age, sex, socioeconomic deprivation and interactions and (iv) construct a summary measure and assess its association with mortality.We included five dimensions of the physical environment: air pollution, climate, drinking water quality, green space availability and industry proximity. PT-MEDIx score ranged from -1 (least environmental deprivation) to +4 (most) and depicted a clear spatial pattern: least deprived municipalities in the depopulated rural areas and most deprived in urban and industrial settings. Comparing with those in the intermediate category of environment deprivation, less deprived municipalities showed lower mortality rate ratios (MRRs) and vice versa: MRRs for all-cause mortality were 0.962 (95% confidence interval: 0.934-0.991) and 1.209 (1.086-1.344), in the least and most deprived municipalities, respectively, and for cancer, 0.957 (0.911-1.006) and 1.345 (1.123-1.598).<br>More details here:Ribeiro, A. I., Pina, M. d. F. d., & Mitchell, R. (2015). Development of a measure of multiple physical environmental deprivation. After United Kingdom and New Zealand, Portugal. European Journal of Public Health, 25(4), 610-617. doi:10.1093/eurpub/cku242<br>
DOI: 10.6084/m9.figshare.7611140
title: Absorption study of porphyrin 1 on NiO

description: Absorption spectroscopy study of porphyrin 1 (bearing acid benzoic group) on NiO.
DOI: 10.7284/126825
title: Gyrocompass data collected during research cruise EN593 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7611143.v1
title: Portuguese measure of multiple environmental deprivation (PT-MEDIx)

description: PT-MEDIx was built at municipality level in four stages: (i) identify health-relevant environmental factors; (ii) acquire datasets about selected environmental factors and calculate municipality-level measures using Geographical Information Systems; (iii) test associations between selected environmental factors and mortality using negative binomial models, adjusting for age, sex, socioeconomic deprivation and interactions and (iv) construct a summary measure and assess its association with mortality.We included five dimensions of the physical environment: air pollution, climate, drinking water quality, green space availability and industry proximity. PT-MEDIx score ranged from -1 (least environmental deprivation) to +4 (most) and depicted a clear spatial pattern: least deprived municipalities in the depopulated rural areas and most deprived in urban and industrial settings. Comparing with those in the intermediate category of environment deprivation, less deprived municipalities showed lower mortality rate ratios (MRRs) and vice versa: MRRs for all-cause mortality were 0.962 (95% confidence interval: 0.934-0.991) and 1.209 (1.086-1.344), in the least and most deprived municipalities, respectively, and for cancer, 0.957 (0.911-1.006) and 1.345 (1.123-1.598).<br>More details here:Ribeiro, A. I., Pina, M. d. F. d., & Mitchell, R. (2015). Development of a measure of multiple physical environmental deprivation. After United Kingdom and New Zealand, Portugal. European Journal of Public Health, 25(4), 610-617. doi:10.1093/eurpub/cku242<br>
DOI: 10.6084/m9.figshare.7611140.v2
title: Absorption study of porphyrin 1 on NiO

description: Absorption spectroscopy study of porphyrin 1 (bearing acid benzoic group) on NiO.
DOI: 10.7284/126826
title: Gyrocompass data collected during research cruise EN593 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7611140.v1
title: Absorption study of porphyrin 1

description: Absorption spectroscopy study of porphyrin 1 (bearing acid benzoic group).
DOI: 10.7284/126832
title: Meteorological Station data collected during research cruise EN593 using a RM Young 26800 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7611005
title: Dry season soil water potential maps of a 50 hectare tropical forest plot on Barro Colorado Island, Panama

description: This file includes an input and output folder. The input folder includes soil moisture measurements fromt the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI) in Panama and R code to create custom soil water potential maps for the plot. The output folder contains soil water potential maps on a 5 m resolution for early, mid and late dry season conditions during a regular year and mid dry season during a drought year.
DOI: 10.6084/m9.figshare.7611044
title: Portuguese version of the European Deprivation Index (version 2001)

