cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16867400
title: Supplementary Table S5. Conclusions of the phylogenetic reconstruction. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867394
title: Supplementary Table S3. A classification of ABR genes into chromosomal and plasmid genes according to their relative frequency on both replicon types. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867400.v1
title: Supplementary Table S5. Conclusions of the phylogenetic reconstruction. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16867397.v1
title: Supplementary Table S1. A list of genomes used in this study. from Gene sharing among plasmids and chromoomes reveals barriers for antibiotic resistance gene transfer

description: The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison to core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 <i>Enterobacteriaceae</i> isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison to core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to the total <i>Escherichia</i> genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability.This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.
DOI: 10.6084/m9.figshare.16689220
title: Global extent and composition of tree pests

description: Data used in "Host phylogenetic diversity predicts the global extent and composition of tree pests." Separate datasheets are available for genus- and species-level pest hosts. <br>Columns include:<b>countriesWithHosts:</b> number of countries where the pest and hosts co-occur<b>countrySaturation:</b> proportion of potential host countries where pests occur<b>ntaxa:</b> number of host taxa<b>mpdses/mpdPval:</b> mean pairwise distance standard effect size and p-value<b>mntdses/mntdPval:</b> mean nearest taxon distance standard effect size and p-value<b>PD:</b> host phylogenetic diversity<b>PSV:</b> Phylogenetic species variability of hosts<b>PSR:</b> Phylogenetic species richness of hosts<b>PSE:</b> Phylogenetic species evenness of hosts<b>PSC:</b> Phylogenetic species clustering of hosts<br>Pest species with only one host have NA's for host range information. Pests with zero saturation, have only been reported in countries outside the native range of their hosts.
DOI: 10.5522/04/16866628
title: Data supporting the article: Health system influences on potentially avoidable hospital admissions by secondary mental health service use: A national ecological study

description: These materials relate to the following publication: Woodhead, C., Martin, P., Osborn, D., Barratt, H., & Raine, R. (2021). Health system influences on potentially avoidable hospital admissions by secondary mental health service use: A national ecological study. Journal of Health Services Research & Policy. https://journals.sagepub.com/doi/full/10.1177/13558196211036739 <b> </b> <br> The materials are designed to enable independent researchers to reproduce the analyses presented in the section “Predictors of variation in CCG-level PAAs”. We are not permitted to share HES data and thus have not included data or code to reproduce the calculation of Potentially Avoidable Admission (PAA) rates. Only the prediction of PAA rates by CCG characteristics is covered in the code presented. <b>Data</b> · The main data set to be read into R is: “MH_Avoidable.csv” · Explanation of variables in: “Avoidable Admissions - List of variables.xlsx” · Lists of CCG identifiers that completeness thresholds for diagnostic information in the MHSDS data set (for sensitivity analyses) are: o “CCGs with fewer than 50pct missing.csv” o “CCGs with fewer than 70pct missing.csv” <b>R code</b> To run R code, first open the R Studio project “Potentially avoidable admissions - data and code.Rproj”. · Code for implementing MIRL to investigate predictors of PAA rates: o in secondary mental health service users: “MIRL stages 2,3,4 - MHSDS patients - physical admissions.R” o in the comparator group: “MIRL stages 2,3,4 - No MHSDS - physical admissions.R” · code for sensitivity analyses: o “Sensitivity analysis.R” o “Sensitivity analysis 70pct missing.R” · code for fractional polynomials: “MH avoidable – fractional polynomials.R” All other R code files contained within the project are called from within these five files via the source command.
DOI: 10.21227/vcx2-e039
title: SAMPLE EMG SIGNAL

description: TEST
DOI: 10.5522/04/16866628.v1
title: Data supporting the article: Health system influences on potentially avoidable hospital admissions by secondary mental health service use: A national ecological study

