cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.8382828
title: THz driven field emission: energy and time-of-flight spectra of ions (DATASET)

description: We present an experimental and numerical study of ion field evaporation from LaB6 nanotips using single-cycle terahertz (THz) transients and a static bias voltage. Varying the amplitude and phase of the THz pulses and the value of the<br> bias, we explore the THz-induced reshaping of the ions energy and their time-of-flight spectra. These results prove that short THz transient of about 1 ps can induce ionization and emission of ions from LaB6 samples by a field effect: the THz<br> transient acts as an ultra-short electrical pulse. Moreover, comparing numerical and experimental results, we prove that the response time of surface atoms to the THz transient is shorter than 1 ps, corresponding to the vibration times of acoustic phonons<br> in LaB6. In the following dataset, you can find data from THz-APT obtained from LaB6 sample and results of simulation of ions under THz Field done with Lorentz
DOI: 10.5281/zenodo.8382827
title: THz driven field emission: energy and time-of-flight spectra of ions (DATASET)

description: We present an experimental and numerical study of ion field evaporation from LaB6 nanotips using single-cycle terahertz (THz) transients and a static bias voltage. Varying the amplitude and phase of the THz pulses and the value of the<br> bias, we explore the THz-induced reshaping of the ions energy and their time-of-flight spectra. These results prove that short THz transient of about 1 ps can induce ionization and emission of ions from LaB6 samples by a field effect: the THz<br> transient acts as an ultra-short electrical pulse. Moreover, comparing numerical and experimental results, we prove that the response time of surface atoms to the THz transient is shorter than 1 ps, corresponding to the vibration times of acoustic phonons<br> in LaB6. In the following dataset, you can find data from THz-APT obtained from LaB6 sample and results of simulation of ions under THz Field done with Lorentz
DOI: 10.57745/ssxynh
title: environment.yml

description: load this environment file in Anaconda to have all the necessary libraries and dependencies to run the code
DOI: 10.57745/1sv9mw
title: OPEN_SOURCE_CODE.py

description: Python code to recompute the regression between subjective assessment and objective indicators, and to generate the figures included in the paper.
DOI: 10.57745/gz3shv
title: data.csv

description: values of the subjective assessment (CAHQRS score) and the 39 handling indicators + the mean speed and the segment considered for every trial (385) and segment (5) combinations
DOI: 10.57745/xvlxpq
title: regression_results.csv

description: Results of the regressions for each indicator, segment, and speed considered (for those who do not want to regenerate these results using the Python code provided)
DOI: 10.57745/gfu9ie
title: readme_en.pdf

description: :unav
DOI: 10.57745/kosnep
title: readme_en.md

description: :unav
DOI: 10.5281/zenodo.8144189
title: Non-additive interaction between genotypes: implications for competitive fitness assays

description: Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged <em>Drosophila simulans</em> populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: 1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. 2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype x environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.
DOI: 10.5281/zenodo.8144190
title: Non-additive interaction between genotypes: implications for competitive fitness assays

description: Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged <em>Drosophila simulans</em> populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: 1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. 2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype x environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.
DOI: 10.5281/zenodo.8382826
title: Non-additive interaction between genotypes: implications for competitive fitness assays

description: Competitive fitness assays are widely used in evolutionary biology and typically rely on a reference strain to compare different focal genotypes. This approach implicitly relies on the absence of interaction between the competing genotypes. In other words, the performance of the reference strain must not depend on the competitor. This report scrutinized this assumption by competing diverged <em>Drosophila simulans</em> populations against a common reference strain. We detected strong evidence for interaction between the competing genotypes: 1) Frequency-dependent selection was common with opposite effects in genetically diverged populations. 2) Temporal heterogeneity of fitness estimates, which can be partially attributed to a competitor-specific delay in the eclosion of the reference strain. We propose that this inconsistent behavior of the reference strain can be considered a specific case of a genotype x environment interaction. Focal populations could modify the environment of the reference strain, either indirectly by altering the microbiome composition and food availability or directly by genotype-specific cannibalism. Our results provide new insights into the interaction of diverged genotypes and have important implications for the interpretation of competitive fitness assays.
DOI: 10.5281/zenodo.8375230
title: Raw Data

description: Raw NMR Data
DOI: 10.5281/zenodo.8375229
title: Raw Data

description: Raw NMR Data
DOI: 10.6084/m9.figshare.23122511.v1
title: <strong>What drives a researcher’s preferences for chemical compounds? Evidence from conjoint analysis</strong>