description: The European Deprivation Index was developed under the Townsend theorization of deprivation. Using data from the European Union - Statistics on Income and Living Conditions Survey, we obtained an indicator of individual deprivation. This indicator became the gold-standard variable, based on what we selected the variables at aggregate level (census 2001) to be included in the European Deprivation Index, a total of eight. The European Deprivation Index was produced for the smallest area unit possible (n = 16 094, mean/area = 643 inhabitants), parish level and municipality level, and resulted from the weighted sum of the previous variables. It was then classified into quintiles.<br>More details here:Ribeiro, A. I., Mayer, A., Miranda, A., & Pina, M. F. (2017). The Portuguese Version of the European Deprivation Index: An Instrument to Study Health Inequalities. Acta Med Port, 30(1), 17-25. <br>Guillaume, E., Pornet, C., Dejardin, O., Launay, L., Lillini, R., Vercelli, M., . . . Launoy, G. (2016). Development of a cross-cultural deprivation index in five European countries. Journal of Epidemiology and Community Health, 70(5), 493-499. doi:10.1136/jech-2015-205729<br>
DOI: 10.7284/126828
title: Radiometer data collected during research cruise EN593 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7611005.v1
title: Dry season soil water potential maps of a 50 hectare tropical forest plot on Barro Colorado Island, Panama

description: This file includes an input and output folder. The input folder includes soil moisture measurements fromt the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI) in Panama and R code to create custom soil water potential maps for the plot. The output folder contains soil water potential maps on a 5 m resolution for early, mid and late dry season conditions during a regular year and mid dry season during a drought year.
DOI: 10.6084/m9.figshare.7610987
title: Archaeological grape seeds genotype data

description: Genotype data for the archaeological grape seeds sequenced for Ramos-Madrigal J <i>et al.</i> Nat Plants 2018 10.1038/s41477-019-0437-5<br>
DOI: 10.7284/126829
title: Radiometer data collected during research cruise EN593 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126827
title: TSG (Thermosalinograph) data collected during research cruise EN593 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25392/leicester.data.7610933
title: Clinical level agent-based model of pathological airway remodeling in asthma

description: The following contains information regarding the uploaded agent-based model capturing asthma pathogenesis in a virtual human airway to make clinical-level predictions. This model was developed considering a Strahler Order 3 airway and is based on interactions between the epithelial, mesenchymal, and inflammatory elements of an airway. Pathological remodeling during asthma in this model, therefore, emerges as a result of dynamic interplay between these elements across multiple spatial and temporal scales. The model was developed to be drug agnostic and used to predict the impact of two drugs, with different pharmacodynamics, on the muscle mass of the virtual airway with severe asthma. Model outcomes were validated by comparing against clinical data and in vitro studies.<br>
DOI: 10.25392/leicester.data.7610933.v1
title: Clinical level agent-based model of pathological airway remodeling in asthma

description: The following contains information regarding the uploaded agent-based model capturing asthma pathogenesis in a virtual human airway to make clinical-level predictions. This model was developed considering a Strahler Order 3 airway and is based on interactions between the epithelial, mesenchymal, and inflammatory elements of an airway. Pathological remodeling during asthma in this model, therefore, emerges as a result of dynamic interplay between these elements across multiple spatial and temporal scales. The model was developed to be drug agnostic and used to predict the impact of two drugs, with different pharmacodynamics, on the muscle mass of the virtual airway with severe asthma. Model outcomes were validated by comparing against clinical data and in vitro studies.<br>
DOI: 10.7284/126833
title: TSG (Thermosalinograph) data collected during research cruise EN593 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.17633/rd.brunel.7610924
title: Numerical modelling of acoustic streaming during the ultrasonic melt treatment of direct-chill (DC) casting dataset

description: This collection contains data from the article:G.S.B. Lebon, G. Salloum-Abou-Jaoude, D. Eskin, I. Tzanakis, K. Pericleous, and P. Jarry. Numerical modelling of acoustic streaming during the ultrasonic melt treatment of direct-chill (DC) casting. Ultrasonics Sonochemistry.
DOI: 10.17633/rd.brunel.7610924.v1
title: Numerical modelling of acoustic streaming during the ultrasonic melt treatment of direct-chill (DC) casting dataset

