cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26886070.v1
title: A global dataset of gross nitrogen transformation rates across terrestrial ecosystems

description: Rates of nitrogen transformations support quantitative descriptions and predictive understanding of the complex nitrogen cycle, but measuring these rates is expensive and not readily available to researchers. Here, we compiled a dataset of gross nitrogen transformation rates (GNTR) of mineralization, nitrification, ammonium immobilization, nitrate immobilization, and dissimilatory nitrate reduction to ammonium in terrestrial ecosystems. Data were extracted from 331 studies published from 1984-2022, covering 581 sites. Globally, 1552 observations were appended with standardized soil, vegetation, and climate data (49 variables in total) potentially contributing to the observed variations of GNTR. We used machine learning-based data imputation to fill in partially missing GNTR, which improved statistical relationships between theoretically correlated processes. The dataset is currently the most comprehensive overview of terrestrial ecosystem GNTR and serves as a global synthesis of the extent and variability of GNTR across a wide range of environmental conditions. Future research can utilize the dataset to identify measurement gaps with respect to climate, soil, and ecosystem types, delineate GNTR for certain ecoregions, and help validate process-based models.
DOI: 10.6084/m9.figshare.782261.v4
title: Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes.

description: TRAMS (Tool for Rapid Annotation of Microbial SNPs) is a program for functional annotation of genomic SNPs which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. TRAMS needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. TRAMS annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. We have also developed a workflow for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs. TRAMS is a simple program for rapid and accurate annotation of SNPs that will be very useful for microbiologists in analysing genomic diversity in microbial populations. Availability: TRAMS is available here to download as Python script and single file executable for WINDOWS and also in the Galaxy tool shed (http://toolshed.g2.bx.psu.edu/view/rreumerman/snptools). <strong>Please cite</strong> Reumerman, R. A., Tucker, N. P., Herron, P. R., Hoskisson, P. A., & Sangal, V. (2013). Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes. Antonie van Leeuwenhoek, 104, 431-434. doi:10.1007/s10482-013-9953-x The full published manuscript is available http://link.springer.com/article/10.1007%2Fs10482-013-9953-x UPDATED 24th September 2013 see Changelog.txt ==[Version1.0.2]== 130923:Fixed issue where program crashed on absence of certain features in genbank file. ==[Version1.0.1]== 130919:Fixed issue where'Gene'and'Source' were not recognized as'gene'and'source'. 130919:Fixed issue where features' strands were mysteriously no longer recognized if on +1 strand.
DOI: 10.17632/fv653hjw88
title: Itaconate is a lysosomal inducer that promotes antibacterial innate immunity

description: Unprocessed immunoblotting data
DOI: 10.17632/s6y74d2wm5
title: Data for: A Simple Structural Control Model for Earthquake Excited Structures
DOI: 10.6084/m9.figshare.29150516.v1
title: Literature Review WIP

description: Ballona Wetlands literature review WIP document
DOI: 10.17632/5cv85nrmnm
title: PISA 2015

description: This data is Programme for International Student Assessment (PISA) 2015 dataset. It includes cognitive items dataset, student questionnaire data file and school questionnaire data file. They are also public available online: http://www.oecd.org/pisa/data/2015database/. It also includes data file to recover the item order in each student's test.
DOI: 10.17632/gr2dy9grdn
title: High CO2 in the mantle source of ocean island basanites

description: These two supplementary material files contain important information regarding the analyses for studying melt inclusions (MIs) from Fogo, Cape Verde Archipelago. In details, the Supplementary Material comprises an .xlsx file labelled as Supplementary Material S1, containing multiple sheets with detailed data information: Whole rock; Sample ubication; Host olivine analysis; Scoria analysis; Uncorrected MIs analysis; Corrected MIs analysis; Total MI CO2 contents; MI Saturation Pressures. Additionally, there is a .pdf file labelled as Supplementary Material S2, which includes the calibration of Nano-SIMS standards (Figure S1) and the Raman tomography of MI Fog 43-6-2 (Figure S2).
DOI: 10.6084/m9.figshare.25939360.v2
title: Benchmark code and data including ENCODE RNA-seq

description: The zipped file contains the data and jupyter notebooks for generating scripts and results in Benchmark.
DOI: 10.17632/b98dcs5jtw
title: LINF_180015300

description: Mitochondrial carrier protein | MCP14; Leishmania infantum (strain JPCM5)
DOI: 10.6084/m9.figshare.25820893.v1
title: Weight Data

description: Data used in the book "Data Science and Analytics with Python" by J Rogel-Salazar. Demo data describing users' weight together with information about exercise and eating habits. Features:gender - Gender of the user (1, 2)exercise - Exercise habit (A - always, B - sometimes, C - never)breakfast - Do you eat breakfast? (Y/N)weight - User weight in kg<br>
DOI: 10.6084/m9.figshare.23282882.v1
title: Changes in aerosol/gas-phase distribution ratio of semi-volatile products

