cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8218538
title: nonlinear-15-grams

description: 15-grams
DOI: 10.6084/m9.figshare.8218532
title: nonlinear-14-grams-number

description: 14-grams
DOI: 10.6084/m9.figshare.8218544
title: nonlinear-15-grams-number

description: 15-grams
DOI: 10.6084/m9.figshare.8218544.v1
title: nonlinear-15-grams-number

description: 15-grams
DOI: 10.6084/m9.figshare.8218538.v1
title: nonlinear-15-grams

description: 15-grams
DOI: 10.6084/m9.figshare.8218529
title: nonlinear-14-grams

description: 14-grams
DOI: 10.6084/m9.figshare.8218532.v1
title: nonlinear-14-grams-number

description: 14-grams
DOI: 10.6084/m9.figshare.8218514
title: Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar

description: To develop a greater understanding of hyporheic zone microbial biogeochemistry, we sampled pore fluids from a piezometer array associated with the McCarran Ranch channel bar (MRCB); a partially submerged cobble island in the Truckee River, NV, USA. Flowing surface water and pumped pore fluids were characterized by prokaryotic community structure, metabolic potential, and aqueous physicochemistry. Concentrations of potential respiratory electron acceptors were highest in surface water and riverbed porewater and sequentially depleted in porewaters along the inferred flowpath (O<sub>2</sub>, then NO<sub>3</sub><sup>−</sup>, then SO<sub>4</sub><sup>2−</sup>). Correspondingly, cultivable nitrate reducers/denitrifiers were most abundant in surface water and riverbed porewater, despite oxic conditions. Cultivable sulfate reducers were overall most abundant in surface water. Prokaryotic community reconstruction from 16S rRNA gene sequences indicates that the surface water community was less diverse than that of porewater and supports a shift in metabolic strategy, from aerobic heterotrophy in surface water (e.g., Comamonadaceae and Sporichthyaceae) to chemolithotrophy and anaerobic metabolisms (e.g., <i>Hydrogenophaga</i> spp., <i>Ferribacterium</i> spp., <i>Methanobacterium</i> spp.) along the hyporheic flow path. These data indicate that prokaryotic communities within the MRCB are phylogenetically and metabolically diverse and contribute to biogeochemical cycling in this common yet relatively understudied habitat.
DOI: 10.6084/m9.figshare.8218529.v1
title: nonlinear-14-grams

description: 14-grams
DOI: 10.6084/m9.figshare.8218514.v2
title: Microbial Community Structure and Metabolic Potential of the Hyporheic Zone of a Large Mid-Stream Channel Bar

description: To develop a greater understanding of hyporheic zone microbial biogeochemistry, we sampled pore fluids from a piezometer array associated with the McCarran Ranch channel bar (MRCB); a partially submerged cobble island in the Truckee River, NV, USA. Flowing surface water and pumped pore fluids were characterized by prokaryotic community structure, metabolic potential, and aqueous physicochemistry. Concentrations of potential respiratory electron acceptors were highest in surface water and riverbed porewater and sequentially depleted in porewaters along the inferred flowpath (O<sub>2</sub>, then NO<sub>3</sub><sup>−</sup>, then SO<sub>4</sub><sup>2−</sup>). Correspondingly, cultivable nitrate reducers/denitrifiers were most abundant in surface water and riverbed porewater, despite oxic conditions. Cultivable sulfate reducers were overall most abundant in surface water. Prokaryotic community reconstruction from 16S rRNA gene sequences indicates that the surface water community was less diverse than that of porewater and supports a shift in metabolic strategy, from aerobic heterotrophy in surface water (e.g., Comamonadaceae and Sporichthyaceae) to chemolithotrophy and anaerobic metabolisms (e.g., <i>Hydrogenophaga</i> spp., <i>Ferribacterium</i> spp., <i>Methanobacterium</i> spp.) along the hyporheic flow path. These data indicate that prokaryotic communities within the MRCB are phylogenetically and metabolically diverse and contribute to biogeochemical cycling in this common yet relatively understudied habitat.
DOI: 10.6084/m9.figshare.8218475
title: nonlinear-13-grams-number

description: 13-grams
DOI: 10.6084/m9.figshare.8218463
title: nonlinear-13-grams-number