description: These materials relate to the following publication: Woodhead, C., Martin, P., Osborn, D., Barratt, H., & Raine, R. (2021). Health system influences on potentially avoidable hospital admissions by secondary mental health service use: A national ecological study. Journal of Health Services Research & Policy. https://journals.sagepub.com/doi/full/10.1177/13558196211036739 <b> </b> <br> The materials are designed to enable independent researchers to reproduce the analyses presented in the section “Predictors of variation in CCG-level PAAs”. We are not permitted to share HES data and thus have not included data or code to reproduce the calculation of Potentially Avoidable Admission (PAA) rates. Only the prediction of PAA rates by CCG characteristics is covered in the code presented. <b>Data</b> · The main data set to be read into R is: “MH_Avoidable.csv” · Explanation of variables in: “Avoidable Admissions - List of variables.xlsx” · Lists of CCG identifiers that completeness thresholds for diagnostic information in the MHSDS data set (for sensitivity analyses) are: o “CCGs with fewer than 50pct missing.csv” o “CCGs with fewer than 70pct missing.csv” <b>R code</b> To run R code, first open the R Studio project “Potentially avoidable admissions - data and code.Rproj”. · Code for implementing MIRL to investigate predictors of PAA rates: o in secondary mental health service users: “MIRL stages 2,3,4 - MHSDS patients - physical admissions.R” o in the comparator group: “MIRL stages 2,3,4 - No MHSDS - physical admissions.R” · code for sensitivity analyses: o “Sensitivity analysis.R” o “Sensitivity analysis 70pct missing.R” · code for fractional polynomials: “MH avoidable – fractional polynomials.R” All other R code files contained within the project are called from within these five files via the source command.
DOI: 10.5281/zenodo.5117845
title: Ocean Bottom Seismometer data of line OBS2017-2 in the South China Sea

description: Dataset line OBS2017-2 was collected in June 2017, using R/V “Shiyan 2” that belongs to the South China Sea Institute of Oceanology, CAS. The spacing of OBSs was ~9.6 km. The seismic source consisted of an array of four BOLT air-guns with a total volume of 6,000 cubic inches and was towed at ~10 m depth below sea level. 1,767 shots had been fired along OBS2017-2 from south to north, and the shooting intervals were set at 80-110 s with a nominal ship speed of ~4.5 knots, resulting in a shooting interval of ~200 m on average. The format of seismic data is SAC. Please send the purpose of the data requesting, as well as the name and affiliation of the applicant to go223@scsio.ac.cn. The updated SEGY format data can be accessed through http://www.doi.org/10.11922/sciencedb.01267.
DOI: 10.5281/zenodo.3604262
title: Ocean Bottom Seismometer data of line OBS2017-2 in the South China Sea

description: Dataset line OBS2017-2 was collected in June 2017, using R/V “Shiyan 2” that belongs to the South China Sea Institute of Oceanology, CAS. The spacing of OBSs was ~9.6 km. The seismic source consisted of an array of four BOLT air-guns with a total volume of 6,000 cubic inches and was towed at ~10 m depth below sea level. 1,767 shots had been fired along OBS2017-2 from south to north, and the shooting intervals were set at 80-110 s with a nominal ship speed of ~4.5 knots, resulting in a shooting interval of ~200 m on average. The format of seismic data is SAC. Please send the purpose of the data requesting, as well as the name and affiliation of the applicant to go223@scsio.ac.cn. The updated SEGY format data can be accessed through http://www.doi.org/10.11922/sciencedb.01267.
DOI: 10.5281/zenodo.3604263
title: Ocean Bottom Seismometer data of line OBS2017-2 in the South China Sea

description: Dataset line OBS2017-2 was collected in June, 2017, using R/V “Shiyan 2” that belongs to the South China Sea Institute of Oceanology, CAS. The spacing of OBSs was ~9.6 km. The seismic source consisted of an array of four BOLT air-guns with a total volume of 6,000 cubic inches and was towed at ~10 m depth below sea level. 1,767 shots had been fired along OBS2017-2 from south to north, and the shooting intervals were set at 80-110 s at nominal ship speed of ~4.5 knots, resulting in a shooting interval of ~200 m on average. The format of seismic data is SAC. Please send the purpose of the data requesting, as well as the name and affiliation of the applicant to go223@scsio.ac.cn. The updated SEGY format data can be accessed through http://www.doi.org/10.11922/sciencedb.01267.
DOI: 10.15468/4n5wmr
title: Review of Gibberifera Obraztsov (Lepidoptera: Tortricidae) from China, with description of a new species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Zhang, Aihuan (2021): Review of Gibberifera Obraztsov (Lepidoptera: Tortricidae) from China, with description of a new species. Zootaxa 5039 (3): 409-416, DOI: https://doi.org/10.11646/zootaxa.5039.3.5
DOI: 10.18113/d3zq0b
title: Nitrous oxide emissions in a landscape transitioning from Conservation Reserve Program grassland to energy crops switchgrass and Miscanthus