description: Α-pinene is an important precursor of secondary organic aerosol (SOA) in the atmosphere. However, the effects of NOx on the SOA derived from α-pinene photooxidation are still not fully understood. the temporal evolution of SOA formation from α-pinene photooxidation with different initial NOx concentrations was investigated in a photooxidation chamber.
DOI: 10.6084/m9.figshare.28738787.v1
title: Point-of-Care Detection of <i>Burkholderia pseudomallei</i>: A Method Integrating LAMP and LFSA with RNase HII Hydrolysis

description: Melioidosis, caused by <i>Burkholderia pseudomallei</i>, is a tropical disease known for its long incubation period and high mortality rate. However, the traits of this “great imitator” present significant challenges for clinical diagnosis and pose a serious threat to populations in epidemic regions. A rapid, accurate, and low environment requirement diagnostic method is needed to enable timely diagnoses. Here, we developed a strategy for point-of-care testing (POCT) using loop-mediated isothermal amplification (LAMP) with RNase HII for efficient detection of <i>B. pseudomallei</i>, through real-time fluorescence analysis or lateral flow strip assay (LFSA). Briefly, RNase HII-based cleavage dual-functional probe LAMP (RCDP-LAMP) utilizes.
DOI: 10.6084/m9.figshare.7654916.v1
title: Scaling in the space-time of the Internet

description: The Internet on router level, is a complex network embedded in a geographical space. We provide experimental evidences which prove that the average travel time for a message increases roughly as the square root of the geographical distance. To explain this scaling law and other measurable topological properties of the Internet as a graph, we introduce and study a simple network model. The model is based on a few realistic socio-economic facts/assumptions and qualitatively reproduces the experimentally observed stylized facts. <br>
DOI: 10.17632/bwkm69ycrc
title: Evaluation of an Adaptive Game-Based Math Learning Program for Improving Early Elementary School Children's Math Knowledge

description: The data were collected as a part of a randomized control trial of an adaptive game-based math learning program. The goal was to understand the extent to which the intervention could improve math learning outcomes and engagement for kindergartners and first graders. The student assessment data include pre- and post- intervention administrations of a measure comprised of standards-based items selected from Certica item bank. Teachers were asked to complete a beginning-of-study survey and end-of-study survey. A sample of the treatment and control group teachers were also invited to take part in end-of-study interviews. Additionally, classroom observations were conducted to gain insights about the math instruction in both treatment and control classrooms. The qualitative data collected from teachers and through observations provide context for how the intervention was implemented and the effects it had on their students and their classroom instruction.
DOI: 10.17632/5cw5rghg7m
title: Microbiome-driven IBS metabotypes influence response to the low FODMAP diet: Insights from the faecal volatome

description: WORKING GROUP
Thomas Edward Conley 1,2, Rachael Slater 1, Stephen Moss 3,4, David Bulmer 5, Juan de la Revilla Negro 3, Umer Zeeshan Ijaz 6, David Mark Pritchard 1,2, Miles Parkes 3,4, Chris Probert 1,2

1. University of Liverpool Institute of Systems, Molecular and Integrative Biology, Liverpool, UK
2. Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
3. Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
4. University of Cambridge Department of Medicine, Gastroenterology and Hepatology, Cambridge, Cambridgeshire, UK
5. University of Cambridge Department of Pharmacology, Cambridge, Cambridgeshire, UK
6. University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, UK


ABSTRACT:
BACKGROUND Irritable bowel syndrome (IBS) is a common and debilitating disorder manifesting with abdominal pain and bowel dysfunction. A mainstay of treatment is dietary modification, including restriction of FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols). A greater response to a low FODMAP diet has been reported in those with a distinct IBS microbiome termed IBS-P. We investigated whether this is linked to specific changes in the metabolome in IBS-P. 
METHODS Solid phase microextraction gas chromatography-mass spectrometry was used to examine the faecal headspace of 56 IBS cases (each paired with a non-IBS household control) at baseline, and after four-weeks of a low FODMAP diet (39 pairs). 50% cases had the IBS-P microbial subtype, while the others had a microbiome that more resembled healthy controls (termed IBS-H). Clinical response to restriction of FODMAPs was measured with the IBS-symptom severity scale, from which a pain sub score was calculated. 
FINDINGS Two distinct metabotypes were identified and mapped onto the microbial subtypes. IBS-P was characterised by a fermentative metabolic profile rich in short chain fatty acids (SCFAs). After FODMAP restriction significant reductions in SCFAs were observed in IBS-P. SCFA levels did not change significantly in the IBS-H group. The magnitude of pain and overall symptom improvement were significantly greater in IBS-P compared to IBS-H (p=0.016 and p=0.026, respectively). Using just five metabolites, a biomarker model could predict microbial subtype with accuracy (AUROC 0.797, sensitivity 78.6% (95% CI:0.78–0.94), specificity 71.4% (95% CI:0.55–0.88).
INTERPREATATION A metabotype high in SCFAs can be manipulated by restricting fermentable carbohydrate, and is associated with an enhanced clinical response to this dietary restriction. This implies that SCFAs harbour pro-nociceptive potential when produced in a specific IBS niche. By ascertaining metabotype, microbial subtype can be predicted with accuracy. This could allow targeted FODMAP restriction in those seemingly primed to respond best.

