cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8118689
title: Role of a hairpin-stabilized pause in the <i>Escherichia coli thiC</i> riboswitch function

description: Transcriptional pauses have been reported in bacterial riboswitches and, in some cases, their specific positioning has been shown to be important for gene regulation. Here, we show that a hairpin structure in the <i>Escherichia coli</i> thiamin pyrophosphate (TPP) <i>thiC</i> riboswitch is involved in transcriptional pausing and ligand sensitivity. Using <i>in vitro</i> transcription kinetic experiments, we show that all three major transcriptional pauses in the <i>thiC</i> riboswitch are affected by NusA, a transcriptional factor known to stimulate hairpin-stabilized pauses. Using a truncated region of the riboswitch, we isolated the hairpin structure responsible for stabilization of the most upstream pause. Destabilization of this structure led to a weaker pause and a decreased NusA effect. In the context of the full-length riboswitch, this same mutation also led to a weaker pause, as well as a decreased TPP binding affinity. Our work suggests that RNA structures involved in transcriptional pausing in riboswitches are important for ligand sensitivity, most likely by increasing the time allowed to the ligand for binding to the riboswitch.
DOI: 10.6084/m9.figshare.8118689.v2
title: Role of a hairpin-stabilized pause in the <i>Escherichia coli thiC</i> riboswitch function

description: Transcriptional pauses have been reported in bacterial riboswitches and, in some cases, their specific positioning has been shown to be important for gene regulation. Here, we show that a hairpin structure in the <i>Escherichia coli</i> thiamin pyrophosphate (TPP) <i>thiC</i> riboswitch is involved in transcriptional pausing and ligand sensitivity. Using <i>in vitro</i> transcription kinetic experiments, we show that all three major transcriptional pauses in the <i>thiC</i> riboswitch are affected by NusA, a transcriptional factor known to stimulate hairpin-stabilized pauses. Using a truncated region of the riboswitch, we isolated the hairpin structure responsible for stabilization of the most upstream pause. Destabilization of this structure led to a weaker pause and a decreased NusA effect. In the context of the full-length riboswitch, this same mutation also led to a weaker pause, as well as a decreased TPP binding affinity. Our work suggests that RNA structures involved in transcriptional pausing in riboswitches are important for ligand sensitivity, most likely by increasing the time allowed to the ligand for binding to the riboswitch.
DOI: 10.6084/m9.figshare.8118545
title: Data from Capo et al. (2019) Environmental DNA "Effects of filtration methods and water volume on quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) fish eDNA concentrations via droplet digital PCR"

description: Dataset showing the number of DNA copy for each DNA extract (from char and trout cultivation tanks). For each DNA extracts, the filtered volume, dilution factors for the ddPCR and the raw outputs are presented.<br>
DOI: 10.6084/m9.figshare.8118545.v1
title: Data from the Manuscript of Capo et al. entitled "Effects of filtration methods and water volume on quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) fish eDNA concentrations via droplet digital PCR"

description: Dataset showing the number of DNA copy for each DNA extract (from char and trout cultivation tanks). For each DNA extracts, the filtered volume, dilution factors for the ddPCR and the raw outputs are presented.<br>
DOI: 10.6084/m9.figshare.8118431
title: Psoriasis treatment patterns: a retrospective claims study

description: <b>Objective:</b> The objective was to characterize psoriasis treatment patterns, including estimating persistence and describing subsequent events (i.e. switching and restarting) for all systemic therapies. <b>Methods</b>: This retrospective cohort study utilized Truven MarketScan databases from 1 January 2014 to 31 December 2016 to investigate persistence, switching and restarting in new users of systemic psoriasis medications. Descriptive statistics, time-to-event analyses and a Cox proportional hazards regression were conducted. <b>Results:</b> A total of 5205 patients met inclusion criteria. Regardless of treatment type, &gt;50% lost persistence by 12 months. Patients newly initiating acitretin or non-TNF biologic experienced the highest loss of persistence (85.2%, 73.8%, respectively). Patients initiating a TNF-α inhibitor or apremilast experienced the lowest loss (51.8%, 56.4% respectively). Treatment type had a statistically significant effect on persistence loss (adjusted hazard ratio: 0.86, 95% CI: 0.81, 0.91). Restarting was the most commonly observed event for patients on an oral or biologic (60.2%, 79.9%, respectively). The most common switch from an oral was to a TNF-α inhibitor, while apremilast often followed biologics. <b>Conclusion:</b> Most patients lost persistence on initial treatment by 12 months, and the majority restarted treatment. This may indicate poor compliance or the cyclical nature of psoriasis. More patients switched from an oral to biologic than vice versa, likely due to formulary design and preference for orals. Studies are needed to investigate underlying reasons and patient characteristics that differentiate treatment utilization.
DOI: 10.6084/m9.figshare.8118431.v1
title: Psoriasis treatment patterns: a retrospective claims study