description: This collection contains data from the article:G.S.B. Lebon, G. Salloum-Abou-Jaoude, D. Eskin, I. Tzanakis, K. Pericleous, and P. Jarry. Numerical modelling of acoustic streaming during the ultrasonic melt treatment of direct-chill (DC) casting. Ultrasonics Sonochemistry.
DOI: 10.6084/m9.figshare.7610918
title: Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

description: <i>CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene-independent manner. In contrast, amplifications caused by whole chromosomal duplication have little to no impact on fitness. This effect is cell line specific and dependent on the ploidy status. We devise a copy-number ratio metric that substantially improves the detection of gene-independent cell fitness effects in CRISPR-Cas9 screens. Furthermore, we develop a computational tool, called Crispy, to account for these effects on a single sample basis and provide corrected gene fitness effects. Our analysis demonstrates the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage, with implications for the use of CRISPR-Cas9 gene-editing in cancer cells.</i><br>
DOI: 10.7284/126836
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN594 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7610903
title: Mathematica code (.nb) from The efficacy of good genes sexual selection under environmental change

description: .nb version of the mathematica code supporting this study
DOI: 10.6084/m9.figshare.7610903.v1
title: Mathematica code (.nb) from The efficacy of good genes sexual selection under environmental change

description: .nb version of the mathematica code supporting this study
DOI: 10.6084/m9.figshare.7610918.v2
title: Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

description: <i>CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene-independent manner. In contrast, amplifications caused by whole chromosomal duplication have little to no impact on fitness. This effect is cell line specific and dependent on the ploidy status. We devise a copy-number ratio metric that substantially improves the detection of gene-independent cell fitness effects in CRISPR-Cas9 screens. Furthermore, we develop a computational tool, called Crispy, to account for these effects on a single sample basis and provide corrected gene fitness effects. Our analysis demonstrates the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage, with implications for the use of CRISPR-Cas9 gene-editing in cancer cells.</i><br>
DOI: 10.7284/126844
title: Anemometer data collected during research cruise EN594 using a RM Young 05103 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7610918.v1
title: Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

description: <i>CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene-independent manner. In contrast, amplifications caused by whole chromosomal duplication have little to no impact on fitness. This effect is cell line specific and dependent on the ploidy status. We devise a copy-number ratio metric that substantially improves the detection of gene-independent cell fitness effects in CRISPR-Cas9 screens. Furthermore, we develop a computational tool, called Crispy, to account for these effects on a single sample basis and provide corrected gene fitness effects. Our analysis demonstrates the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage, with implications for the use of CRISPR-Cas9 gene-editing in cancer cells.</i><br>
DOI: 10.7284/126845
title: Anemometer data collected during research cruise EN594 using a RM Young 05103 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7610825
title: Assessing the terrestrial capacity for Negative Emission Technologies in Ireland

description: Negative emissions technologies (NETs) and their potential role in meeting emission targets is a rapidly growing and contentious area of climate change mitigation research. The literature ranges in scope from general reviews of NETs options to research and development through applied case studies. Within this field, a gap exists in the application of this growing body of research to the unique limitations and opportunities of a specific nation. Ireland is a small developed island nation in the EU with a unique emissions profile, as 32% of the total comes from agriculture due to the high number of cattle. In this study we aim to assess the potential capacity of terrestrial NETs options for Ireland and review the nation-specific context for their deployment. Despite the proportionally high representation of biochar and carbon capture and storage in the international NETs research, in an Irish context afforestation and bioenergy crops are much more established practices and could readily be considered in possible emission pathways that use NETs. Higher capacities were found for NETs options that are currently unavailable (direct air carbon capture and storage and bioenergy with carbon capture and storage), while options available to deploy at scale (afforestation, soil carbon management and biochar) have capacities limited by saturation of soil carbon stock and have higher risk of reversibility due to impermanence. Hence, while we estimate a reasonable technical capacity for NETs in Ireland, emission reduction remains the highest priority for feasibly meeting a Paris-aligned carbon quota for Ireland.
DOI: 10.6084/m9.figshare.7610828
title: Dataset from Host density predicts the probability of parasitism by avian brood parasites

