cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5008415.v1
title: Median log2ratios for comparative fitness profiling by microarray from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress

description: For microarray data generated for each deletion collection and drug or environmental experimental condition relative to its control, median log2ratios for condition replicates are given.
DOI: 10.6073/pasta/8344a28cfa3a7d3cdb6867da1bc231c0
title: Jornada Basin LTER: Wireless meteorological station at NPP P-TOBO site: Daily summary data: 2013 - ongoing

description: Daily summary data at NPP P-TOBO met station. Average/maximum/minimum air temperature; average/maximum relative humidity and wind speed and average wind direction; solar radiation; albedo. These are measured and calculated based on 1-second scan rate of all sensors located at an automated meteorological station installed at Jornada LTER NPP P-TOBO site. Wind speed is measured at 75 cm, 150 cm, and 300 cm, wind direction at approximately 3m, and air temperature and relative humidity at approximate 2.5m. Solar radiation is measured at 3m. This climate station is operated by the Jornada LTER Program. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.5008481
title: Genetic roster of each deletion collection by microarray intensity from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress.

description: Presence/absence calls were determined by microarray hybridization signal intensity collection-specific background thresholds as described (Methods)
DOI: 10.6084/m9.figshare.5008481.v2
title: Genetic roster of each deletion collection by microarray intensity from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress.

description: Presence/absence calls were determined by microarray hybridization signal intensity collection-specific background thresholds as described (Methods)
DOI: 10.6084/m9.figshare.5008481.v1
title: Genetic roster of each deletion collection by microarray intensity from Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress

description: Presence/absence calls were determined by microarray hybridization signal intensity collection-specific background thresholds as described (Methods)
DOI: 10.6073/pasta/13095b82eec4f219c1fd9301e6ee8092
title: Jornada Basin LTER: Wireless meteorological station at NPP P-TOBO site: 1-second summary precipitation data: 2013 - ongoing

description: 1-second summary precipitation data at NPP P-TOBO met station. Total precipitation per second is recorded only if there is measurable precipitation. This is recorded at an automated meteorological station installed at Jornada LTER NPP P-TOBO site.. This climate station is operated by the Jornada LTER Program. IMPORTANT: Rainfall is only recorded when a bucket tip occurs on the tipping bucket rain gauge. If there is missing data due to equipment or other problems, there will be no indication of this within this dataset. The user needs to review precipitation values in the 30 minute or hourly summary datasets to determine if there are missing data in this 1 second detailed precipitation dataset. Reference the package i.d.'s knb-lter-jrn.210437027, knb-lter-jrn.210437042, and knb-lter-jrn.210437057 for the NPP P-TOBO met station 30 minute, hourly, and daily summary datasets, respectively. This is an ONGOING dataset.
DOI: 10.21227/w1cg-qf28
title: Model6_2

