cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7038481
title: Data and code for the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models"

description: This is the repository for the data and code to reproduce the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models".

Summary:

·  Background and Aims

Lidar is a promising tool for fast and accurate measurements of trees. There are several approaches to estimate aboveground woody biomass using lidar point clouds. One of the most widely used methods involves fitting geometric primitives (e.g. cylinders) to the point cloud, thereby reconstructing both the geometry and topology of the tree. However, current algorithms are not suited for accurate estimation of the volume of finer branches, because of the unreliable point dispersions from e.g. beam footprint compared to the structure diameter.

·  Methods

We propose a new method that couples point cloud-based skeletonization and multi-linear statistical modelling based on structural data to make a model (structural model) that accurately estimates the aboveground woody biomass of trees from high-quality lidar point clouds, including finer branches. The structural model was tested at segment, axis, and branch level, and compared to a cylinder fitting algorithm and to the pipe model theory.

·  Key Results

The model accurately predicted the biomass with 1.6% nRMSE at the segment scale from a k-fold cross-validation. It also gave satisfactory results when up-scaled to the branch level with a significantly lower error (13% nRMSE) and bias (-5%) compared to conventional cylinder fitting to the point cloud (nRMSE: 92%, bias: 82%), or using the pipe model theory (nRMSE: 31%, bias: -27%).

The model was then applied to the whole-tree scale and showed that the sampled trees had more than 1.7km of structures on average and that 96% of that length was coming from the twigs (i.e. <5 cm diameter). Our results showed that neglecting twigs can lead to a significant underestimation of tree aboveground woody biomass (-21%).

·  Conclusions

The structural model approach is an effective method that allows a more accurate estimation of the volumes of smaller branches from lidar point clouds. This method is versatile but requires manual measurements on branches for calibration. Nevertheless, once the model is calibrated, it can provide unbiased and large-scale estimations of tree structure volumes, making it an excellent choice for accurate 3D reconstruction of trees and estimating standing biomass.
DOI: 10.5281/zenodo.7038482
title: Data and code for the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models"

description: This is the repository for the data and code to reproduce the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models". Summary: LiDAR is a promising tool for fast and accurate measurements of trees. There are several approaches to estimate aboveground woody biomass using LiDAR point clouds. One of the most widely used method consists in fitting geometric primitives (<em>e.g.</em> cylinders) to the point cloud, thereby reconstructing both the geometry and topology of the tree. However, current algorithms are not suited for accurate estimation of the biomass of finer branches, because of the unreliable point dispersions from the movements induced by wind, occlusion in the upper canopy, or the relatively large laser footprint compared to the structure diameter. We propose a new method that couples point cloud-based reconstructions and structural models to estimate accurately the aboveground woody biomass of trees from high-quality LiDAR point clouds, including finer branches. The model was trained using branch samples from trees, and accurately predicted the biomass with 1.6% nRMSE at the segment scale from a k-fold cross-validation. It also gave satisfactory results when up-scaled to the branch level with a significantly lower error (13% nRMSE) and bias (-5%) compared to fitting cylinders to the point cloud (nRMSE: 92%), or using the pipe model theory (nRMSE: 31%). The model was then applied to the whole-tree scale, and showed that the sampled trees had more than 1.7km of structures on average, and that 96% of that length was coming from the twigs (<em>i.e.</em> &lt;5 cm diameter). Our results showed that neglecting twigs can lead to a significant underestimation of tree aboveground woody biomass (-21%). The structural model approach is promising for unbiased large-scale estimations when high-quality LiDAR point clouds are available. It offers an accurate alternative for estimating standing biomass without requiring tree cutting.
DOI: 10.5281/zenodo.10489728
title: The role of a mammalian network in regulating ischemic stroke outcome

description: QUICK GUIDE ABOUT THE FOLDERS AND FILES

This repository contains the code used to align the sequences and to analyse the counts used in the paper: The role of a mammalian network in regulating ischemic stroke outcome. Plus, it has intermediary files regarding steps of data processing. For example, the output files produced with fastqc, multiqc, PCA and other methods. The raw fastq files of the aligned sequences can be downloaded from GEO database using the links provided in the publication.

"Alignments" folder contains the code used to align and quantify the sequencing data. Each subfolder is associated to a specific sequencing dataset used in the paper.For miRNA and total RNA sequences, we used the corresponding nf-core pipeline.For circular sequences, we used ciriquant software pulled into a local docker.For each run of nf-core pipeline and ciriquant, we kept the most important intermediary files like the ones related to quality control from "fastqc" and "multiqc".For each run of nf-core pipeline, the subfolder "pipeline_info" contains the report of the execution of the nf-core pipeline and the command used to call it.For ciriquant run, config.yml and op0_CIRIquant.sh show which has been the setting and files used for the execution.The alignment of total RNA sequencing data has been performed twice.Standard alignment with default parameters.Edited_genome alignment with the mm10 genome annotation modified to include Cdr1as.Mus_musculus folder contains the mm10 genome annotation modified to include Cdr1as.

"Analysis" folder contains the code to analyse the counts produced with the nf-core and ciriquant pipelines.Each subfolder is associated to a specific sequencing dataset used in the paper.The scripts of a folder are always indipendent from the files belonging to other folders.The scripts are ordered based on how they must be executed, so op1, op2, op3 ...The scripts always elaborate the data coming from their "data" folder, use the functions inside their own "funs" folder and produce the results in their own "output" folder; changing the structure of a folder may give errors during the execution of a script.

"Analysis_revision" folder contains the code to add to the "Analysis" folder.This code has been added to reply to reviewer's comments.

BE CAREFULL: both the code for the alignments and analysis includes pointers to file paths which must be changed in order to be run in your system.
DOI: 10.5281/zenodo.7233808
title: The role of a mammalian network in regulating ischemic stroke outcome

description: QUICK GUIDE ABOUT THE FOLDERS AND FILES

This repository contains the code used to align the sequences and to analyse the counts used in the paper: The role of a mammalian network in regulating ischemic stroke outcome. Plus, it has intermediary files regarding steps of data processing. For example, the output files produced with fastqc, multiqc, PCA and other methods. The raw fastq files of the aligned sequences can be downloaded from GEO database using the links provided in the publication.

"Alignments" folder contains the code used to align and quantify the sequencing data. Each subfolder is associated to a specific sequencing dataset used in the paper.For miRNA and total RNA sequences, we used the corresponding nf-core pipeline.For circular sequences, we used ciriquant software pulled into a local docker.For each run of nf-core pipeline and ciriquant, we kept the most important intermediary files like the ones related to quality control from "fastqc" and "multiqc".For each run of nf-core pipeline, the subfolder "pipeline_info" contains the report of the execution of the nf-core pipeline and the command used to call it.For ciriquant run, config.yml and op0_CIRIquant.sh show which has been the setting and files used for the execution.The alignment of total RNA sequencing data has been performed twice.Standard alignment with default parameters.Edited_genome alignment with the mm10 genome annotation modified to include Cdr1as.Mus_musculus folder contains the mm10 genome annotation modified to include Cdr1as.

"Analysis" folder contains the code to analyse the counts produced with the nf-core and ciriquant pipelines.Each subfolder is associated to a specific sequencing dataset used in the paper.The scripts of a folder are always indipendent from the files belonging to other folders.The scripts are ordered based on how they must be executed, so op1, op2, op3 ...The scripts always elaborate the data coming from their "data" folder, use the functions inside their own "funs" folder and produce the results in their own "output" folder; changing the structure of a folder may give errors during the execution of a script.

"Analysis_revision" folder contains the code to add to the "Analysis" folder.This code has been added to reply to reviewer's comments.