description: The spatial distribution of hosts can be a determining factor in the reproductive success of parasites. Highly aggregated hosts may offer more opportunities for reproduction but can have better defences than isolated hosts. Here we connect macro- and micro-evolutionary processes to understand the link between host density and parasitism, using avian brood parasites as a model system. We analyse data across more than 200 host species using phylogenetic comparative analyses and quantify parasitism rate and host reproductive success in relation to spatial distribution using field data collected on one host species over 6 years. Our comparative analysis reveals that hosts occurring at intermediate densities are more likely to be parasitized than colonial or widely dispersed hosts. Correspondingly, our intraspecific field data show that individuals living at moderate densities experience higher parasitism rates than individuals at either low or high densities. Moreover, we show for the first time that the effect of host density on host reproductive success varies according to the intensity of parasitism; hosts have greater reproductive success when living at high densities if parasitism rates are high, but fare better at low densities when parasitism rates are low. We provide the first evidence of the trade-off between host density and parasitism at both macro- and micro-evolutionary scales in brood parasites.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
DOI: 10.6084/m9.figshare.7610825.v1
title: Assessing the terrestrial capacity for Negative Emission Technologies in Ireland

description: Negative emissions technologies (NETs) and their potential role in meeting emission targets is a rapidly growing and contentious area of climate change mitigation research. The literature ranges in scope from general reviews of NETs options to research and development through applied case studies. Within this field, a gap exists in the application of this growing body of research to the unique limitations and opportunities of a specific nation. Ireland is a small developed island nation in the EU with a unique emissions profile, as 32% of the total comes from agriculture due to the high number of cattle. In this study we aim to assess the potential capacity of terrestrial NETs options for Ireland and review the nation-specific context for their deployment. Despite the proportionally high representation of biochar and carbon capture and storage in the international NETs research, in an Irish context afforestation and bioenergy crops are much more established practices and could readily be considered in possible emission pathways that use NETs. Higher capacities were found for NETs options that are currently unavailable (direct air carbon capture and storage and bioenergy with carbon capture and storage), while options available to deploy at scale (afforestation, soil carbon management and biochar) have capacities limited by saturation of soil carbon stock and have higher risk of reversibility due to impermanence. Hence, while we estimate a reasonable technical capacity for NETs in Ireland, emission reduction remains the highest priority for feasibly meeting a Paris-aligned carbon quota for Ireland.
DOI: 10.6084/m9.figshare.7610828.v1
title: Dataset from Host density predicts the probability of parasitism by avian brood parasites

description: The spatial distribution of hosts can be a determining factor in the reproductive success of parasites. Highly aggregated hosts may offer more opportunities for reproduction but can have better defences than isolated hosts. Here we connect macro- and micro-evolutionary processes to understand the link between host density and parasitism, using avian brood parasites as a model system. We analyse data across more than 200 host species using phylogenetic comparative analyses and quantify parasitism rate and host reproductive success in relation to spatial distribution using field data collected on one host species over 6 years. Our comparative analysis reveals that hosts occurring at intermediate densities are more likely to be parasitized than colonial or widely dispersed hosts. Correspondingly, our intraspecific field data show that individuals living at moderate densities experience higher parasitism rates than individuals at either low or high densities. Moreover, we show for the first time that the effect of host density on host reproductive success varies according to the intensity of parasitism; hosts have greater reproductive success when living at high densities if parasitism rates are high, but fare better at low densities when parasitism rates are low. We provide the first evidence of the trade-off between host density and parasitism at both macro- and micro-evolutionary scales in brood parasites.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
DOI: 10.7284/126837
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN594 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126834
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN594 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition