cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1608860.v3
title: The stress-related, rhizobial small RNA RcsR1 destabilizes the autoinducer synthase encoding mRNA <i>sinI</i> in <i>Sinorhizobium meliloti</i>

description: Quorum sensing is a cell density-dependent communication system of bacteria relying on autoinducer molecules. During the analysis of the post-transcriptional regulation of quorum sensing in the nitrogen fixing plant symbiont <i>Sinorhizobium meliloti,</i> we predicted and verified a direct interaction between the 5'-UTR of <i>sinI</i> mRNA encoding the autoinducer synthase and a small RNA (sRNA), which we named RcsR1. <i>In vitro</i>, RcsR1 prevented cleavage in the 5'-UTR of <i>sinI</i> by RNase E and impaired <i>sinI</i> translation. In line with low ribosomal occupancy and transcript destabilization upon binding of RcsR1 to <i>sinI</i>, overproduction of RcsR1 in <i>S. meliloti</i> resulted in lower level and shorter half-life of <i>sinI</i> mRNA, and in decreased autoinducer amount. Although RcsR1 can influence quorum sensing via <i>sinI</i>, its level did not vary at different cell densities, but decreased under salt stress and increased at low temperature. We found that RcsR1 and its stress-related expression pattern, but not the interaction with <i>sinI</i> homologs, are conserved in <i>Sinorhizobium</i>, <i>Rhizobium</i> and <i>Agrobacterium.</i> Consistently, overproduction of RcsR1 in <i>S. meliloti</i> and <i>Agrobacterium tumefaciens</i> inhibited growth at high salinity. We identified conserved targets of RcsR1 and showed that most conserved interactions and the effect on growth under salt stress are mediated by the first stem-loop of RcsR1, while its central part is responsible for the species-specific interaction with <i>sinI</i>. We conclude that RcsR1 is an ancient, stress-related riboregulator in rhizobia and propose that it links stress responses to quorum sensing in <i>S. meliloti.</i>
DOI: 10.6084/m9.figshare.1608860
title: The stress-related, rhizobial small RNA RcsR1 destabilizes the autoinducer synthase encoding mRNA <i>sinI</i> in <i>Sinorhizobium meliloti</i>

description: Quorum sensing is a cell density-dependent communication system of bacteria relying on autoinducer molecules. During the analysis of the post-transcriptional regulation of quorum sensing in the nitrogen fixing plant symbiont <i>Sinorhizobium meliloti,</i> we predicted and verified a direct interaction between the 5'-UTR of <i>sinI</i> mRNA encoding the autoinducer synthase and a small RNA (sRNA), which we named RcsR1. <i>In vitro</i>, RcsR1 prevented cleavage in the 5'-UTR of <i>sinI</i> by RNase E and impaired <i>sinI</i> translation. In line with low ribosomal occupancy and transcript destabilization upon binding of RcsR1 to <i>sinI</i>, overproduction of RcsR1 in <i>S. meliloti</i> resulted in lower level and shorter half-life of <i>sinI</i> mRNA, and in decreased autoinducer amount. Although RcsR1 can influence quorum sensing via <i>sinI</i>, its level did not vary at different cell densities, but decreased under salt stress and increased at low temperature. We found that RcsR1 and its stress-related expression pattern, but not the interaction with <i>sinI</i> homologs, are conserved in <i>Sinorhizobium</i>, <i>Rhizobium</i> and <i>Agrobacterium.</i> Consistently, overproduction of RcsR1 in <i>S. meliloti</i> and <i>Agrobacterium tumefaciens</i> inhibited growth at high salinity. We identified conserved targets of RcsR1 and showed that most conserved interactions and the effect on growth under salt stress are mediated by the first stem-loop of RcsR1, while its central part is responsible for the species-specific interaction with <i>sinI</i>. We conclude that RcsR1 is an ancient, stress-related riboregulator in rhizobia and propose that it links stress responses to quorum sensing in <i>S. meliloti.</i>
DOI: 10.6084/m9.figshare.1608835
title: data_Sten2014

description: Suporting data for the manuscript submitted to Ecology
DOI: 10.6084/m9.figshare.11688504
title: Born to be young? Prenatal thyroid hormones increase early-life telomere length in wild collared flycatcher