BE CAREFULL: both the code for the alignments and analysis includes pointers to file paths which must be changed in order to be run in your system.
DOI: 10.4121/e971ae20-c4a1-4ea8-87eb-987f2362bda4
title: Data underlying the paper: "Reconstructing Intimate Contexts through Data Donation: A Case Study in Menstrual Tracking Technologies." Included in Chapter 3 of the PhD thesis: Sensitive Data Donation

description: This project investigates the data donation experience of 22 people who donated their menstrual tracking logs collected by the menstrual tracking app Clue via a digital data donation platform. They participated in a semi-structured interview where they explored and contextualized their data, represented visually. The dataset includes the interview protocol, the visual representation of the data, and the thematic structure of the results.
DOI: 10.4121/e971ae20-c4a1-4ea8-87eb-987f2362bda4.v1
title: Data underlying the paper: "Reconstructing Intimate Contexts through Data Donation: A Case Study in Menstrual Tracking Technologies." Included in Chapter 3 of the PhD thesis: Sensitive Data Donation

description: This project investigates the data donation experience of 22 people who donated their menstrual tracking logs collected by the menstrual tracking app Clue via a digital data donation platform. They participated in a semi-structured interview where they explored and contextualized their data, represented visually. The dataset includes the interview protocol, the visual representation of the data, and the thematic structure of the results.
DOI: 10.48597/pduv-f694
title: Measurement of Inorganics in precipitation at Valdalen

description: Measurement of Inorganics in precipitation at Valdalen
DOI: 10.48597/pduw-qrus
title: Measurement of Inorganics in precipitation at Hurdal

description: Measurement of Inorganics in precipitation at Hurdal
DOI: 10.48597/pgw6-2y35
title: Measurement of Inorganics in precipitation at Skreådalen

description: Measurement of Inorganics in precipitation at Skreådalen
DOI: 10.48597/pxad-jby2
title: Measurement of Inorganics in precipitation at Svratouch

description: Measurement of Inorganics in precipitation at Svratouch
DOI: 10.48597/pzbg-kcb2
title: Measurement of Inorganics in precipitation at Hurdal

description: Measurement of Inorganics in precipitation at Hurdal
DOI: 10.48597/q7qd-3qjh
title: Measurement of Sulphate_corrected at Nausta

description: Measurement of Sulphate_corrected at Nausta
DOI: 10.48597/qcas-gm2c
title: Measurement of Inorganics in precipitation at Valdalen

description: Measurement of Inorganics in precipitation at Valdalen
DOI: 10.48597/qf6p-yv8p
title: Measurement of Sulphate_corrected at Nausta

description: Measurement of Sulphate_corrected at Nausta
DOI: 10.48597/reyy-bfrw
title: Measurement of Inorganics in precipitation at Solhomfjell

description: Measurement of Inorganics in precipitation at Solhomfjell
DOI: 10.48597/rgtk-vyhn
title: Measurement of Sulphate_corrected at Nausta

description: Measurement of Sulphate_corrected at Nausta
DOI: 10.48597/rppq-snjf
title: Measurement of Inorganics in precipitation at Møsvatn

description: Measurement of Inorganics in precipitation at Møsvatn
DOI: 10.48597/s5fw-88fa
title: Measurement of Inorganics in precipitation at Møsvatn

description: Measurement of Inorganics in precipitation at Møsvatn
DOI: 10.48597/s6rg-hftr
title: Measurement of Inorganics in precipitation at Hurdal

description: Measurement of Inorganics in precipitation at Hurdal
DOI: 10.48597/tk3a-s7wc
title: Measurement of Inorganics in precipitation at Svratouch

description: Measurement of Inorganics in precipitation at Svratouch
DOI: 10.48597/tz8p-6f28
title: Measurement of Sum_ammonia_and_ammonium at Lardal

description: Measurement of Sum_ammonia_and_ammonium at Lardal
DOI: 10.48597/u94w-4tyh
title: Measurement of Inorganics in precipitation at Møsvatn

description: Measurement of Inorganics in precipitation at Møsvatn
DOI: 10.48597/unys-rw37
title: Measurement of Inorganics in precipitation at Solhomfjell

description: Measurement of Inorganics in precipitation at Solhomfjell
DOI: 10.5281/zenodo.10731921
title: Data archive accompanying "Assimilating space-based Thermospheric Neutral Density (TND) data into the TIE-GCM coupled model during periods with low and high solar activity"

description: This dataset contains the main data assimilation results in analysis and forecasting mode as well as original model (TIE-GCM). The process has been done during 3 experiments: E1(4-8 March 2008), E2 (13-16 August 2004) and E3 (4-8 February 3015). All files are in mat file format. 