description: Model 6.2
DOI: 10.6084/m9.figshare.5008490
title: ESM 3 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish abundance data from the five survey sites around Utila.</b> Each individual lionfish is represented by a unique row. ‘depth’ gives the transect depth in m, ‘transect’ represents which of the four transects (numbered: 2, 3, 4, 5) conducted at that site and depth, ‘site’ gives the survey site (CV – Coral View, RC – Raggedy Cay, TM – The Maze, RP – Rocky Point).
DOI: 10.6084/m9.figshare.5008490.v2
title: ESM 3 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish abundance data from the five survey sites around Utila.</b> Each individual lionfish is represented by a unique row. ‘depth’ gives the transect depth in m, ‘transect’ represents which of the four transects (numbered: 2, 3, 4, 5) conducted at that site and depth, ‘site’ gives the survey site (CV – Coral View, RC – Raggedy Cay, TM – The Maze, RP – Rocky Point).
DOI: 10.6084/m9.figshare.5008490.v1
title: ESM 3 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>Raw lionfish abundance data from the five survey sites around Utila.</b> Each individual lionfish is represented by a unique row. ‘depth’ gives the transect depth in m, ‘transect’ represents which of the four transects (numbered: 2, 3, 4, 5) conducted at that site and depth, ‘site’ gives the survey site (CV – Coral View, RC – Raggedy Cay, TM – The Maze, RP – Rocky Point).
DOI: 10.6084/m9.figshare.5008418
title: ESM 7 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw code for analysis.</b> Raw R code to conduct all analysis contained within this paper.
DOI: 10.6084/m9.figshare.5008418.v2
title: ESM 7 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw code for analysis.</b> Raw R code to conduct all analysis contained within this paper.
DOI: 10.6084/m9.figshare.5008418.v1
title: ESM 7 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>Raw code for analysis.</b> Raw R code to conduct all analysis contained within this paper.
DOI: 10.6084/m9.figshare.5008433
title: ESM 6 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish stomach data from Utila.</b> Each row represents a unique lionfish. Columns include: ‘lionfish.ID’ – unique lionfish identifier, ‘item’ – stomach item type, ‘digestion’ – digestion state following Green et al. [29], ‘weight.g’ – the stomach item weight in g, ‘tl.mm’ – the stomach item total length, ‘family’ – the stomach item family if a fish.
DOI: 10.6084/m9.figshare.5008433.v2
title: ESM 6 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish stomach data from Utila.</b> Each row represents a unique lionfish. Columns include: ‘lionfish.ID’ – unique lionfish identifier, ‘item’ – stomach item type, ‘digestion’ – digestion state following Green et al. [29], ‘weight.g’ – the stomach item weight in g, ‘tl.mm’ – the stomach item total length, ‘family’ – the stomach item family if a fish.
DOI: 10.6084/m9.figshare.5008433.v1
title: ESM 6 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>Raw lionfish stomach data from Utila.</b> Each row represents a unique lionfish. Columns include: ‘lionfish.ID’ – unique lionfish identifier, ‘item’ – stomach item type, ‘digestion’ – digestion state following Green et al. [29], ‘weight.g’ – the stomach item weight in g, ‘tl.mm’ – the stomach item total length, ‘family’ – the stomach item family if a fish.
DOI: 10.6084/m9.figshare.5008523
title: ESM 5 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish alert distance data from Utila and Tela.</b> Each row represents a unique lionfish. Columns include: ‘Lionfish.ID’ – unique lionfish identifier, ‘region’ – whether from Utila or Tela, ‘site’ – dive center name for dive site around Utila or Tela, ‘depth.m’ – depth the lionfish was observed at in m, ‘alert.distance.cm’ – alert distance in cm, ‘total.length.cm’ – the total length of the lionfish in cm.
DOI: 10.6084/m9.figshare.5008523.v2
title: ESM 5 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish alert distance data from Utila and Tela.</b> Each row represents a unique lionfish. Columns include: ‘Lionfish.ID’ – unique lionfish identifier, ‘region’ – whether from Utila or Tela, ‘site’ – dive center name for dive site around Utila or Tela, ‘depth.m’ – depth the lionfish was observed at in m, ‘alert.distance.cm’ – alert distance in cm, ‘total.length.cm’ – the total length of the lionfish in cm.
DOI: 10.6084/m9.figshare.5008523.v1
title: ESM 5 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>Raw lionfish alert distance data from Utila and Tela.</b> Each row represents a unique lionfish. Columns include: ‘Lionfish.ID’ – unique lionfish identifier, ‘region’ – whether from Utila or Tela, ‘site’ – dive center name for dive site around Utila or Tela, ‘depth.m’ – depth the lionfish was observed at in m, ‘alert.distance.cm’ – alert distance in cm, ‘total.length.cm’ – the total length of the lionfish in cm.
DOI: 10.6073/pasta/e6f5393cb8a733b05dd45b7c97acfea5
title: Jornada Basin LTER: Wireless meteorological station at NPP P-TOBO site: 30-minute soil volumetric water content data: 2013 - ongoing

description: 30-minute Soil Moisture data at NPP P-TOBO met station. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured every 30 minutes at an automated meteorological station installed at Jornada LTER NPP P-TOBO site. Measurements are made every 30 minutes at 10 cm, 20 cm, and 30 cm soil depths. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.5008541
title: ESM 4 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish dissection data from Utila.</b> Each row represents a unique lionfish. Columns include: ‘Lionfish.ID’ – unique lionfish identifier, ‘Dive.site’ – dive center name for dive site around Utila, ‘TL.mm’ – total length of the lionfish in mm, ‘Weight.with.spines.g’ – lionfish weight in g, ‘Sex’ ’ the lionfish sex (M – Male, F – Female, I – Immature unable to be sexed), ‘Maturity’ – lionfish maturity number (see methods), ‘Gonad.weight.g’ – weight of both gonads in g, ‘Year’ – the year of collection, ‘depth.zone’ – the depth category (1 – 0-25 m, 2 – 25–40 m, 3 – &gt;40m).
DOI: 10.6084/m9.figshare.5008541.v2
title: ESM 4 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?.