description: Datasets used in Stier et al. 2020: "Born to be young? Prenatal thyroid hormones increase early-life telomere length in wild collared flycatcher". Each .csv file contain the data presented in Fig. 1 (Ageing standard curves) and Fig. 2 (effects of prenatal TH).<br>
DOI: 10.6084/m9.figshare.11688504.v1
title: Born to be young? Prenatal thyroid hormones increase early-life telomere length in wild collared flycatcher

description: Datasets used in Stier et al. 2020: "Born to be young? Prenatal thyroid hormones increase early-life telomere length in wild collared flycatcher". Each .csv file contain the data presented in Fig. 1 (Ageing standard curves) and Fig. 2 (effects of prenatal TH).<br>
DOI: 10.6084/m9.figshare.1608717
title: Entiology enteric diseases data

description: Data sets used to estimate the etiology of diarrhoea incidence and mortality in children under 5 and the population over 5
DOI: 10.6084/m9.figshare.1608716
title: A GIS-based comparison of long-distance supply of energy wood for future needs from young forests to the coast of Finland

description: With increasing demand and competition for forest biomass, the future will see its transportation distances increase in Finland. The aim of the study was to evaluate long-distance transportation solutions and intermodal handling of energy wood for its journey from young forests to a combined heat and power plant in Kokkola, Finland. Via a case study, the costs of various supply chains were estimated on the basis of spatially explicit data. The potentials were estimated from National Forest Inventory data. With GIS assistance, supply points were determined, and supply costs with nine distinct supply chains were calculated for each point on the basis of transport distances and productivity models. Both whole-tree and delimbed stemwood chains were included. The transport modes considered were trains, traditional 60-tonne trucks, and combinations with new high-capacity transport (HCT) vehicles of 68 and 76 tonnes and train transportation. Whole trees were assumed to be transported either as chips or in uncomminuted form to train terminals, whereas delimbed stemwood remained uncomminuted. Use of interchangeable containers was assumed in two of the whole-tree chains. In our study, the whole-tree supply chains did not prove to be competitive with the stemwood chains. Train-based chains proved to be cost-competitive with the traditional truck chain only in very limited areas around the terminals. The costs of the supply chains based on use of HCT vehicles were always lower than the costs associated with the train-based chains. The greatest barrier in long-distance and intermodal transport of forest chips is the high cost of transport by rail.
DOI: 10.6084/m9.figshare.1608717.v1
title: Entiology enteric diseases data

description: Data sets used to estimate the etiology of diarrhoea incidence and mortality in children under 5 and the population over 5
DOI: 10.6084/m9.figshare.1608715
title: Relevant data

description: snp
DOI: 10.6084/m9.figshare.1608716.v1
title: A GIS-based comparison of long-distance supply of energy wood for future needs from young forests to the coast of Finland

description: With increasing demand and competition for forest biomass, the future will see its transportation distances increase in Finland. The aim of the study was to evaluate long-distance transportation solutions and intermodal handling of energy wood for its journey from young forests to a combined heat and power plant in Kokkola, Finland. Via a case study, the costs of various supply chains were estimated on the basis of spatially explicit data. The potentials were estimated from National Forest Inventory data. With GIS assistance, supply points were determined, and supply costs with nine distinct supply chains were calculated for each point on the basis of transport distances and productivity models. Both whole-tree and delimbed stemwood chains were included. The transport modes considered were trains, traditional 60-tonne trucks, and combinations with new high-capacity transport (HCT) vehicles of 68 and 76 tonnes and train transportation. Whole trees were assumed to be transported either as chips or in uncomminuted form to train terminals, whereas delimbed stemwood remained uncomminuted. Use of interchangeable containers was assumed in two of the whole-tree chains. In our study, the whole-tree supply chains did not prove to be competitive with the stemwood chains. Train-based chains proved to be cost-competitive with the traditional truck chain only in very limited areas around the terminals. The costs of the supply chains based on use of HCT vehicles were always lower than the costs associated with the train-based chains. The greatest barrier in long-distance and intermodal transport of forest chips is the high cost of transport by rail.
DOI: 10.6084/m9.figshare.1608714
title: Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance

description: Additional supplementary file for eLife article "Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance" (2014, eLife 2014;3:e02678, doi: 10.7554/eLife.02678).
DOI: 10.6084/m9.figshare.1608835.v1
title: data_Sten2014