Units of variable as follows:



latitude and longitude are in degree.

Heights are in km.

Neutral densities are in kg/m3.

Electron densities are in 1/cm3.


This dataset is used in the article by M. Kosary et al. "Assimilating space-based Thermospheric Neutral Density (TND) data into the TIE-GCM coupled model during periods with low and high solar activity", currently in review in AGU Space Weather.
DOI: 10.48597/us5v-st6v
title: Measurement of Inorganics in precipitation at Hurdal

description: Measurement of Inorganics in precipitation at Hurdal
DOI: 10.48597/wdhw-hnp2
title: Measurement of Inorganics in precipitation at Møsvatn

description: Measurement of Inorganics in precipitation at Møsvatn
DOI: 10.48597/xefq-spks
title: Measurement of Inorganics in precipitation at Svratouch

description: Measurement of Inorganics in precipitation at Svratouch
DOI: 10.15468/dl.br3cpb
title: Occurrence Download

description: A dataset containing 385757 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Glyceria fluitans"
 ]
}

 The dataset includes 385757 records from 1531 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016408-250827131500795/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.30025378
title: The 'Medicine Baba' Goes Door to Door

description: The "Medicine Baba," Omkar Nath Sharma, 75, spends his days knocking on doors in Delhi's upper and middle class neighborhoods, collecting their leftover medicines and giving them to the poor. Mr. Sharma, a former medical technician, was jolted out of retirement in 2008, after an under-construction Delhi Metro bridge collapsed in Laxmi Nagar, claiming two lives and injuring several construction workers and passers by. Many of those people had no access to health care or medicine. "I was moved by the plight of the people who were running here and there searching desperately for medicine," said Mr. Sharma in a recent interview. He said he visited the site of the accident and decided "I will do something to help society." Mr. Sharma starts his day at 6 a.m., when he leaves his rented home in Manglapuri, a southern Delhi suburb, and travels by buses on his senior citizen pass to wealthier parts of the city. He has built up a pool of regular contributors in neighborhoods like Green Park, who he calls on when they have medicines they no longer need. Mr. Sharma estimates he walks about three miles a day, collecting everything from<br>
DOI: 10.6084/m9.figshare.30025378.v1
title: The 'Medicine Baba' Goes Door to Door

description: The "Medicine Baba," Omkar Nath Sharma, 75, spends his days knocking on doors in Delhi's upper and middle class neighborhoods, collecting their leftover medicines and giving them to the poor. Mr. Sharma, a former medical technician, was jolted out of retirement in 2008, after an under-construction Delhi Metro bridge collapsed in Laxmi Nagar, claiming two lives and injuring several construction workers and passers by. Many of those people had no access to health care or medicine. "I was moved by the plight of the people who were running here and there searching desperately for medicine," said Mr. Sharma in a recent interview. He said he visited the site of the accident and decided "I will do something to help society." Mr. Sharma starts his day at 6 a.m., when he leaves his rented home in Manglapuri, a southern Delhi suburb, and travels by buses on his senior citizen pass to wealthier parts of the city. He has built up a pool of regular contributors in neighborhoods like Green Park, who he calls on when they have medicines they no longer need. Mr. Sharma estimates he walks about three miles a day, collecting everything from<br>
DOI: 10.15468/dl.rh6yf6
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nandus nebulosus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 38 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016510-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yjwx2v
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coreopsis grandiflora",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 150 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016511-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wcuh55
title: Occurrence Download

description: A dataset containing 11016 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Living Specimen)",
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nautilus pompilius",
 "Year 2000-2025"
 ]
}

 The dataset includes 11016 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016512-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pzjaqw
title: Occurrence Download

description: A dataset containing 19085 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Información florística del Proyecto Mapa de Vegetación para la Clasificación de Ecosistemas del Ecuador Continental"
 ]
}

 The dataset includes 19085 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016509-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kuxw2h
title: Occurrence Download

description: A dataset containing 3006588822 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 3006588822 records from 64602 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015862-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1182856.08fu
title: SH1182856.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1182857.08fu
title: SH1182857.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.