description: 13-grams
DOI: 10.6084/m9.figshare.8218475.v1
title: nonlinear-13-grams-number

description: 13-grams
DOI: 10.6084/m9.figshare.8218436
title: nonlinear-12-grams

description: 12-grams
DOI: 10.6084/m9.figshare.8218439
title: nonlinear-12-grams-number

description: 12-grams
DOI: 10.6084/m9.figshare.8218442
title: nonlinear-12-grams-plot

description: 12-grams
DOI: 10.6084/m9.figshare.8218463.v1
title: nonlinear-13-grams-number

description: 13-grams
DOI: 10.6084/m9.figshare.8218439.v1
title: nonlinear-12-grams-number

description: 12-grams
DOI: 10.6084/m9.figshare.8218442.v1
title: nonlinear-12-grams-plot

description: 12-grams
DOI: 10.6084/m9.figshare.8218430
title: nonlinear-11-grams-number

description: 11-grams
DOI: 10.6084/m9.figshare.8218436.v1
title: nonlinear-12-grams

description: 12-grams
DOI: 10.6084/m9.figshare.8218424
title: nonlinear-11-grams

description: 11-grams
DOI: 10.6084/m9.figshare.8218430.v1
title: nonlinear-11-grams-number

description: 11-grams
DOI: 10.6084/m9.figshare.8218424.v1
title: nonlinear-11-grams

description: 11-grams
DOI: 10.6084/m9.figshare.8218388
title: RGG-motif self-association regulates eIF4G-binding translation repressor protein Scd6

description: Regulation of mRNA translation plays a key role in the control of gene expression. Scd6, a conserved RGG-motif containing protein represses translation by binding to translation initiation factor eIF4G1. Here we report that Scd6 binds itself in RGG-motif dependent manner and self-association regulates its repression activity. Scd6 self-interaction competes with eIF4G1 binding and methylation of Scd6 RGG-motif by Hmt1 negatively affects self-association. Results pertaining to Sbp1 indicate that self-association could be a general feature of RGG-motif containing translation repressor proteins. Taken together, our study reveals a mechanism of regulation of eIF4G-binding RGG-motif translation repressors.
DOI: 10.6084/m9.figshare.8218385
title: Olive orchard microbiome: characterisation of bacterial communities in soil-plant compartments and their comparison between sustainable and conventional soil management systems

description: <b>Background</b>: Beneficial bacteria-plant interactions play an important role in agriculture, positively affecting plant status and improving product quality. Bacterial endophytes contribute to host plant protection and survival. <b>Aim</b>: This study characterised the bacterial communities present in soil, leaf surface and xylem sap of olive trees, and investigated their response under a sustainable (Smng) or a conventional (Cmng) management system in an olive grove located in southern Italy. The aims are: (a) to understand if soil bacteria enter xylem and reach leaves and (b) to verify if the bacterial communities in the two management systems deeply differ due to the different agronomic practices applied in Smng and in Cmng. <b>Methods</b>: Therefore, a metagenomic approach was used to detect microorganisms, in order to estimate bacterial diversity and abundance, and to identify the bacterial taxa in the three analysed compartments in plants subjected to Smng and Cmng systems. <b>Results</b>: Bacterial communities came from the soil and reached aerial plant parts through xylem sap. The application of different agronomic practices influenced the composition of soil bacterial communities. <b>Conclusions</b>: The potential benefits of the specific bacterial taxa detected under the Smng system could improve plant growth protection and provide a higher crop quality in fruit plants.
DOI: 10.6084/m9.figshare.8218385.v1
title: Olive orchard microbiome: characterisation of bacterial communities in soil-plant compartments and their comparison between sustainable and conventional soil management systems

