All DEGs and primers sequences for qRT-PCR validation.
This data set contains:
1) Isothermal titration calorimety (ITC) heat flow for Thisted brine (TB) titrated into Berea sandstone aged with TB and 2*DTB titrated into Berea sandstone aged with TB
2) Pressure measurements from coreflooding experiments
3) Effluent analysis: Ionic composition, alkalinity and iron concentration
Contributors:Martin Bitomský, Pavla Mládková, Robin Pakeman, Martin Duchoslav
Data from: Bitomský M., Mládková P., Pakeman RJ, & Duchoslav M. (2020). Clade composition of a plant community indicates its phylogenetic diversity. Ecology and Evolution. doi: 10.1002/ece3.6170
Data summarises results from the case studies and simulations presented in our paper. In addition, we provide an R script for calculation of proposed phylogenetic diversity metrics (the clade indices).
Brief description of each file:
1. Grasslands_DNA_markers_info.xls - Accession numbers of all DNA markers used for phylogeny inference in grasslands
2. Grasslands_DNA_alignment_BEFORE_GBlocks.fasta - DNA alignment matrix before utilisation of the GBlocks tool
3. Grasslands_DNA_alignment_AFTER_GBlocks.fasta - DNA alignment matrix after utilisation of the GBlocks tool
4. Grasslands_BEAST_file.xml - BEAST .xml file submitted to the CIPRES portal (www.phylo.org)
5. Grasslands_tree.txt - Dated MCC tree, grasslands (newick format)
6. Grasslands_tree.nex - Dated MCC tree, grasslands (nexus format)
7. Phyto-database_pruned_tree.txt - Pruned dated tree from the super tree of European flora (Durka & Michalski 2012, Ecology), phytosociological database (newick format)
8. Plot_data.slx - plot data of all case studies + species lists
9. Simulation_results.txt - Summary of R2 values (phylogeny-based metric ~ the clade index) for simulated phylogenies and community matrices (manipulated: phylogenetic scale, species pool size and species richness range)
10. Bitomsky2020EE_R_script_indices.R - An R script for computation of the clade indices (with notes and examples)
Study Objective: To compare the rate of post-operative urinary retention (POUR) after total laparoscopic hysterectomy (TLH) using the autofill versus the backfill void trial. Secondary objectives were to compare the time to discharge from the recovery room, rate of post-operative urinary tract infection (UTI), perceived bladder condition, bladder function impact on life, and patient satisfaction.
Design: Randomized controlled trial (Canadian Task Force classification I).
Setting: Single academic medical center.
Patients: Women who underwent TLH by conventional laparoscopy or robotic-assisted laparoscopy for benign non-urogynecologic indications.
Interventions: After TLH, participants were randomized to have an autofill void trial (group A) or a backfill void trial (group B). Failure rate, time to discharge, and UTI rate were assessed. Participants completed the patient perception of bladder condition (PPBC) and the incontinence impact questionnaire-short form (IIQ-7) questionnaires. Patient satisfaction was assessed. Multiple regression analysis was performed to determine predictors of POUR.
Measurements and Main Results: 82 participants completed the study after randomization: 42 in group A and 40 in group B. There were no statistically significant differences in demographic or perioperative outcomes. Seven participants had POUR in group A (16.7%) and 11 in group B (27.5%) (p = .36). The median time to discharge was 176 minutes for group A [160.5, 255.5] and 218 minutes for group B [180, 265] (p = 0.01). There were no statistically significant differences in rate of post-operative UTI (p = 1.00), PPBC scores (p = 0.24), IIQ-7 scores (p = 0.23), and patient satisfaction scores (p = 0.26). A stepwise logistic regression analysis demonstrated that pre-operative consumption of progesterone and non-same-day discharge may be weak predictors of POUR (p = .059 and p = .058, respectively).
Conclusion: Autofill and backfill void trials result in a comparable rate of POUR with the autofill void trial resulting in faster same-day discharge.
Contributors:Eefje Poppelaars, Johannes Klackl, Belinda Pletzer, Eva Jonas
Open data and R analysis scripts for the paper as submitted for publication: "Poppelaars, E. S., Klackl, J., Pletzer, B., & Jonas, E. (2020). Delta-beta cross-frequency coupling as an index of stress regulation during social-evaluative threat."
Hypotheses and analyses were preregistered: Poppelaars, E. S., Klackl, J., Pletzer, B., & Jonas, E. (2018). Delta-beta cross-frequency coupling as an index of stress regulation during social-evaluative threat. Open Science Framework. https://osf.io/8gchf/register/565fb3678c5e4a66b5582f67.
Description of the dataset:
A dataset of 37 men and 30 women (tested in the luteal phase of their menstrual cycle) participated in a public speaking task to induce social-evaluative threat. Responses of multiple stress systems were measured (sympathetic and parasympathetic nervous system activity, self-reported affect, and hypothalamic–pituitary–adrenal axis activity), as well as personality traits (e.g. trait social anxiety), and EEG delta-beta cross-frequency coupling (e.g., frontal and parietal amplitude-amplitude correlation and phase-amplitude coupling).
Description of analyses files:
- File 'README.txt' contains the description of the files (metadata).
- File 'SET_CFC_MatlabOutput.xlsx' contains the delta-beta coupling data, calculated using MATLAB scripts from https://github.com/ESPoppelaars/Cross-frequency-coupling.
- File 'SETData.sav' contains the raw stress and personality data, taken from https://doi.org/10.17632/7vj8r76s6f.
- Files 'SET_CFC.outl.del.RData' contains the complete dataset with missing values and outliers deleted.