description: We investigated which attribute and attribute level affect researchers’ preferences for chemical compounds. Drawing on survey data for Korean researchers using chemical compounds provided by the Korean Chemical Bank (KCB), we conducted a conjoint analysis, through which the part-worth utility for each attribute’s level was estimated, the relative importance values of attributes were calculated, and user segmentation with different patterns was classified. The results of this study show that the structure database offers the highest part-worth utility to the researchers, followed by high new functionality, price, screening service, and drug action data provided only by the KCB. Notably, researchers view the offer of a structured database and high new functionality as more important in decision-making about the research and development (R&D) use of chemical compounds than other attributes. Furthermore, the results of user segmentation present different patterns of the use of chemical compounds: researchers group the most appealing to structure database and improved new functionality attributes. We discussed some policy and strategic implications based on the findings of this study and proposed some limitations.
DOI: 10.25345/c5vm4375s
title: MassIVE MSV000092973 - Overcoming therapeutic resistance in GBM
title: To reveal specific mechanisms of drug resistance about bevacizumab treatment in GBM patients who have prolonged disease free survival (DFS), but retained overall survival (OV), we established systemic drug-resistance murine GBM model in the context of tumor evolutionary with time series brain tissue collection. And to trace the change of specific functional molecules along the bevacizumab resistance, we performed LC-MS/MS-based global, phospho-proteomic analysis and NGS-based transcriptomic analysis using the time series murine GBM model.
DOI: 10.5281/zenodo.8358757
title: CLOE MCMC mock data and covariance

description: Input files (data, Gaussian and SSC covariance) for the upcoming CLOE MCMC runs
DOI: 10.5281/zenodo.8358758
title: CLOE MCMC mock data and covariance

description: Input files (data, Gaussian and SSC covariance) for the upcoming CLOE MCMC runs
DOI: 10.5281/zenodo.8382926
title: DataSet-Nursing Leadership

description: Data Collected from Nurses for an empirical research study
DOI: 10.5281/zenodo.8382925
title: DataSet-Nursing Leadership

description: Data Collected from Nurses for an empirical research study
DOI: 10.6084/m9.figshare.24204348
title: <b>R</b><b>o</b><b>le of dark septate endophyte mycelial networks in nitrogen transfer between buckwheat and alfalfa: a </b><sup><strong>15</strong></sup><b>N tracer study</b>

description: The dataset includes the growth, physiological properties and nutritional status of plants and the colonization of microorganisms, and other data needed for this study.
DOI: 10.6084/m9.figshare.24204348.v2
title: <b>R</b><b>o</b><b>le of dark septate endophyte mycelial networks in nitrogen transfer between buckwheat and alfalfa: a </b><sup><strong>15</strong></sup><b>N tracer study</b>

description: The dataset includes the growth, physiological properties and nutritional status of plants and the colonization of microorganisms, and other data needed for this study.
DOI: 10.6084/m9.figshare.24204348.v1
title: <b>R</b><b>o</b><b>le of dark septate endophyte mycelial networks in nitrogen transfer between buckwheat and alfalfa: a </b><sup><strong>15</strong></sup><b>N tracer study</b>

description: The dataset includes the growth, physiological properties and nutritional status of plants and the colonization of microorganisms, and other data needed for this study.
DOI: 10.6084/m9.figshare.23122511
title: <strong>What drives a researcher’s preferences for chemical compounds? Evidence from conjoint analysis</strong>

description: We investigated which attribute and attribute level affect researchers’ preferences for chemical compounds. Drawing on survey data for Korean researchers using chemical compounds provided by the Korean Chemical Bank (KCB), we conducted a conjoint analysis, through which the part-worth utility for each attribute’s level was estimated, the relative importance values of attributes were calculated, and user segmentation with different patterns was classified. The results of this study show that the structure database offers the highest part-worth utility to the researchers, followed by high new functionality, price, screening service, and drug action data provided only by the KCB. Notably, researchers view the offer of a structured database and high new functionality as more important in decision-making about the research and development (R&D) use of chemical compounds than other attributes. Furthermore, the results of user segmentation present different patterns of the use of chemical compounds: researchers group the most appealing to structure database and improved new functionality attributes. We discussed some policy and strategic implications based on the findings of this study and proposed some limitations.
DOI: 10.6084/m9.figshare.23122511.v3
title: <strong>What drives a researcher’s preferences for chemical compounds? Evidence from conjoint analysis</strong>