description: <b>Background</b>: Beneficial bacteria-plant interactions play an important role in agriculture, positively affecting plant status and improving product quality. Bacterial endophytes contribute to host plant protection and survival. <b>Aim</b>: This study characterised the bacterial communities present in soil, leaf surface and xylem sap of olive trees, and investigated their response under a sustainable (Smng) or a conventional (Cmng) management system in an olive grove located in southern Italy. The aims are: (a) to understand if soil bacteria enter xylem and reach leaves and (b) to verify if the bacterial communities in the two management systems deeply differ due to the different agronomic practices applied in Smng and in Cmng. <b>Methods</b>: Therefore, a metagenomic approach was used to detect microorganisms, in order to estimate bacterial diversity and abundance, and to identify the bacterial taxa in the three analysed compartments in plants subjected to Smng and Cmng systems. <b>Results</b>: Bacterial communities came from the soil and reached aerial plant parts through xylem sap. The application of different agronomic practices influenced the composition of soil bacterial communities. <b>Conclusions</b>: The potential benefits of the specific bacterial taxa detected under the Smng system could improve plant growth protection and provide a higher crop quality in fruit plants.
DOI: 10.6084/m9.figshare.8218358
title: Strain names and corresponding HA IDs

description: Data Citation 2---Strain names and corresponding HA IDs
DOI: 10.6084/m9.figshare.8218388.v3
title: RGG-motif self-association regulates eIF4G-binding translation repressor protein Scd6

description: Regulation of mRNA translation plays a key role in the control of gene expression. Scd6, a conserved RGG-motif containing protein represses translation by binding to translation initiation factor eIF4G1. Here we report that Scd6 binds itself in RGG-motif dependent manner and self-association regulates its repression activity. Scd6 self-interaction competes with eIF4G1 binding and methylation of Scd6 RGG-motif by Hmt1 negatively affects self-association. Results pertaining to Sbp1 indicate that self-association could be a general feature of RGG-motif containing translation repressor proteins. Taken together, our study reveals a mechanism of regulation of eIF4G-binding RGG-motif translation repressors.
DOI: 10.6084/m9.figshare.8218358.v1
title: Strain names and corresponding HA IDs

description: Data Citation 2---Strain names and corresponding HA IDs
DOI: 10.6084/m9.figshare.8218388.v2
title: RGG-motif self-association regulates eIF4G-binding translation repressor protein Scd6

description: Regulation of mRNA translation plays a key role in the control of gene expression. Scd6, a conserved RGG-motif containing protein represses translation by binding to translation initiation factor eIF4G1. Here we report that Scd6 binds itself in RGG-motif dependent manner and self-association regulates its repression activity. Scd6 self-interaction competes with eIF4G1 binding and methylation of Scd6 RGG-motif by Hmt1 negatively affects self-association. Results pertaining to Sbp1 indicate that self-association could be a general feature of RGG-motif containing translation repressor proteins. Taken together, our study reveals a mechanism of regulation of eIF4G-binding RGG-motif translation repressors.
DOI: 10.6084/m9.figshare.8218349
title: Raw data of HI test of IVA/H3N2

description: Data Citation 1---Hemagglutination-inhibition reaction
DOI: 10.6084/m9.figshare.8218349.v1
title: Raw data of HI test of IVA/H3N2

description: Data Citation 1---Hemagglutination-inhibition reaction
DOI: 10.6084/m9.figshare.8218340
title: Raw data of HI test of IVA/H3N2

description: Data Citation 1---Hemagglutination- inhibition reaction
DOI: 10.6084/m9.figshare.8218328
title: Adjuvanted versus nonadjuvanted influenza vaccines and risk of hospitalizations for pneumonia and cerebro/cardiovascular events in the elderly

description: <b>Background</b>: The higher effectiveness of MF59®-adjuvanted trivalent influenza vaccine (MF59-TIV) vs. nonadjuvanted TIV in preventing influenza-related hospitalizations was found considering few influenza seasons, local and heterogeneous settings. This study evaluated the relative vaccine effectiveness (rVE) of MF59-TIV vs. nonadjuvanted TIV on the risk of hospitalization for pneumonia and cerebro/cardiovascular events across 15 consecutive influenza seasons. <b>Research design and methods</b>: Using Health Search Database, a case–control study was nested in a cohort of elderly vaccinated with MF59-TIV or TIV. Conditional logistic regression was used to estimate the odds ratio with 95% confidence intervals (CI) of hospitalizations potentially related to influenza in patients vaccinated with MF59-TIV or TIV. <b>Results</b>: Of 43,000 patients vaccinated with MF59-TIV (66.2%) and TIV (33.8%) for the first time, 103 cases of hospitalization for pneumonia or cerebro/cardiovascular events (0.11 per 1,000 person-weeks) during 15 influenza seasons were identified. The MF59-TIV was associated with a reduced risk of hospitalizations for pneumonia and cerebro/cardiovascular events vs. TIV [rVE: 39% (95% CI: 4–61%)]. <b>Conclusions</b>: In a 15-season cohort of elderly, MF59-TIV seems to reduce the risk of hospitalizations for pneumonia and cerebro/cardiovascular events when compared with nonadjuvanted TIV. Our findings support the recommendation for MF59-TIV in the elderly population.
DOI: 10.6084/m9.figshare.8218304
title: Deformable image registration for radiation therapy: principle, methods, applications and evaluation