description: <b>Objective:</b> The objective was to characterize psoriasis treatment patterns, including estimating persistence and describing subsequent events (i.e. switching and restarting) for all systemic therapies. <b>Methods</b>: This retrospective cohort study utilized Truven MarketScan databases from 1 January 2014 to 31 December 2016 to investigate persistence, switching and restarting in new users of systemic psoriasis medications. Descriptive statistics, time-to-event analyses and a Cox proportional hazards regression were conducted. <b>Results:</b> A total of 5205 patients met inclusion criteria. Regardless of treatment type, &gt;50% lost persistence by 12 months. Patients newly initiating acitretin or non-TNF biologic experienced the highest loss of persistence (85.2%, 73.8%, respectively). Patients initiating a TNF-α inhibitor or apremilast experienced the lowest loss (51.8%, 56.4% respectively). Treatment type had a statistically significant effect on persistence loss (adjusted hazard ratio: 0.86, 95% CI: 0.81, 0.91). Restarting was the most commonly observed event for patients on an oral or biologic (60.2%, 79.9%, respectively). The most common switch from an oral was to a TNF-α inhibitor, while apremilast often followed biologics. <b>Conclusion:</b> Most patients lost persistence on initial treatment by 12 months, and the majority restarted treatment. This may indicate poor compliance or the cyclical nature of psoriasis. More patients switched from an oral to biologic than vice versa, likely due to formulary design and preference for orals. Studies are needed to investigate underlying reasons and patient characteristics that differentiate treatment utilization.
DOI: 10.6084/m9.figshare.8118413
title: tcnibmg

description: <b>This is an R data package</b>. This contains transcriptome data from TCGA (https://portal.gdc.cancer.gov/) for 17 cancers.
DOI: 10.6084/m9.figshare.8118413.v1
title: tcnibmg

description: <b>This is an R data package</b>. This contains transcriptome data from TCGA (https://portal.gdc.cancer.gov/) for 17 cancers.
DOI: 10.6084/m9.figshare.8118413.v3
title: tcnibmg

description: <b>This is an R data package</b>. This contains transcriptome data from TCGA (https://portal.gdc.cancer.gov/) for 17 cancers.
DOI: 10.6084/m9.figshare.8118413.v2
title: tcnibmg

description: <b>This is an R data package</b>. This contains transcriptome data from TCGA (https://portal.gdc.cancer.gov/) for 17 cancers.
DOI: 10.6084/m9.figshare.8118401
title: GADO HPO Predictions spiked 01-02-2018

description: Data used to run GADO command line: https://github.com/molgenis/systemsgenetics/wiki/GADO-Command-line<br>
DOI: 10.6084/m9.figshare.8118401.v1
title: GADO HPO Predictions spiked 01-02-2018

description: Data used to run GADO command line: https://github.com/molgenis/systemsgenetics/wiki/GADO-Command-line<br>
DOI: 10.5525/gla.researchdata.1054
title: Purring Wheel: Thermal and Vibrotactile Notifications on the Steering Wheel
DOI: 10.17028/rd.lboro.8118323
title: DICE Personal & Contextual Factors Dataset

description: Thank you for your interest in using our data. As this data was provided to us by a third party, before we provide access to it, we would like you to agree to some terms of use. These are not unnecessarily restrictive - essentially, they enable you to use the full details of the customer complaints that we used, whilst agreeing not to <b>publish</b> details that could (directly or indirectly) identify the rail companies referred to in the complaints. Please contact one of the authors for access. The research team would like to acknowledge the help from mySociety (mySociety.org) who provided this data, which was collected through their FixMyTransport platform. Thank you.
DOI: 10.17028/rd.lboro.8118323.v1
title: DICE Personal & Contextual Factors Dataset