description: <b>Raw lionfish dissection data from Utila.</b> Each row represents a unique lionfish. Columns include: ‘Lionfish.ID’ – unique lionfish identifier, ‘Dive.site’ – dive center name for dive site around Utila, ‘TL.mm’ – total length of the lionfish in mm, ‘Weight.with.spines.g’ – lionfish weight in g, ‘Sex’ ’ the lionfish sex (M – Male, F – Female, I – Immature unable to be sexed), ‘Maturity’ – lionfish maturity number (see methods), ‘Gonad.weight.g’ – weight of both gonads in g, ‘Year’ – the year of collection, ‘depth.zone’ – the depth category (1 – 0-25 m, 2 – 25–40 m, 3 – &gt;40m).
DOI: 10.6084/m9.figshare.5008541.v1
title: ESM 4 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>Raw lionfish dissection data from Utila.</b> Each row represents a unique lionfish. Columns include: ‘Lionfish.ID’ – unique lionfish identifier, ‘Dive.site’ – dive center name for dive site around Utila, ‘TL.mm’ – total length of the lionfish in mm, ‘Weight.with.spines.g’ – lionfish weight in g, ‘Sex’ ’ the lionfish sex (M – Male, F – Female, I – Immature unable to be sexed), ‘Maturity’ – lionfish maturity number (see methods), ‘Gonad.weight.g’ – weight of both gonads in g, ‘Year’ – the year of collection, ‘depth.zone’ – the depth category (1 – 0-25 m, 2 – 25–40 m, 3 – &gt;40m).
DOI: 10.6073/pasta/e0cb55a31df87c5dd476b022aaf8a5c6
title: Jornada Basin LTER: Wireless meteorological station at NPP P-TOBO site: Daily average soil volumetric water content data: 2013 - ongoing

description: Daily average of 30-minute Volumetric Water Content at NPP P-TOBO met station. Collection of soil volumetric water content data at Jornada LTER NPP sites, New Mexico, supports the environmental monitoring objectives of the Jornada LTER monitoring program that look at plant-soil water dynamics. Volumetric water content, bulk electrical conductivity, soil temperature, and bulk dielectric permittivity are measured and calculated at an automated meteorological station installed at Jornada LTER NPP P-TOBO site. The daily average at 3 soil depths is calculated from measurements made every 30 minutes at 10 cm, 20 cm, and 30 cm. This is an ONGOING dataset.
DOI: 10.6084/m9.figshare.5008514
title: MATLAB files from From arteries to boreholes: steady-state response of a poroelastic cylinder to fluid injection.

description: A suite of MATLAB functions that implement the analytical and numerical steady-state solutions described in the manuscript
DOI: 10.6084/m9.figshare.5008514.v1
title: MATLAB files from From arteries to boreholes: steady-state response of a poroelastic cylinder to fluid injection

description: A suite of MATLAB functions that implement the analytical and numerical steady-state solutions described in the manuscript
DOI: 10.6084/m9.figshare.5011694
title: all.J.csv from An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to <i>Streptococcus pneumoniae</i>.

description: The frequency of resistance to antibiotics in <i>Streptococcus pneumoniae</i> has been stable over recent decades. For example, penicillin non-susceptibility in Europe has fluctuated between 12% and 16% without any major time trend. In spite of long-term stability, resistance fluctuates over short time scales, presumably in part due to seasonal fluctuations in antibiotic prescriptions. Here, we develop a model that describes the evolution of antibiotic resistance under selection by multiple antibiotics prescribed at seasonally changing rates. This model was inspired by, and fitted to, published data on monthly antibiotics prescriptions and frequency of resistance in two communities in Israel over 5 years. Seasonal fluctuations in antibiotic usage translate into small fluctuations of the frequency of resistance around the average value. We describe these dynamics using a perturbation approach that encapsulates all ecological and evolutionary forces into a generic model, whose parameters quantify a force stabilizing the frequency of resistance around the equilibrium and the sensitivity of the population to antibiotic selection. Fitting the model to the data revealed a strong stabilizing force, typically two to five times stronger than direct selection due to antibiotics. The strong stabilizing force explains that resistance fluctuates <i>in phase</i> with usage, as antibiotic selection alone would result in resistance fluctuating behind usage with a lag of three months when antibiotic use is seasonal. While most antibiotics selected for increased resistance, intriguingly, cephalosporins selected for decreased resistance to penicillins and macrolides, an effect consistent in the two communities. One extra monthly prescription of cephalosporins per 1000 children decreased the frequency of penicillin-resistant strains by 1.7%. This model emerges under minimal assumptions, quantifies the forces acting on resistance and explains up to 43% of the temporal variation in resistance.
DOI: 10.6084/m9.figshare.5011694.v2
title: all.J.csv from An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to <i>Streptococcus pneumoniae</i>.