description: <b>Background:</b> Deformable image registration (DIR) is increasingly used in the field of radiation therapy (RT) to account for anatomical deformations. The aims of this paper are to describe the main applications of DIR in RT and discuss current DIR evaluation methods. <b>Methods:</b> Articles on DIR published from January 2000 to October 2018 were extracted from PubMed and Science Direct. Our search was restricted to articles that report data obtained from humans, were written in English, and address DIR methods for RT. A total of 207 articles were selected from among 2506 identified in the search process. <b>Results:</b> At planning, DIR is used for organ delineation using atlas-based segmentation, deformation-based planning target volume definition, functional planning and magnetic resonance imaging-based dose calculation. In image-guided RT, DIR is used for contour propagation and dose calculation on per-treatment imaging. DIR is also used to determine the accumulated dose from fraction to fraction in external beam RT and brachytherapy, both for dose reporting and adaptive RT. In the case of re-irradiation, DIR can be used to estimate the cumulated dose of the two irradiations. Finally, DIR can be used to predict toxicity in voxel-wise population analysis. However, the evaluation of DIR remains an open issue, especially when dealing with complex cases such as the disappearance of matter. To quantify DIR uncertainties, most evaluation methods are limited to geometry-based metrics. Software companies have now integrated DIR tools into treatment planning systems for clinical use, such as contour propagation and fraction dose accumulation. <b>Conclusions:</b> DIR is increasingly important in RT applications, from planning to toxicity prediction. DIR is routinely used to reduce the workload of contour propagation. However, its use for complex dosimetric applications must be carefully evaluated by combining quantitative and qualitative analyses.
DOI: 10.6084/m9.figshare.8218328.v1
title: Adjuvanted versus nonadjuvanted influenza vaccines and risk of hospitalizations for pneumonia and cerebro/cardiovascular events in the elderly

description: <b>Background</b>: The higher effectiveness of MF59®-adjuvanted trivalent influenza vaccine (MF59-TIV) vs. nonadjuvanted TIV in preventing influenza-related hospitalizations was found considering few influenza seasons, local and heterogeneous settings. This study evaluated the relative vaccine effectiveness (rVE) of MF59-TIV vs. nonadjuvanted TIV on the risk of hospitalization for pneumonia and cerebro/cardiovascular events across 15 consecutive influenza seasons. <b>Research design and methods</b>: Using Health Search Database, a case–control study was nested in a cohort of elderly vaccinated with MF59-TIV or TIV. Conditional logistic regression was used to estimate the odds ratio with 95% confidence intervals (CI) of hospitalizations potentially related to influenza in patients vaccinated with MF59-TIV or TIV. <b>Results</b>: Of 43,000 patients vaccinated with MF59-TIV (66.2%) and TIV (33.8%) for the first time, 103 cases of hospitalization for pneumonia or cerebro/cardiovascular events (0.11 per 1,000 person-weeks) during 15 influenza seasons were identified. The MF59-TIV was associated with a reduced risk of hospitalizations for pneumonia and cerebro/cardiovascular events vs. TIV [rVE: 39% (95% CI: 4–61%)]. <b>Conclusions</b>: In a 15-season cohort of elderly, MF59-TIV seems to reduce the risk of hospitalizations for pneumonia and cerebro/cardiovascular events when compared with nonadjuvanted TIV. Our findings support the recommendation for MF59-TIV in the elderly population.
DOI: 10.6084/m9.figshare.8218304.v1
title: Deformable image registration for radiation therapy: principle, methods, applications and evaluation