description: Thank you for your interest in using our data. As this data was provided to us by a third party, before we provide access to it, we would like you to agree to some terms of use. These are not unnecessarily restrictive - essentially, they enable you to use the full details of the customer complaints that we used, whilst agreeing not to <b>publish</b> details that could (directly or indirectly) identify the rail companies referred to in the complaints. Please contact one of the authors for access. The research team would like to acknowledge the help from mySociety (mySociety.org) who provided this data, which was collected through their FixMyTransport platform. Thank you.
DOI: 10.6084/m9.figshare.8118311
title: Bicycle Route Comforts and Risks

description: A selection of bicycle routes in Zurich provided by cyclists with calculated relative risk and comfort measures. The user ID's provide identification of the unique cyclists while the route ID's identify unique routes.
DOI: 10.6084/m9.figshare.8118311.v1
title: Bicycle Route Comforts and Risks

description: A selection of bicycle routes in Zurich provided by cyclists with calculated relative risk and comfort measures. The user ID's provide identification of the unique cyclists while the route ID's identify unique routes.
DOI: 10.6084/m9.figshare.8118290
title: Database for estimating CV of VAR

description: Database used for running Appendix Script A1<br>
DOI: 10.6084/m9.figshare.8118290.v1
title: Database for estimating CV of VAR

description: Database used for running Appendix Script A1<br>
DOI: 10.6084/m9.figshare.8118245
title: Risk scores and surgery for infective endocarditis: in search of a good predictive score

description: <i>Objectives</i>: To evaluate scoring systems that have been created to predict the risk of death post-surgery in infective endocarditis (IE). <i>Design</i>: Eight scores – (1) The Society of Thoracic Surgery (STS) risk score for IE, (2) De Feo score, (3) PALSUSE score (prosthetic valve, age ≥70, large intracardiac destruction, Staphylococcus spp, urgent surgery, sex [female], EuroSCORE ≥10), (4) ANCLA score (anemia, New York Heart Association class IV, critical state, large intracardiac destruction, surgery of thoracic aorta), (5) Risk-Endocarditis Score (RISK-E), (6) score for heart valve or prosthesis IE (EndoSCORE), and (7,8) Association pour l'Étude et la Prévention de l'Endocadite Infectieuse (AEPEI) score I and II – were evaluated in 324 (mean age, 61.8 ± 14.6 years) consecutive patients having IE and undergoing cardiac operation (1999–2018, Regione Autonoma Friuli-Venezia Giulia, Italy). <i>Results</i>: There were 45 (13.9%) in-hospital deaths. Despite many differences on the number and the type of variables, all the investigated scores showed good goodness-of-fit (Hosmer-Lemeshow test, <i>p</i> ≥.28). For five scores, accuracy of prediction (receiver-operating characteristic curve analysis) was good (ANCLA score) or fair (STS risk score for IE, PALSUSE score, AEPEI score I and II). When compared one-to-one (Hanley-McNeil method), accuracy of prediction of ANCLA score was higher than all of other risk scores except for AEPEI score I (<i>p</i> = .077). <i>Conclusions</i>: Five of eight scores that were evaluated in this study showed satisfactory performance in predicting in-hospital mortality following surgery for IE. The ANCLA score should be preferred.
DOI: 10.17608/k6.auckland.8118194
title: Seagrass speceis occurrence records

description: Cleaned seagrass occurrence location data from the GBIF and UNEP-WCMC.<br>
DOI: 10.17608/k6.auckland.8118194.v1
title: Seagrass speceis occurrence records

description: Cleaned seagrass occurrence location data from the GBIF and UNEP-WCMC.<br>
DOI: 10.6084/m9.figshare.8118035
title: Data

description: Datasets
DOI: 10.6084/m9.figshare.8118035.v1
title: Data

description: Datasets
DOI: 10.6084/m9.figshare.8117978
title: Methylation counts and methylation level

description: This file contains the raw data of the methylation counts and the methylation level (%). The first column for each CpG site is the number of methylated Cs and the second column in the un-methylated Cs. The third column shows the methylation level in a given CpG site. A dot in the record indicates missing data.
DOI: 10.6084/m9.figshare.8117978.v2
title: Methylation counts and methylation level

description: This file contains the raw data of the methylation counts and the methylation level (%). The first column for each CpG site is the number of methylated Cs and the second column in the un-methylated Cs. The third column shows the methylation level in a given CpG site. A dot in the record indicates missing data.
DOI: 10.6084/m9.figshare.8117978.v1
title: Methylation counts and methylation level