Enclosed:
1. Master table containing clinical & faecal SPME-GC-MS data.
2. File containing correlation coefficients between VOCs & bacterial pathways.
DOI: 10.17632/94csp5czvt
title: Decision matrices for sustainable development strategies assessment using the new Multi-Target TOPSIS Method

description: The dataset includes performance values achieved by considered European countries in relation to implementing the Europe 2020 strategy collected for 2016-2020. The dataset contains also target values of the Europe 2020 strategy which the considered countries should strive to achieve. Data is collected in two-dimensional decision matrices created for each analysed year and one decision matrix with target values. Data achieved by countries and target data are provided in individual XLSX and CSV files for each year and for target data. Detailed data description is provided in PDF file.
DOI: 10.5281/zenodo.15282743
title: Data for the manuscript "The density isobar of water: A comparative study of vdW-DF-cx and RPBE-D3"

description: Data related to the paper "The density isobar of water: A comparative study of vdW-DF-cx and RPBE-D3".

The data are structured as follows:

 

Jupyter notebooks (use the data saved in the directories provided):



density_isobars.ipynb : plots of water densities along the whole molecular dynamics trajectories for RPBE-D3 and vdW-DF-cx, Figure 2 from the paper

Energy_contrib_analysis.ipynb : plots of exchnage-correlation energy contributions for RPBE-D3 and vdW-DF-cx, Figures 6 and 7 from the paper


 

Description of directories:

NNFF_datasets



RPBED3_Cheng_dataset.extxyz : structures, energies and atomic forces of bulk water structures calculated using RPBE-D3

vdW_DF_cx_Cheng_dataset.extxyz : structures, energies and atomic forces of bulk water structures calculated using vdW-DF-cx


struct_HDL_LDL



Structures of the HDL-like and LDL-like structures used for the relative stability evaluation, Figure 7 in the paper (POSCAR files)


data_DFT_energies



3 subdirectories with data for the water dimer (Dimer), expanded/contracted HDL-like structure POSCAR_HDL_like (Bulk_HDL) and LDL-like structure POSCAR_LDL_like (Bulk_LDL)

Each subdirectory contains .npy files with total energies caluclated with RPBE-D3 or vdW-DF-cx and the separate exchnage-correlation contributions ( see more details in the associated jupyther notebook Energy_contrib_analysis.ipynb )


data_REMD_extxyz



contains the 10100 structures taken from the equilibrated trajectories that were used for the structural evaluation using the local structure index (LSI) and radial distribution function


data_REMD_density



contains densities for all 16 replica runs at every 20th timestep caluclated using RPBE-D3 and vdW-DF-cx force fields.

file names logic: density_{temperature_of_replica}_{density_functional}.npy (XC=vdW-DF-cx)
DOI: 10.5281/zenodo.15282744
title: Data for the manuscript "The density isobar of water: A comparative study of vdW-DF-cx and RPBE-D3"

description: Data related to the paper "The density isobar of water: A comparative study of vdW-DF-cx and RPBE-D3".

The data are structured as follows:

 

Jupyter notebooks (use the data saved in the directories provided):



density_isobars.ipynb : plots of water densities along the whole molecular dynamics trajectories for RPBE-D3 and vdW-DF-cx, Figure 2 from the paper

Energy_contrib_analysis.ipynb : plots of exchnage-correlation energy contributions for RPBE-D3 and vdW-DF-cx, Figures 6 and 7 from the paper


 

Description of directories:

NNFF_datasets



RPBED3_Cheng_dataset.extxyz : structures, energies and atomic forces of bulk water structures calculated using RPBE-D3

vdW_DF_cx_Cheng_dataset.extxyz : structures, energies and atomic forces of bulk water structures calculated using vdW-DF-cx


struct_HDL_LDL



Structures of the HDL-like and LDL-like structures used for the relative stability evaluation, Figure 7 in the paper (POSCAR files)


data_DFT_energies



3 subdirectories with data for the water dimer (Dimer), expanded/contracted HDL-like structure POSCAR_HDL_like (Bulk_HDL) and LDL-like structure POSCAR_LDL_like (Bulk_LDL)

