cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17870/bathspa.9619916.v3
title: Empathy Group - Meeting 6 Notes, 26 April 2016

description: This item contains meeting notes for the sixth meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619826
title: Empathy Group - Meeting 5 Notes, 29 February 2016

description: This item contains meeting notes for the fifth meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619826.v2
title: Empathy Group - Meeting 5 Notes, 29 February 2016

description: This item contains meeting notes for the fifth meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619745
title: Empathy Group, Meeting 4 Notes - 10 December 2015

description: This item contains meeting notes for the fourth meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619745.v2
title: Empathy Group, Meeting 4 Notes - 10 December 2015

description: This item contains meeting notes for the fourth meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619460
title: Empathy Group - Meeting 3 Notes, 26 October 2015

description: This item contains meeting notes for the third meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619460.v2
title: Empathy Group - Meeting 3 Notes, 26 October 2015

description: This item contains meeting notes for the third meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619316
title: Empathy Group - Meeting 2 Notes, 2 May 2015

description: This item contains meeting notes for the second meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619316.v3
title: Empathy Group - Meeting 2 Notes, 2 May 2015

description: This item contains meeting notes for the second meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619016
title: Empathy Group - Meeting 1 Notes, 16 March 2015

description: This item contains meeting notes for the first meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.17870/bathspa.9619016.v2
title: Empathy Group - Meeting 1 Notes, 16 March 2015

description: This item contains meeting notes for the first meeting of the Empathy Group, an interdisciplinary research group at Bath Spa University.
DOI: 10.6084/m9.figshare.22354141
title: dataset

description: Chromium dataset
DOI: 10.6073/pasta/e9c8bbb471959f43754c26406038f2e0
title: Leaf Area Index at Harvard Forest HEM and LPH Towers since 1998

description: Leaf area index (LAI) measurements are made to detect changes in forest leaf area that are important in understanding forests’ carbon dioxide (CO2) uptake and water use. Measurements of LAI in different forest types are useful understanding differences between forests in CO2 uptake and water use, while variation in LAI in the same forest type over time helps to explain interannual variation and long-term trends in carbon storage and water use. Within a single year, especially for deciduous forests, seasonal changes in LAI are very important in determining the forest’s cycle of CO2 uptake and water use. LAI measurements at Harvard Forest were begun in the old-growth hemlock stand in 1998 in order to understand and develop a predictive model for its carbon exchange, and were begun at the Little Prospect Hill site in 2002 to better understand CO2 uptake and carbon storage at this site, which were measured by the eddy-covariance method beginning in 2002. Due to a lack of personnel, multiple annual measurements of LAI to examine seasonal change in leaf area did not begin until 2007.
DOI: 10.17028/rd.lboro.22354462
title: Supplementary information files for A genetically-optimised artificial life algorithm for complexity-based synthetic dataset generation

description: Supplementary files for article A genetically-optimised artificial life algorithm for complexity-based synthetic dataset generation <br> Algorithmic evaluation is a vital step in developing new approaches to machine learning and relies on the availability of existing datasets. However, real-world datasets often do not cover the necessary complexity space required to understand an algorithm’s domains of competence. As such, the generation of synthetic datasets to fill gaps in the complexity space has gained attention, offering a means of evaluating algorithms when data is unavailable. Existing approaches to complexity-focused data generation are limited in their ability to generate solutions that invoke similar classification behaviour to real data. The present work proposes a novel method (Sy:Boid) for complexity-based synthetic data generation, adapting and extending the Boid algorithm that was originally intended for computer graphics simulations. Sy:Boid embeds the modified Boid algorithm within an evolutionary multi-objective optimisation algorithm to generate synthetic datasets which satisfy predefined magnitudes of complexity measures. Sy:Boid is evaluated and compared to labelling-based and sampling-based approaches to data generation to understand its ability to generate a wide variety of realistic datasets. Results demonstrate Sy:Boid is capable of generating datasets across a greater portion of the complexity space than existing approaches. Furthermore, the produced datasets were observed to invoke very similar classification behaviours to that of real data. <br> <br>
DOI: 10.17028/rd.lboro.22354462.v1
title: Supplementary information files for A genetically-optimised artificial life algorithm for complexity-based synthetic dataset generation

description: Supplementary files for article A genetically-optimised artificial life algorithm for complexity-based synthetic dataset generation <br> Algorithmic evaluation is a vital step in developing new approaches to machine learning and relies on the availability of existing datasets. However, real-world datasets often do not cover the necessary complexity space required to understand an algorithm’s domains of competence. As such, the generation of synthetic datasets to fill gaps in the complexity space has gained attention, offering a means of evaluating algorithms when data is unavailable. Existing approaches to complexity-focused data generation are limited in their ability to generate solutions that invoke similar classification behaviour to real data. The present work proposes a novel method (Sy:Boid) for complexity-based synthetic data generation, adapting and extending the Boid algorithm that was originally intended for computer graphics simulations. Sy:Boid embeds the modified Boid algorithm within an evolutionary multi-objective optimisation algorithm to generate synthetic datasets which satisfy predefined magnitudes of complexity measures. Sy:Boid is evaluated and compared to labelling-based and sampling-based approaches to data generation to understand its ability to generate a wide variety of realistic datasets. Results demonstrate Sy:Boid is capable of generating datasets across a greater portion of the complexity space than existing approaches. Furthermore, the produced datasets were observed to invoke very similar classification behaviours to that of real data. <br> <br>
DOI: 10.6084/m9.figshare.22332574
title: PDAC

description: <strong>Single-cell data for deconvolution (PDAC)</strong>
DOI: 10.5683/sp2/k57iz1
title: LAPOP: Suriname 2010