description: We investigated which attribute and attribute level affect researchers’ preferences for chemical compounds. Drawing on survey data for Korean researchers using chemical compounds provided by the Korean Chemical Bank (KCB), we conducted a conjoint analysis, through which the part-worth utility for each attribute’s level was estimated, the relative importance values of attributes were calculated, and user segmentation with different patterns was classified. The results of this study show that the structure database offers the highest part-worth utility to the researchers, followed by high new functionality, price, screening service, and drug action data provided only by the KCB. Notably, researchers view the offer of a structured database and high new functionality as more important in decision-making about the research and development (R&D) use of chemical compounds than other attributes. Furthermore, the results of user segmentation present different patterns of the use of chemical compounds: researchers group the most appealing to structure database and improved new functionality attributes. We discussed some policy and strategic implications based on the findings of this study and proposed some limitations.
DOI: 10.6084/m9.figshare.23122511.v2
title: <strong>What drives a researcher’s preferences for chemical compounds? Evidence from conjoint analysis</strong>

description: We investigated which attribute and attribute level affect researchers’ preferences for chemical compounds. Drawing on survey data for Korean researchers using chemical compounds provided by the Korean Chemical Bank (KCB), we conducted a conjoint analysis, through which the part-worth utility for each attribute’s level was estimated, the relative importance values of attributes were calculated, and user segmentation with different patterns was classified. The results of this study show that the structure database offers the highest part-worth utility to the researchers, followed by high new functionality, price, screening service, and drug action data provided only by the KCB. Notably, researchers view the offer of a structured database and high new functionality as more important in decision-making about the research and development (R&D) use of chemical compounds than other attributes. Furthermore, the results of user segmentation present different patterns of the use of chemical compounds: researchers group the most appealing to structure database and improved new functionality attributes. We discussed some policy and strategic implications based on the findings of this study and proposed some limitations.
DOI: 10.6084/m9.figshare.20400975
title: <b>Saxidomus purpuratus genome data</b>

description: <pre># Final result of SPU genome assembly<br><br>## File description<br><br>SPU_genome_v1.build_20211105.genome.fna : genome assembly<br>SPU_genome_v1.build_20211105.gene.faa : Predicted genes, protein sequence<br>SPU_genome_v1.build_20211105.gene.gff3 : Predicted genes, GFF3 formatted<br>SPU_genome_v1.build_20211105.gene.fna : Predicted genes, nucleotide sequence<br><br><br></pre>
DOI: 10.6084/m9.figshare.21408117
title: Supplementary Data: Finding Haplotypic Signatures in Proteins

description: Supplementary data related to the paper "Identifying Protein Haplotypes by Mass Spectrometry" <br> SD1: FASTA file including all target protein sequences (Ensembl reference proteome, protein haplotype sequences, contaminant sequences), excluding decoys SD2: FASTA file including all target and decoy sequences SD3: List of all peptide-spectrum matches (PSMs) with all related metadata and quality control measures SD4: List of substitutions identified, along with IDs of corresponding PSMs SD5: List of variant PSMs and peptide candidates suggested by PepQuery, along with confidence scores for each peptide candidate <br> To reproduce the post-processing steps, you can use the pipeline published at https://github.com/ProGenNo/IdentifyingHaplotypesByMS The repository also contains additional explanations of supplementary files contents.
DOI: 10.6084/m9.figshare.21408117.v2
title: Supplementary Data: Finding Haplotypic Signatures in Proteins

description: Supplementary data related to the paper "Identifying Protein Haplotypes by Mass Spectrometry" <br> SD1: FASTA file including all target protein sequences (Ensembl reference proteome, protein haplotype sequences, contaminant sequences), excluding decoys SD2: FASTA file including all target and decoy sequences SD3: List of all peptide-spectrum matches (PSMs) with all related metadata and quality control measures SD4: List of substitutions identified, along with IDs of corresponding PSMs SD5: List of variant PSMs and peptide candidates suggested by PepQuery, along with confidence scores for each peptide candidate <br> To reproduce the post-processing steps, you can use the pipeline published at https://github.com/ProGenNo/IdentifyingHaplotypesByMS The repository also contains additional explanations of supplementary files contents.
DOI: 10.6084/m9.figshare.24204441
title: Study data

description: The dataset includes the growth, physiological properties and nutritional status of plants and the colonization of microorganisms, and other data needed for this study.
DOI: 10.6084/m9.figshare.24204441.v1
title: Study data