description: Suporting data fof the manuscript submitted to Proc B
DOI: 10.6084/m9.figshare.1608715.v1
title: Relevant data

description: snp
DOI: 10.6084/m9.figshare.1608714.v1
title: Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance

description: Additional supplementary file for eLife article "Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance" (2014, eLife 2014;3:e02678, doi: 10.7554/eLife.02678).
DOI: 10.6084/m9.figshare.1608835.v3
title: data_Sten2014

description: Suporting data for the manuscript submitted to Ecology
DOI: 10.6084/m9.figshare.1608709
title: Simulations of retinogeniculate refinement

description: Supplementary Data to accompany our 2002 paper. http://dx.doi.org/10.1152/jn.00372.2002
DOI: 10.6084/m9.figshare.1608835.v2
title: data_Sten2014

description: Suporting data for the manuscript submitted to Ecology
DOI: 10.6084/m9.figshare.1608709.v2
title: Simulations of retinogeniculate refinement

description: Supplementary Data to accompany our 2002 paper. http://dx.doi.org/10.1152/jn.00372.2002
DOI: 10.6084/m9.figshare.1608709.v1
title: Simulations of retinogeniculate refinement

description: Supplementary Data to accompany our 2002 paper.
DOI: 10.5281/zenodo.4015117
title: What is the clinical course of patients hospitalised for COVID-19 treatment Ireland: a retrospective cohort study in Dublin's North Inner City (the 'Mater 100')

description: <strong>Background: </strong>Since March 2020, Ireland has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While several cohorts from China have been described, there is little data describing the epidemiological and clinical characteristics of patients with COVID-19 in Ireland. <strong>To improve our understanding of this emerging infection we carried out </strong>a retrospective review of patient data to<strong> examine the clinical characteristics </strong>of patients admitted for COVID-19 hospital treatment. <strong>Methods<strong>:</strong></strong> Demographic, clinical and laboratory data on the first 100 adult patients admitted to Mater Misericordiae University Hospital (MMUH) for in-patient COVID-19 treatment after onset of the outbreak in March 2020 was extracted from clinical and administrative records. <strong>R<strong>esults:</strong></strong> Fifty-eight per cent were male, 63% were Irish nationals, and median age was 45 years (interquartile range [IQR] =34-64 years). Patients had symptoms for a median of five days before diagnosis (IQR=2.5-7 days), most commonly cough (72%), fever (65%), dyspnoea (37%), fatigue (28%), myalgia (27%) and headache (24%). Of all cases, 54 had at least one pre-existing chronic illness (most commonly hypertension, diabetes mellitus or asthma). At initial assessment, the most common abnormal findings were: C-reactive protein &gt;7.0mg/L (74%), ferritin &gt;247μg/L (women) or &gt;275μg/L (men) (62%), D-dimer &gt;0.5μg/dL (62%), chest imaging (59%), NEWS Score (modified) of ≥3 (55%) and heart rate &gt;90/min (51%). Twenty-seven required supplemental oxygen, of which 17 were admitted to the intensive care unit - 14 requiring ventilation. Forty received antiviral treatment (most commonly hydroxychloroquine or lopinavir/ritonavir). Four died, 17 were admitted to intensive care, and 74 were discharged home, with nine days the median hospital stay (IQR=6-11). C<strong>onclusion:</strong> Our findings reinforce the emerging consensus of COVID-19 as an acute life-threatening disease and highlights, the importance of laboratory (ferritin, C-reactive protein, D-dimer) and radiological parameters, in addition to clinical parameters. Further cohort studies involving larger samples followed longitudinally are a priority.
DOI: 10.5281/zenodo.4015116
title: What is the clinical course of patients hospitalised for COVID-19 treatment Ireland: a retrospective cohort study in Dublin's North Inner City (the 'Mater 100')

description: <strong>Background: </strong>Since March 2020, Ireland has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While several cohorts from China have been described, there is little data describing the epidemiological and clinical characteristics of patients with COVID-19 in Ireland. <strong>To improve our understanding of this emerging infection we carried out </strong>a retrospective review of patient data to<strong> examine the clinical characteristics </strong>of patients admitted for COVID-19 hospital treatment. <strong>Methods<strong>:</strong></strong> Demographic, clinical and laboratory data on the first 100 adult patients admitted to Mater Misericordiae University Hospital (MMUH) for in-patient COVID-19 treatment after onset of the outbreak in March 2020 was extracted from clinical and administrative records. <strong>R<strong>esults:</strong></strong> Fifty-eight per cent were male, 63% were Irish nationals, and median age was 45 years (interquartile range [IQR] =34-64 years). Patients had symptoms for a median of five days before diagnosis (IQR=2.5-7 days), most commonly cough (72%), fever (65%), dyspnoea (37%), fatigue (28%), myalgia (27%) and headache (24%). Of all cases, 54 had at least one pre-existing chronic illness (most commonly hypertension, diabetes mellitus or asthma). At initial assessment, the most common abnormal findings were: C-reactive protein &gt;7.0mg/L (74%), ferritin &gt;247μg/L (women) or &gt;275μg/L (men) (62%), D-dimer &gt;0.5μg/dL (62%), chest imaging (59%), NEWS Score (modified) of ≥3 (55%) and heart rate &gt;90/min (51%). Twenty-seven required supplemental oxygen, of which 17 were admitted to the intensive care unit - 14 requiring ventilation. Forty received antiviral treatment (most commonly hydroxychloroquine or lopinavir/ritonavir). Four died, 17 were admitted to intensive care, and 74 were discharged home, with nine days the median hospital stay (IQR=6-11). C<strong>onclusion:</strong> Our findings reinforce the emerging consensus of COVID-19 as an acute life-threatening disease and highlights, the importance of laboratory (ferritin, C-reactive protein, D-dimer) and radiological parameters, in addition to clinical parameters. Further cohort studies involving larger samples followed longitudinally are a priority.
DOI: 10.6084/m9.figshare.1608690
title: Data under 5 inpatients

description: Data extraction from systematic review of inpatient studies with diarrhoea (children under 5)
DOI: 10.6084/m9.figshare.1608691
title: Norovirus under 5

description: Data extraction from systematic review of inpatient, outpatient and community studies
DOI: 10.6084/m9.figshare.1608692
title: Norovirus data all ages

description: Data extracted from systematic review on studies isolating norovirus from inpatients, outpatients and community studies.
DOI: 10.6084/m9.figshare.1608693
title: Mapping of topsoil texture in Hungary using classification trees

description: Spatial information about physical soil properties is in great demand, being basic input data in numerous applications. Soil texture can be characterized by different approaches, such as particle size distribution, plasticity index or soil texture classification. In accordance with the increasing demands for spatial soil texture information, our aim was to compile a topsoil texture class map for Hungary with an appropriate spatial resolution, using the United States Department of Agriculture soil texture classes. The ‘Classification and Regression Trees’ method was applied because it is widely used in Digital Soil Mapping, and has numerous advantages. Primary soil data were provided by the Hungarian Soil Information and Monitoring System. A digital elevation model and its derived components, geological and land cover map, and appropriate remotely sensed products together with the soil map featuring overall physical properties provided by the Digital Kreybig Soil Information System were used as auxiliary environmental co-variables. The resulting map can be used as direct input data in meteorological and hydrological modelling as well as in spatial planning.
DOI: 10.6084/m9.figshare.1608693.v1
title: Mapping of topsoil texture in Hungary using classification trees

description: Spatial information about physical soil properties is in great demand, being basic input data in numerous applications. Soil texture can be characterized by different approaches, such as particle size distribution, plasticity index or soil texture classification. In accordance with the increasing demands for spatial soil texture information, our aim was to compile a topsoil texture class map for Hungary with an appropriate spatial resolution, using the United States Department of Agriculture soil texture classes. The ‘Classification and Regression Trees’ method was applied because it is widely used in Digital Soil Mapping, and has numerous advantages. Primary soil data were provided by the Hungarian Soil Information and Monitoring System. A digital elevation model and its derived components, geological and land cover map, and appropriate remotely sensed products together with the soil map featuring overall physical properties provided by the Digital Kreybig Soil Information System were used as auxiliary environmental co-variables. The resulting map can be used as direct input data in meteorological and hydrological modelling as well as in spatial planning.
DOI: 10.6084/m9.figshare.1608688
title: Data under 5 _oupatients and community studies

description: Data extraction from systematic review of outpatients and community studies of peopple with diarrhoea (children under 5)
DOI: 10.6084/m9.figshare.1608689
title: Data pop over 5 _inpatients, outpatients and community studies