- File 'Codebook_SET_CFC.outl.del.csv' contains a description of all variables in the 'SET_CFC.outl.del.RData' file (metadata).
- Files 'SET_CFC.outl.del.imp.RData' and 'SET_CFC.outl.del.imp.extra.RData' contain multiple imputed datasets (without missing values) that can be used to reproduce results from the paper.
- File 'LSA_HSA_brief.RData' contains data to use as informed priors for the Bayesian analyses, calculated from data published at https://doi.org/10.3758/s13415-018-0603-7.
- File 'Codebook_LSA_HSA_brief.csv' contains a description of all variables in the 'LSA_HSA_brief.RData' file (metadata).
- File '01_CalculationOfData.R' is an R analysis script that imports the raw data, calculates new variables, and imputes missing data via multiple imputation using the 'predictorMatrixAdj.xlsx' file.
- File '02_AnalysisOfImputedData.R' is an R analysis script that calculates descriptive statistics, creates plots, and tests hypotheses using t-tests, Bayesian statistics, and multiple lineair regressions. Also uses the custom functions: 'BF.evidence.R', 'cohen.d.magnitude.R' and 'p.value.sig.R', as well as the 'BF_t.R' file as taken from https://doi.org/10.17045/sthlmuni.4981154.v3.
Contributors:Francisco B. Varona, F. Javier Baeza, David Bru, Salvador Ivorra
This database contains experimental results that have been collected on steel-to-concrete bond strength after high temperature exposure. The results are sourced from a state of the art based on the available scientific literature in January 2019. The total number of references is 17, making a total of 466 experiments. The variables that have been identified are the following:
• Type of fibre addition.
• Fibre content expressed as percentage of volume fraction.
• Concrete compressive strength at ambient temperature.
• Bond length to rebar diameter ratio.
• Clear concrete cover to rebar diameter ratio.
• Age at testing.
• Ratio between the duration of the thermal saturation at maximum temperature and the minimum specimen size squared.
• Maximum exposure temperature.
• Normalised bond strength, ratio between the bond strength after high temperature exposure and the original bond strength at ambient temperature.
• The compressive strength after high temperature exposure, whenever the experiments covered this type of test.
• The original peak bond strength value at ambient temperature.
Also included, there is a tabulated representation of the main features of each experimental research.
Contributors:Jianfeng Li, Tongbin Shao, Maoshuang Song
This data set is about the original data on triaxial compression of Fangshan dolomite at effective confining pressures of 50-300 MPa and temperatures of 27-900 ℃ in a Paterson-type gas-medium deformation apparatus. From this data set, one can plot stress-strain curves and determine rheological parameters for building constitutive equations of Fangshan dolomite deformed by low temperature plasticity and dislocation creep.
Shopping center interview about attitudes toward the virus in the midst of the crisis.
This data contains 2129 observations of escape behaviour from 57 bird species from Estonian urban and rural habitats. Data was collected in 2015-2016 by Kunter Tätte. Flight initiation distances are accompanied by starting distances, alert distances and various other covariates.
This data contains observations from four studies (but not observations collected by other authors):
1) Samia, D.S.M., Blumstein, D.T., Díaz, M., Grim, T., Ibáñez-Álamo, J.D., Jokimäki, J., Tätte, K., Markó, G., Tryjanowski, P., Møller, A.P. (2017). Rural-Urban Differences in Escape Behavior of European Birds Across a Latitudinal Gradient. Frontiers in Ecology and Evolution, 5: 66.
2) Tätte, K., Møller, A.P., Mänd, R. (2018). Towards an integrated view of escape decisions in birds: relation between flight initiation distance and distance fled. Animal Behaviour, 136: 75-86.
3) Morelli, F., Benedetti, Y., Díaz, M., Grim, T., Ibáñez-Álamo, J., Jokimaki, J., Kaisanlahti-Jokimäki, M.L., Tätte, K., Marko, G., Jiang, Y., Tryjanowski, P., Møller, A.P. (2018). Contagious fear: Escape behavior increases with flock size in European gregarious birds. Ecology and Evolution, 9(10), 6096-6104.
4) Unpublished data. Mainly for a discontinued project titled "Effects of winter weather and latitude on escape decisions" in 2015 by Anders Pape Møller. There is also excluded data from the first three studies (i.e. either species with too few observations, or species not of interest in a particular study, or repeat observations)
* All distances are in meters, but snow cover in cm
* Temperatures are in celsius.
* This data set is good for urban-rural comparisons because (a) I always collected observations from both habitats on the same day, (b) starting distances between urban and rural habitats are very similar, (c) there is a large overlap between species composition
* Most birds were located on the ground (initial_perch_height = 0)
* Whenever a column name has "repeat_..." as prefix, it indicates a second subsequent approach to the same individual. After the first approach I moved back to a starting distance of about 30 m and then recorded alert distance and FID again. This repeat data has not been analyzed or used anywhere.
* In the column titled sex, M=male, F=female. I am not very certain about how well I was able to sex Motacilla alba, but observations from other species should be fine. Sex data has not been analyzed.
* approach_speed "normal" indicates a walking speed of 1.3 m/s, while "fast" was about 2.6 m/s. However, note that some observations were made during wintertime with snow, meaning that the approach speeds might have been slower then. I would treat winter data with caution. There is also a column "bird_feeder_nearby" that indicates whether a bird feeder was in sight, but it does not necessarily mean that the bird was feeding there.
* Column on flock size does not discriminate between same-species groups and mixed-species groups.
Online data collection about 9 attitudes toward the virus pandemic.