description: The dataset includes the growth, physiological properties and nutritional status of plants and the colonization of microorganisms, and other data needed for this study.
DOI: 10.5281/zenodo.8381079
title: Gold standard annotation of epilepsy clinic letters for the development of information extraction tools

description: This folder contains 200 synthetic letters, based on hospital outpatient epilepsy clinic consultations, written by neurology consultants, specialist trainees, and epilepsy specialist nurses. The letters were double annotated by trained researchers, according to annotation guidelines, uploaded separately (What and How of annotating with Markup). The 200 .ann annotation files are also included. We used Markup (https://getmarkup.com) for annotation (the configuration file is within the uploaded set of annotations) with an epilepsy concept list based on the Unified Medical Language System (UMLS) ontology. All annotations were compared, reviewed, and corrected to form a gold standard annotation set.
description: The annotation guidelines 'What and How of annotating with Markup' accompany the enclosed sets of text and annotation files.
DOI: 10.34740/kaggle/dsv/6553950
title: 📒Meta Kaggle ported to SQLITE DB
DOI: 10.5281/zenodo.8382923
title: Dataset for "Impact of surface anisotropy on the spin-wave dynamics in thin ferromagnetic film"

description: The dataset consist of the data used to prepare the figures for the manusript entitled <em>Impact of surface anisotropy on the spin-wave dynamics in thin ferromagnetic film.</em> Please read README.txt file to see the description of the data in the files.
description: We acknowledge the financial support from National Science Centre, Poland, grants no. UMO-2020/39/I/ST3/02413 and UMO-2021/41/N/ST3/04478. The research leading to these results has received funding from the Norwegian Financial Mechanism 2014-2021 project no. UMO-2020/37/K/ST3/02450. K.S. acknowledges the financial support from the Foundation for Polish Science (FNP).
DOI: 10.5281/zenodo.8382924
title: Dataset for "Impact of surface anisotropy on the spin-wave dynamics in thin ferromagnetic film"

description: The dataset consist of the data used to prepare the figures for the manusript entitled <em>Impact of surface anisotropy on the spin-wave dynamics in thin ferromagnetic film.</em> Please read README.txt file to see the description of the data in the files.
description: We acknowledge the financial support from National Science Centre, Poland, grants no. UMO-2020/39/I/ST3/02413 and UMO-2021/41/N/ST3/04478. The research leading to these results has received funding from the Norwegian Financial Mechanism 2014-2021 project no. UMO-2020/37/K/ST3/02450. K.S. acknowledges the financial support from the Foundation for Polish Science (FNP).
DOI: 10.6084/m9.figshare.24204501
title: Appendices to BEH 3837

description: Appendix A. Detailed description of a standardized protocol for diver placement and feeding procedures, ensuring consistency in timing and the quantity of food released.Appendix B. Details raw data from 651 dives, with durations varying between 25 min (deeper sites) and 45 min (shallower sites), resulting in a total of 2813 individual observation sessions. For the purpose of assessing personality, we focused on 31 adult bull sharks, each identified by a unique number followed by either an F for female or an M for male.
DOI: 10.6084/m9.figshare.24204501.v1
title: Appendices to BEH 3837

description: Appendix A. Detailed description of a standardized protocol for diver placement and feeding procedures, ensuring consistency in timing and the quantity of food released.Appendix B. Details raw data from 651 dives, with durations varying between 25 min (deeper sites) and 45 min (shallower sites), resulting in a total of 2813 individual observation sessions. For the purpose of assessing personality, we focused on 31 adult bull sharks, each identified by a unique number followed by either an F for female or an M for male.
DOI: 10.5258/soton/d2655
title: Data supporting the University of Southampton Doctoral Thesis "Integration of health informatics: 'big data' for clinical translation in inflammatory bowel disease".

description: Data supporting the University of Southampton Doctoral Thesis "Integration of health informatics: ‘big data’ for clinical translation in inflammatory bowel disease". The data is a supplementary information. This supplementary data predominantly consists of computational script that enable the reproducibility of genomic data processing, and the generation of machine learning models discussed throughout the thesis. Supplementary files are zipped in folders according to the chapter they are used in, aside from the folder "gene panels and lists", as these text files are used in multiple chapters in the thesis. These zipped folders are as follows: - chapter 3 genomic data processing - chapter 4 machine learning scripts - chapters 5 and 6 scripts qc stricturing genes - chapter 7 supplementary information - gene panels and lists Related Funders: Institute for Life Sciences, National Institute for Health Research Biomedical Research Centre Southampton