description: Data extraction from systematic review of inpatient, outpatient and community studies with diarrhoea (population over 5)
DOI: 10.6084/m9.figshare.1608690.v1
title: Data under 5 inpatients

description: Data extraction from systematic review of inpatient studies with diarrhoea (children under 5)
DOI: 10.6084/m9.figshare.1608691.v1
title: Norovirus under 5

description: Data extraction from systematic review of inpatient, outpatient and community studies
DOI: 10.6084/m9.figshare.1608688.v1
title: Data under 5 _oupatients and community studies

description: Data extraction from systematic review of outpatients and community studies of peopple with diarrhoea (children under 5)
DOI: 10.6084/m9.figshare.1608347
title: Data from: The effects of phylogenetic relatedness on invasion success and impact: deconstructing Darwin’s naturalization conundrum

description: Darwin’s naturalization conundrum describes the paradox that the relatedness of exotic species to native residents could either promote or hinder their success through opposing mechanisms: niche pre-adaptation or competitive interactions. Previous studies focusing on single snapshots of invasion patterns have provided support to both sides of the conundrum. Here, by examining invasion dynamics of 480 plots over 40 years, we show that exotic species more closely related to native species were more likely to enter, establish and dominate the resident communities, and that native residents more closely related to these successful exotics were more likely to go locally extinct. Therefore, non-random displacement of natives during invasion could weaken or even reverse the negative effects of exotic-native phylogenetic distances on invasion success. The scenario that exotics more closely related to native residents are more successful, but tend to eliminate their closely related natives, may help to reconcile the 150-year-old conundrum.
DOI: 10.6084/m9.figshare.1608322
title: #RefugeesWelcome Co-Retweeted Network from 9/3/2015

description: The co-retweeted network of users discussing #refugeeswelcome on September 3rd, 2015.
DOI: 10.6084/m9.figshare.1608321
title: #RefugeesWelcome Co-Retweeted Network from 11/18/2015

description: The co-retweeted network of users discussing #refugeeswelcome on November 18th, 2015.
DOI: 10.6084/m9.figshare.1608322.v1
title: #RefugeesWelcome Co-Retweeted Network from 9/3/2015

description: The co-retweeted network of users discussing #refugeeswelcome on September 3rd, 2015.
DOI: 10.6084/m9.figshare.1608347.v1
title: Data from: The effects of phylogenetic relatedness on invasion success and impact: deconstructing Darwin’s naturalization conundrum

description: Darwin’s naturalization conundrum describes the paradox that the relatedness of exotic species to native residents could either promote or hinder their success through opposing mechanisms: niche pre-adaptation or competitive interactions. Previous studies focusing on single snapshots of invasion patterns have provided support to both sides of the conundrum. Here, by examining invasion dynamics of 480 plots over 40 years, we show that exotic species more closely related to native species were more likely to enter, establish and dominate the resident communities, and that native residents more closely related to these successful exotics were more likely to go locally extinct. Therefore, non-random displacement of natives during invasion could weaken or even reverse the negative effects of exotic-native phylogenetic distances on invasion success. The scenario that exotics more closely related to native residents are more successful, but tend to eliminate their closely related natives, may help to reconcile the 150-year-old conundrum.
DOI: 10.6084/m9.figshare.1608317
title: TDP43

description: Correction to TDP43 paper published in Plos
DOI: 10.6084/m9.figshare.1608318
title: Bait Preference of Free-Ranging Feral Swine for Delivery of a Novel Toxicant

description: Columns Site = location of camera Treatment = type of treatment at site Day = day of study TotalPhotos = number of images taken per day per site PigPhotos = number of images with feral swine per day per site AdultPigPhotos = number of images with adult feral swine per day per site DeerPhotos = number of images with deer per day per site RaccoonPhotos = number of images with raccoons per day per site BirdPhotos = number of images with birds per day per site NonTargetPhotos = number of images with all nontarget species combined per day per site
DOI: 10.6084/m9.figshare.1608321.v1
title: #RefugeesWelcome Co-Retweeted Network from 11/18/2015

description: The co-retweeted network of users discussing #refugeeswelcome on November 18th, 2015.
DOI: 10.6084/m9.figshare.1608317.v1
title: TDP43

description: Correction to TDP43 paper published in Plos