description: <b>Background:</b> Deformable image registration (DIR) is increasingly used in the field of radiation therapy (RT) to account for anatomical deformations. The aims of this paper are to describe the main applications of DIR in RT and discuss current DIR evaluation methods. <b>Methods:</b> Articles on DIR published from January 2000 to October 2018 were extracted from PubMed and Science Direct. Our search was restricted to articles that report data obtained from humans, were written in English, and address DIR methods for RT. A total of 207 articles were selected from among 2506 identified in the search process. <b>Results:</b> At planning, DIR is used for organ delineation using atlas-based segmentation, deformation-based planning target volume definition, functional planning and magnetic resonance imaging-based dose calculation. In image-guided RT, DIR is used for contour propagation and dose calculation on per-treatment imaging. DIR is also used to determine the accumulated dose from fraction to fraction in external beam RT and brachytherapy, both for dose reporting and adaptive RT. In the case of re-irradiation, DIR can be used to estimate the cumulated dose of the two irradiations. Finally, DIR can be used to predict toxicity in voxel-wise population analysis. However, the evaluation of DIR remains an open issue, especially when dealing with complex cases such as the disappearance of matter. To quantify DIR uncertainties, most evaluation methods are limited to geometry-based metrics. Software companies have now integrated DIR tools into treatment planning systems for clinical use, such as contour propagation and fraction dose accumulation. <b>Conclusions:</b> DIR is increasingly important in RT applications, from planning to toxicity prediction. DIR is routinely used to reduce the workload of contour propagation. However, its use for complex dosimetric applications must be carefully evaluated by combining quantitative and qualitative analyses.
DOI: 10.6084/m9.figshare.8218055
title: Raw Data of Aggression Scoring from Aggression and discrimination among closely versus distantly related species of <i>Drosophila</i>

description: Excel spreadsheet with raw data from aggression trials.
DOI: 10.6084/m9.figshare.8218055.v1
title: Raw Data of Aggression Scoring from Aggression and discrimination among closely versus distantly related species of <i>Drosophila</i>

description: Excel spreadsheet with raw data from aggression trials.
DOI: 10.26180/5cf4f64629f6a
title: Original data for Species-energy relationships of indigenous and invasive species may arise in different ways – a demonstration using springtails

description: A dataset of abundance of springtails on sub-Antarctic Marion Island (Prince Edwrad Islands) across the full elevational gradient, from Transvaal Cove on the eastern coast, past Katedraalkrans, across the central high areas of 1000 m, and down to Mixed Pickle Cove in the west. All species were collected by core sampling of several types and numbers reflect actual abundance. The data were collected between June 2008 and March 2009 by regular sampling of the sites. The data were collected mainly by Anne M. Treasure (anne.m.treasure@gmail.com) who is the main contact for it. Otherwise try Steven Chown (steven.chown@monash.edu)
DOI: 10.6084/m9.figshare.8217944
title: NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution

description: The advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. However, little is known, at such high resolution, how transcription factors directly influence RNA Pol II pausing and directionality. To map the impact of transcription/elongation factors on transcription dynamics genome-wide at base pair resolution, we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). Application of NET-prism on elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals their inherent command on transcription dynamics, with regards to directionality and pausing over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity during gene expression.
DOI: 10.6084/m9.figshare.8217935
title: The aligned matrix of 12S+16S+COI DNA sequences of the manuscript A new species of the genus Microhyla (Amphibia Anura Microhylidae) from Guizhou Province, China

description: The aligned matrix of 12S+16S+COI DNA sequences of the manuscript A new species of the genus Microhyla (Amphibia Anura Microhylidae) from Guizhou Province, China
DOI: 10.6084/m9.figshare.8217944.v1
title: NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution

description: The advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. However, little is known, at such high resolution, how transcription factors directly influence RNA Pol II pausing and directionality. To map the impact of transcription/elongation factors on transcription dynamics genome-wide at base pair resolution, we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). Application of NET-prism on elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals their inherent command on transcription dynamics, with regards to directionality and pausing over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity during gene expression.
DOI: 10.6084/m9.figshare.8217935.v1
title: The aligned matrix of 12S+16S+COI DNA sequences of the manuscript A new species of the genus Microhyla (Amphibia Anura Microhylidae) from Guizhou Province, China

description: The aligned matrix of 12S+16S+COI DNA sequences of the manuscript A new species of the genus Microhyla (Amphibia Anura Microhylidae) from Guizhou Province, China