description: uture liquid fuel demand from renewable sources may, in part, be met by converting the seasonally wet portions of the landscape currently managed for soil and water conservation to perennial energy crops. However, this shift may increase nitrous oxide (N2O) emissions, thus limiting the carbon (C) benefits of energy crops. Particularly high emissions may occur during the transition period when the soil is disturbed, plants are establishing, and nitrate and water accumulation may favor emissions. We measured N2O emissions and associated environmental drivers during the transition of perennial grassland in a Conservation Reserve Program (CRP) to switchgrass (Panicum virgatum L.) and Miscanthus x giganteus in the bottom 3-ha of a watershed in the Ridge and Valley ecoregion of the northeastern United States. Replicated treatments of CRP (unconverted), unfertilized switchgrass (switchgrass), nitrogen (N) fertilized switchgrass (switchgrass-N), and Miscanthus were randomized in four blocks. Each plot was divided into shoulder, backslope, and footslope positions based on the slope and moisture gradient. Soil N2O flux, soil moisture, and soil mineral nitrogen availability were monitored during the growing season of 2013, the year after the land conversion. Growing season N2O flux showed a significant vegetation-bylandscape position interaction (P < 0.009). Switchgrass-N and Miscanthus treatments had 3 and 6-times higher cumulative flux respectively than the CRP in the footslope, but at other landscape positions fluxes were similar among land uses. A peak N2O emission event, contributing 26% of the cumulative flux, occurred after a 10.8-cm of rain during early June. Prolonged subsoil saturation coinciding with high mineral N concentration fueled N2O emission hot spots in the footslopes under energy crops. Our results suggest that mitigating N2O emissions
DOI: 10.21227/p3am-2r25
title: Indoor Corridor and Outdoor Open area Received Power Data at 28 GHz using PXI Channel Sounder

description: The dataset is divided into two parts. The measurement dataset and simulation dataset. The measurement dataset contains received power measurements at 28 GHz in an indoor corridor and outdoor open area. The received power and other channel statistics, e.g., root mean square delay spread, power and time of arrival of multipath components, and path loss were obtained using the PXI channel sounder system. Two different gain antennas 17 dBi and 23 dBi were used. The transmitter was fixed, whereas the receiver was moved in a straight line aligned to the boresight of the transmitter antenna. Simulations of the measurement scenario were also carried out using the Wireless InSite ray-tracing software.
DOI: 10.25822/0y1h-vs11
title: Urban Poor in India
DOI: 10.5281/zenodo.5597021
title: Belowground nitrogen cycling in a montane grassland exposed to elevated CO2, warming and drought

description: #### Data description<br> Data from a multi-factorial global change experiment (elevated CO<sub>2</sub>, warming and drought) in a montane grassland experiment in Austria (ClimGrass). Variables presented are soil nitrogen cycling rates measured using isotope pool dilutions. Companion paper will be linked following manuscript publication. #### Metadata<br> climgrass_soil_N_cycling.csv data description Year: 2017<br> Harvest: three harvests (May 30, July 25, October 3)<br> Season: numerical column for harvest number<br> Plot: location of plot within the ClimGrass experiment<br> Treatment: eight treatment levels<br> c0t0 (ambient CO<sub>2</sub>, ambient temperature)<br> c0t1 (ambient CO<sub>2</sub>, + 1.5°C)<br> c0t2 (ambient CO<sub>2</sub>, + 3°C)<br> c1t1 (+150 ppm, +1.5°C)<br> c2t0 (+300 ppm, ambient temperature)<br> c2t2 (+300 ppm, +3°C)<br> c0t0-d (ambient CO<sub>2</sub>, ambient temperature, extended drought)<br> c2t2-d (+300 ppm, +3°C, extended drought)<br> CO2_ppm: three values of carbon dioxide enrichment treatment (+0, +150, or +300 ppm)<br> Temp_C: three values of elevated temperature treatment (+0, +1.5, +3°C)<br> Drought: two levels (control, drought)<br> Prot_depoly: gross protein depolymerization rates (micrograms nitrogen per grams dry soil per day = µg N g-1 d-1)<br> FAA_uptake: gross free amino acid uptake rates (µg N g-1 d-1)<br> MRT_FAA_hrs: mean residence time of free amino acids (hours)<br> FAA: free amino acids (µg N g-1)<br> Mineralization: gross mineralization rates (µg N g-1 d-1)<br> Nitrification: gross nitrification rates (µg N g-1 d-1) #### References<br> Additional information on the experimental design can be found in the following paper:<br> Piepho, H.-P., Herndl, M., Pötsch, E.M., Bahn, M., 2017. Designing an experiment with quantitative treatment factors to study the effects of climate change. Journal of Agronomy and Crop Science 203, 584–592. doi:https://doi.org/10.1111/jac.12225 More information on the isotope pool dilution method used can be found in the following paper:<br> Wanek, W., Mooshammer, M., Blöchl, A., Hanreich, A., Richter, A., 2010. Determination of gross rates of amino acid production and immobilization in decomposing leaf litter by a novel 15 N isotope pool dilution technique. Soil Biology and Biochemistry 42, 1293–1302. doi:10.1016/j.soilbio.2010.04.001
DOI: 10.5281/zenodo.5597020
title: Belowground nitrogen cycling in a montane grassland exposed to elevated CO2, warming and drought