description: This file contains the raw data of the methylation counts and the methylation level (%). The first column for each CpG site is the number of methylated Cs and the second column in the un-methylated Cs. The third column shows the methylation level in a given CpG site. A dot in the record indicates missing data.
DOI: 10.25377/sussex.8117975.v1
title: Dataset for Everyday Childhoods research project. David - Day in a Life

description: This data was collected as part of David's day in a life observation, carried out on the 06/02/2014 with Sue Sharpe. This item belongs to the Everyday Childhoods project dataset. For more information, click on the project or collection link.
DOI: 10.6084/m9.figshare.8117939
title: Predicting the spatial dynamics of Wolbachia infections in Aedes aegypti arbovirus vector populations in heterogeneous landscapes, 2019, Journal of Applied Ecology

description: 1. Mosquito age class abundances (first instar larvae, total number of larvae, and number of newly eclosed pupae) on each day from the Low Food (LF) field-cage experimental population.2. Number of pupae per house per day recorded during the pupal surveys conducted by Koenraadt et al. (2008).
DOI: 10.6084/m9.figshare.8117939.v1
title: Predicting the spatial dynamics of Wolbachia infections in Aedes aegypti arbovirus vector populations in heterogeneous landscapes, 2019, Journal of Applied Ecology

description: 1. Mosquito age class abundances (first instar larvae, total number of larvae, and number of newly eclosed pupae) on each day from the Low Food (LF) field-cage experimental population.2. Number of pupae per house per day recorded during the pupal surveys conducted by Koenraadt et al. (2008).
DOI: 10.6084/m9.figshare.8117867
title: DATA-NGS.zip

description: This is the sequence and analysis data of 16S high throughput sequencing of 40 nematode symbiotic bacteria.<br>
DOI: 10.6084/m9.figshare.8117867.v1
title: DATA-NGS.zip

description: This is the sequence and analysis data of 16S high throughput sequencing of 40 nematode symbiotic bacteria.<br>
DOI: 10.6084/m9.figshare.8117858
title: Source Data.xlsx

description: Synthetic mimics of chlorophyll, which is designed by replacing the Mg center of porphyrin unit with other metal atoms (Au, Cu, Co) on metal-organic frameworks, may maximize atom utilization and optimize catalytic activity. Simultaneously, porphyrin ligand can be easily interfered by light filed, which offers an opportunity to develop light-coupled electrocatalyst for CO<sub>2</sub> reduction. The single-Au-atom catalyst exhibits a record-high turnover frequency of 28332 h<sup>-1</sup> at -1.1 V and CO faradaic efficiency of 94.2% at -0.9 V. Interestingly, with visible light interfered (67% solar intensity), the electrocatalyst reaches an approximate turnover frequency value and faradaic efficiency with reduced potential of 130 mV. The similar trend is also observed on single-Cu-atom electrocatalyst under visible light, displaying a positive shift of 100 mV with a highest HCOOH faradaic efficiency of 77.3% at -0.7 V versus RHE. Interestingly, the light-induced positive shifts of 20, 100 and 130 mV for single-Co-atom, single-Cu-atom and single-Au-atom electrocatalysts are in consistent with their energy gaps of 0, 1.5 and 1.7 eV, respectively, suggesting the porphyrin not only serves as ligand, but also photoswitch to regulate electron transfer pathway to metal atom.<br>
DOI: 10.6084/m9.figshare.8117858.v1
title: Source Data.xlsx

description: Synthetic mimics of chlorophyll, which is designed by replacing the Mg center of porphyrin unit with other metal atoms (Au, Cu, Co) on metal-organic frameworks, may maximize atom utilization and optimize catalytic activity. Simultaneously, porphyrin ligand can be easily interfered by light filed, which offers an opportunity to develop light-coupled electrocatalyst for CO<sub>2</sub> reduction. The single-Au-atom catalyst exhibits a record-high turnover frequency of 32853 h<sup>-1</sup> at -1.1 V and CO faradaic efficiency of 94.2% at -0.9 V. Interestingly, with visible light interfered (67% solar intensity), the electrocatalyst reaches an approximate turnover frequency value and faradaic efficiency with reduced potential of 130 mV. The similar trend is also observed on single-Cu-atom electrocatalyst under visible light, displaying a positive shift of 100 mV with a highest HCOOH faradaic efficiency of 77.3% at -0.7 V versus RHE. Interestingly, the light-induced positive shifts of 20, 100 and 130 mV for single-Co-atom, single-Cu-atom and single-Au-atom electrocatalysts are in consistent with their energy gaps of 0, 1.5 and 1.7 eV, respectively, suggesting the porphyrin not only serves as ligand, but also photoswitch to regulate electron transfer pathway to metal atom.<br>
DOI: 10.6084/m9.figshare.8117858.v2
title: Source Data.xlsx