Each subdirectory contains .npy files with total energies caluclated with RPBE-D3 or vdW-DF-cx and the separate exchnage-correlation contributions ( see more details in the associated jupyther notebook Energy_contrib_analysis.ipynb )


data_REMD_extxyz



contains the 10100 structures taken from the equilibrated trajectories that were used for the structural evaluation using the local structure index (LSI) and radial distribution function


data_REMD_density



contains densities for all 16 replica runs at every 20th timestep caluclated using RPBE-D3 and vdW-DF-cx force fields.

file names logic: density_{temperature_of_replica}_{density_functional}.npy (XC=vdW-DF-cx)
DOI: 10.15468/dl.uf75s8
title: Occurrence Download

description: A dataset containing 44689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Potentilla crantzii (Crantz) Beck ex Fritsch",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 44689 records from 325 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001767-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fe9v7y
title: Occurrence Download

description: A dataset containing 347 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hosackia repens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 347 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003735-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z92njv
title: Occurrence Download

description: A dataset containing 356 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pinguipes brasilianus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 356 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003736-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28418344
title: Optimized formulas of the gravitational field of a vertical cylindrical prism

description: Modeling the gravitational effects of the topography and other layers of the Earth is the basis not only for gravity corrections and reductions in geodesy but also for gravity inversions and interpretations in geophysics. Previous formulas of the Gravitational Potential (GP), Gravitational Vector (GV), and Gravitational Gradient Tensor (GGT) of a vertical cylindrical prism were derived from complex conversion relations, the result of which is relatively complicated. In this contribution, we are able to optimize such formulas through a particular geometrical relation between the computation point and integration point. The consistency between our newly derived formulas and previous formulas is confirmed analytically. By extending the cylindrical prism to a cylindrical shell, the analytical formulas of the GP, GV, and GGT of a cylindrical shell are derived when the computation point is located on the polar axis. Based on these analytical formulas, a cylindrical shell benchmark is put forward to evaluate the numerical properties of the cylindrical prism, that is to discrete a whole cylindrical shell into cylindrical prisms. For actual numerical calculations, we propose to approximate the cylindrical prism with a second-order 3D Taylor series expansion. Beyond the improved simplicity, our optimized formulas help to save computation time (particularly for the GGT up to 20%). Numerical results reveal that when the computation point’s vertical distance changes, the relative and absolute errors are symmetric with respect to the center vertical distance of the cylindrical shell. Using the second-order 3D Taylor series expansion method provides sufficient computation precision, i.e. all relative errors of the GP, GV, and GGT are smaller than 10<sup>−2</sup> in the numerical experiments. The new expressions for the GP, GV, and GGT of a vertical cylindrical prism using the second-order 3D Taylor series expansion and a cylindrical shell are provided for practical applications of gravity forward modeling in the Python language at the GitHub website https://www.github.com/xiaoledeng/optimized-formulas-of-gp-gv-ggt.
DOI: 10.6084/m9.figshare.28418344.v1
title: Optimized formulas of the gravitational field of a vertical cylindrical prism

description: Modeling the gravitational effects of the topography and other layers of the Earth is the basis not only for gravity corrections and reductions in geodesy but also for gravity inversions and interpretations in geophysics. Previous formulas of the Gravitational Potential (GP), Gravitational Vector (GV), and Gravitational Gradient Tensor (GGT) of a vertical cylindrical prism were derived from complex conversion relations, the result of which is relatively complicated. In this contribution, we are able to optimize such formulas through a particular geometrical relation between the computation point and integration point. The consistency between our newly derived formulas and previous formulas is confirmed analytically. By extending the cylindrical prism to a cylindrical shell, the analytical formulas of the GP, GV, and GGT of a cylindrical shell are derived when the computation point is located on the polar axis. Based on these analytical formulas, a cylindrical shell benchmark is put forward to evaluate the numerical properties of the cylindrical prism, that is to discrete a whole cylindrical shell into cylindrical prisms. For actual numerical calculations, we propose to approximate the cylindrical prism with a second-order 3D Taylor series expansion. Beyond the improved simplicity, our optimized formulas help to save computation time (particularly for the GGT up to 20%). Numerical results reveal that when the computation point’s vertical distance changes, the relative and absolute errors are symmetric with respect to the center vertical distance of the cylindrical shell. Using the second-order 3D Taylor series expansion method provides sufficient computation precision, i.e. all relative errors of the GP, GV, and GGT are smaller than 10<sup>−2</sup> in the numerical experiments. The new expressions for the GP, GV, and GGT of a vertical cylindrical prism using the second-order 3D Taylor series expansion and a cylindrical shell are provided for practical applications of gravity forward modeling in the Python language at the GitHub website https://www.github.com/xiaoledeng/optimized-formulas-of-gp-gv-ggt.