description: #### Data description<br> Data from a multi-factorial global change experiment (elevated CO<sub>2</sub>, warming and drought) in a montane grassland experiment in Austria (ClimGrass). Variables presented are soil nitrogen cycling rates measured using isotope pool dilutions. Companion paper will be linked following manuscript publication. #### Metadata<br> climgrass_soil_N_cycling.csv data description Year: 2017<br> Harvest: three harvests (May 30, July 25, October 3)<br> Season: numerical column for harvest number<br> Plot: location of plot within the ClimGrass experiment<br> Treatment: eight treatment levels<br> c0t0 (ambient CO<sub>2</sub>, ambient temperature)<br> c0t1 (ambient CO<sub>2</sub>, + 1.5°C)<br> c0t2 (ambient CO<sub>2</sub>, + 3°C)<br> c1t1 (+150 ppm, +1.5°C)<br> c2t0 (+300 ppm, ambient temperature)<br> c2t2 (+300 ppm, +3°C)<br> c0t0-d (ambient CO<sub>2</sub>, ambient temperature, extended drought)<br> c2t2-d (+300 ppm, +3°C, extended drought)<br> CO2_ppm: three values of carbon dioxide enrichment treatment (+0, +150, or +300 ppm)<br> Temp_C: three values of elevated temperature treatment (+0, +1.5, +3°C)<br> Drought: two levels (control, drought)<br> Prot_depoly: gross protein depolymerization rates (micrograms nitrogen per grams dry soil per day = µg N g-1 d-1)<br> FAA_uptake: gross free amino acid uptake rates (µg N g-1 d-1)<br> MRT_FAA_hrs: mean residence time of free amino acids (hours)<br> FAA: free amino acids (µg N g-1)<br> Mineralization: gross mineralization rates (µg N g-1 d-1)<br> Nitrification: gross nitrification rates (µg N g-1 d-1) #### References<br> Additional information on the experimental design can be found in the following paper:<br> Piepho, H.-P., Herndl, M., Pötsch, E.M., Bahn, M., 2017. Designing an experiment with quantitative treatment factors to study the effects of climate change. Journal of Agronomy and Crop Science 203, 584–592. doi:https://doi.org/10.1111/jac.12225 More information on the isotope pool dilution method used can be found in the following paper:<br> Wanek, W., Mooshammer, M., Blöchl, A., Hanreich, A., Richter, A., 2010. Determination of gross rates of amino acid production and immobilization in decomposing leaf litter by a novel 15 N isotope pool dilution technique. Soil Biology and Biochemistry 42, 1293–1302. doi:10.1016/j.soilbio.2010.04.001
DOI: 10.5517/cc6yd9t
title: CCDC 206996: Experimental Crystal Structure Determination

description: Related Article: S.Rannabauer, T.Habereder, H.Noth, W.Schnick|2003|Z.Naturforsch.,B:Chem.Sci.|58|745|
DOI: 10.5517/ccdc.csd.cc28dysf
title: CCDC 2097825: Experimental Crystal Structure Determination

description: Related Article: Guang-Xu Yao, Jin-Qiang Zhang, Peng Li, Hui Liu, Li Wang, Yin-Xia Sun, Wen-Kui Dong|2022|Inorg.Chim.Acta|529|120642|doi:10.1016/j.ica.2021.120642
DOI: 10.5517/ccdc.csd.cc28dytg
title: CCDC 2097826: Experimental Crystal Structure Determination

description: Related Article: Guang-Xu Yao, Jin-Qiang Zhang, Peng Li, Hui Liu, Li Wang, Yin-Xia Sun, Wen-Kui Dong|2022|Inorg.Chim.Acta|529|120642|doi:10.1016/j.ica.2021.120642