description: Synthetic mimics of chlorophyll, which is designed by replacing the Mg center of porphyrin unit with other metal atoms (Au, Cu, Co) on metal-organic frameworks, may maximize atom utilization and optimize catalytic activity. Simultaneously, porphyrin ligand can be easily interfered by light filed, which offers an opportunity to develop light-coupled electrocatalyst for CO<sub>2</sub> reduction. The single-Au-atom catalyst exhibits a record-high turnover frequency of 28332 h<sup>-1</sup> at -1.1 V and CO faradaic efficiency of 94.2% at -0.9 V. Interestingly, with visible light interfered (67% solar intensity), the electrocatalyst reaches an approximate turnover frequency value and faradaic efficiency with reduced potential of 130 mV. The similar trend is also observed on single-Cu-atom electrocatalyst under visible light, displaying a positive shift of 100 mV with a highest HCOOH faradaic efficiency of 77.3% at -0.7 V versus RHE. Interestingly, the light-induced positive shifts of 20, 100 and 130 mV for single-Co-atom, single-Cu-atom and single-Au-atom electrocatalysts are in consistent with their energy gaps of 0, 1.5 and 1.7 eV, respectively, suggesting the porphyrin not only serves as ligand, but also photoswitch to regulate electron transfer pathway to metal atom.<br>
DOI: 10.6084/m9.figshare.8117858.v3
title: Source Data.xlsx

description: Synthetic mimics of chlorophyll, which is designed by replacing the Mg center of porphyrin unit with other metal atoms (Au, Cu, Co) on metal-organic frameworks, may maximize atom utilization and optimize catalytic activity. Simultaneously, porphyrin ligand can be easily interfered by light filed, which offers an opportunity to develop light-coupled electrocatalyst for CO<sub>2</sub> reduction. The single-Au-atom catalyst exhibits a record-high turnover frequency of 28332 h<sup>-1</sup> at -1.1 V and CO faradaic efficiency of 94.2% at -0.9 V. Interestingly, with visible light interfered (67% solar intensity), the electrocatalyst reaches an approximate turnover frequency value and faradaic efficiency with reduced potential of 130 mV. The similar trend is also observed on single-Cu-atom electrocatalyst under visible light, displaying a positive shift of 100 mV with a highest HCOOH faradaic efficiency of 77.3% at -0.7 V versus RHE. Interestingly, the light-induced positive shifts of 20, 100 and 130 mV for single-Co-atom, single-Cu-atom and single-Au-atom electrocatalysts are in consistent with their energy gaps of 0, 1.5 and 1.7 eV, respectively, suggesting the porphyrin not only serves as ligand, but also photoswitch to regulate electron transfer pathway to metal atom.<br>
DOI: 10.6084/m9.figshare.8117858.v4
title: Source Data.xlsx

description: Synthetic mimics of chlorophyll, which is designed by replacing the Mg center of porphyrin unit with other metal atoms (Au, Cu, Co) on metal-organic frameworks, may maximize atom utilization and optimize catalytic activity. Simultaneously, porphyrin ligand can be easily interfered by light filed, which offers an opportunity to develop light-coupled electrocatalyst for CO<sub>2</sub> reduction. The single-Au-atom catalyst exhibits a record-high turnover frequency of 28332 h<sup>-1</sup> at -1.1 V and CO faradaic efficiency of 94.2% at -0.9 V. Interestingly, with visible light interfered (67% solar intensity), the electrocatalyst reaches an approximate turnover frequency value and faradaic efficiency with reduced potential of 130 mV. The similar trend is also observed on single-Cu-atom electrocatalyst under visible light, displaying a positive shift of 100 mV with a highest HCOOH faradaic efficiency of 77.3% at -0.7 V versus RHE. Interestingly, the light-induced positive shifts of 20, 100 and 130 mV for single-Co-atom, single-Cu-atom and single-Au-atom electrocatalysts are in consistent with their energy gaps of 0, 1.5 and 1.7 eV, respectively, suggesting the porphyrin not only serves as ligand, but also photoswitch to regulate electron transfer pathway to metal atom.<br>