description: The frequency of resistance to antibiotics in <i>Streptococcus pneumoniae</i> has been stable over recent decades. For example, penicillin non-susceptibility in Europe has fluctuated between 12% and 16% without any major time trend. In spite of long-term stability, resistance fluctuates over short time scales, presumably in part due to seasonal fluctuations in antibiotic prescriptions. Here, we develop a model that describes the evolution of antibiotic resistance under selection by multiple antibiotics prescribed at seasonally changing rates. This model was inspired by, and fitted to, published data on monthly antibiotics prescriptions and frequency of resistance in two communities in Israel over 5 years. Seasonal fluctuations in antibiotic usage translate into small fluctuations of the frequency of resistance around the average value. We describe these dynamics using a perturbation approach that encapsulates all ecological and evolutionary forces into a generic model, whose parameters quantify a force stabilizing the frequency of resistance around the equilibrium and the sensitivity of the population to antibiotic selection. Fitting the model to the data revealed a strong stabilizing force, typically two to five times stronger than direct selection due to antibiotics. The strong stabilizing force explains that resistance fluctuates <i>in phase</i> with usage, as antibiotic selection alone would result in resistance fluctuating behind usage with a lag of three months when antibiotic use is seasonal. While most antibiotics selected for increased resistance, intriguingly, cephalosporins selected for decreased resistance to penicillins and macrolides, an effect consistent in the two communities. One extra monthly prescription of cephalosporins per 1000 children decreased the frequency of penicillin-resistant strains by 1.7%. This model emerges under minimal assumptions, quantifies the forces acting on resistance and explains up to 43% of the temporal variation in resistance.
DOI: 10.6084/m9.figshare.5011694.v1
title: all.J.csv from An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to <i>Streptococcus pneumoniae</i>

description: The frequency of resistance to antibiotics in <i>Streptococcus pneumoniae</i> has been stable over the last decades. For example, penicillin non-susceptibility in Europe has fluctuated between 12% and 16% without any major time trend. In spite of long-term stability, resistance fluctuates over short time-scales, presumably in part due to seasonal fluctuations in antibiotic prescriptions. Here, we develop a model that describes the evolution of antibiotic resistance under selection by multiple antibiotics prescribed at seasonally changing rates. This model was inspired by, and fitted to, published data on monthly antibiotics prescriptions and frequency of resistance, in two communities in Israel, over 5 years. Seasonal fluctuations in antibiotic usage translate into small fluctuations of the frequency of resistance around the average value. We describe these dynamics using a perturbation approach that encapsulates all ecological and evolutionary forces into a generic model, whose parameters quantify a force stabilizing the frequency of resistance around the equilibrium, and the sensitivity of the population to antibiotic selection. Fitting the model to the data revealed a strong stabilizing force, typically two to five times stronger than direct selection due to antibiotics. The strong stabilizing force explains that resistance fluctuates <i>in phase</i> with usage, as antibiotic selection alone would result in resistance fluctuating behind usage with a lag of three months when antibiotic use is seasonal. While most antibiotics selected for increased resistance, intriguingly, cephalosporins selected for decreased resistance to penicillins and macrolides, an effect consistent in the two communities. One extra monthly prescription of cephalosporins per 1000 children decreased the frequency of penicillin-resistant strains by 1.7%. This model emerges under minimal assumptions, quantifies the forces acting on resistance and explains up to 43% of the temporal variation in resistance.
DOI: 10.6084/m9.figshare.5011712
title: Read me file with details on the R codes from An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to <i>Streptococcus pneumoniae</i>.

description: The frequency of resistance to antibiotics in <i>Streptococcus pneumoniae</i> has been stable over recent decades. For example, penicillin non-susceptibility in Europe has fluctuated between 12% and 16% without any major time trend. In spite of long-term stability, resistance fluctuates over short time scales, presumably in part due to seasonal fluctuations in antibiotic prescriptions. Here, we develop a model that describes the evolution of antibiotic resistance under selection by multiple antibiotics prescribed at seasonally changing rates. This model was inspired by, and fitted to, published data on monthly antibiotics prescriptions and frequency of resistance in two communities in Israel over 5 years. Seasonal fluctuations in antibiotic usage translate into small fluctuations of the frequency of resistance around the average value. We describe these dynamics using a perturbation approach that encapsulates all ecological and evolutionary forces into a generic model, whose parameters quantify a force stabilizing the frequency of resistance around the equilibrium and the sensitivity of the population to antibiotic selection. Fitting the model to the data revealed a strong stabilizing force, typically two to five times stronger than direct selection due to antibiotics. The strong stabilizing force explains that resistance fluctuates <i>in phase</i> with usage, as antibiotic selection alone would result in resistance fluctuating behind usage with a lag of three months when antibiotic use is seasonal. While most antibiotics selected for increased resistance, intriguingly, cephalosporins selected for decreased resistance to penicillins and macrolides, an effect consistent in the two communities. One extra monthly prescription of cephalosporins per 1000 children decreased the frequency of penicillin-resistant strains by 1.7%. This model emerges under minimal assumptions, quantifies the forces acting on resistance and explains up to 43% of the temporal variation in resistance.