description: The Latin American Public Opinion Project (LAPOP) is an academic institution hosted by Vanderbilt University that began with the study of democratic values in Costa Rica, but today carries out surveys in much of Latin America, Canada, the United States, and the Caribbean. In 2004, LAPOP established the AmericasBarometer as multi-country, regularly conducted survey of democratic values and behaviors in the Americas, and the first round included voting-age respondents from 11 countries. LAPOP collected opinions on major problems facing the country and community, threats to security, attitudes towards the country's political system, and trust in government institutions. Also measured were respondents' participation in community organizations, attitudes towards government critics, voting behavior, confidence in local government, and the prevalence of crime. Demographic information collected includes nationality, ethnicity, native language, age, gender, education level, occupation, religion, and whether the respondent lives in an urban or rural area.
DOI: 10.6073/pasta/74ebb1d4a3f073a58d6a53c283c57aa1
title: CO2 Profile at Harvard Forest HEM and LPH Towers since 2009

description: Carbon dioxide profile measurements are designed to supplement eddy flux measurements in calculating the carbon exchange of a forest. In the case of the Harvard Forest flux towers, the change in CO2 storage between the ground and the height of the eddy flux system during each half hour must be added to the eddy flux measured above the forest to determine the total carbon exchange. The profile measurements are also necessary in order to calculate CO2 movement by advection, or horizontal air transport. The amount of CO2 removed from a particular site by advection is the product of the total CO2 within the air a given range of height above the ground, and the average velocity of airflow parallel to the ground surface within that height range.
DOI: 10.5683/sp2/6khach
title: LAPOP: Trinidad Tobago 2010

description: The Latin American Public Opinion Project (LAPOP) is an academic institution hosted by Vanderbilt University that began with the study of democratic values in Costa Rica, but today carries out surveys in much of Latin America, Canada, the United States, and the Caribbean. In 2004, LAPOP established the AmericasBarometer as multi-country, regularly conducted survey of democratic values and behaviors in the Americas, and the first round included voting-age respondents from 11 countries. LAPOP collected opinions on major problems facing the country and community, threats to security, attitudes towards the countrys political system, and trust in government institutions. Also measured were respondents participation in community organizations, attitudes towards government critics, voting behavior, confidence in local government, and the prevalence of crime. Demographic information collected includes nationality, ethnicity, native language, age, gender, education level, occupation, religion, and whether the respondent lives in an urban or rural area.
DOI: 10.34992/awm0-sm20
title: Lake Winnipeg Rivers
DOI: 10.5203/yj2e-r534
title: Census Division Cartographic Boundary Files - 2011 Census
DOI: 10.5683/sp2/mjc1ts
title: LAPOP: Uruguay 2007

description: The Latin American Public Opinion Project (LAPOP) is an academic institution hosted by Vanderbilt University that began with the study of democratic values in Costa Rica, but today carries out surveys in much of Latin America, Canada, the United States, and the Caribbean. In 2004, LAPOP established the AmericasBarometer as multi-country, regularly conducted survey of democratic values and behaviors in the Americas, and the first round included voting-age respondents from 11 countries. LAPOP collected opinions on major problems facing the country and community, threats to security, attitudes towards the country's political system, and trust in government institutions. Also measured were respondents' participation in community organizations, attitudes towards government critics, voting behavior, confidence in local government, and the prevalence of crime. Demographic information collected includes nationality, ethnicity, native language, age, gender, education level, occupation, religion, and whether the respondent lives in an urban or rural area.
DOI: 10.5683/sp2/vdepaz
title: LAPOP: Uruguay 2008

description: The Latin American Public Opinion Project (LAPOP) is an academic institution hosted by Vanderbilt University that began with the study of democratic values in Costa Rica, but today carries out surveys in much of Latin America, Canada, the United States, and the Caribbean. In 2004, LAPOP established the AmericasBarometer as multi-country, regularly conducted survey of democratic values and behaviors in the Americas, and the first round included voting-age respondents from 11 countries. LAPOP collected opinions on major problems facing the country and community, threats to security, attitudes towards the country's political system, and trust in government institutions. Also measured were respondents' participation in community organizations, attitudes towards government critics, voting behavior, confidence in local government, and the prevalence of crime. Demographic information collected includes nationality, ethnicity, native language, age, gender, education level, occupation, religion, and whether the respondent lives in an urban or rural area.
DOI: 10.6084/m9.figshare.22354573
title: Supplementary Material 1

description: Supplementary material (PDF file) containing: <br> Supplemental Table 1: A. fumigatus strains used in this study. <br> Supplemental Table 2: Primers used in this study for the construction of mutant strains. <br> Supplemental Table 3: Real time PCR primers used in this study
DOI: 10.6084/m9.figshare.22354573.v1
title: Supplementary Material 1

description: Supplementary material (PDF file) containing: <br> Supplemental Table 1: A. fumigatus strains used in this study. <br> Supplemental Table 2: Primers used in this study for the construction of mutant strains. <br> Supplemental Table 3: Real time PCR primers used in this study
DOI: 10.6073/pasta/0e989d80764d5f13eeb77325210875f6
title: Microclimate at Harvard Forest HDW Tower since 2014

description: The HDW (Hardwood) microclimate and walkup tower at Harvard Forest became operational in April 2014. The site was chosen to represent the mixed hardwood forest around the EMS and NEON towers and to provide a platform for research projects without access to those towers. Microclimate data are archived annually and recent data are available upon request. Measured values include air temperature, relative humidity, PAR, net radiation, albedo, wind speed and direction, soil temperature and soil moisture.
DOI: 10.14278/rodare.2085
title: Data publication: A network-based approach to identifying correlations between phylogeny, morphological traits and occurrence of fish species in US river basins.

description: There are three primary datasets used in this work.These were obtained from Dr. Guohuan Su (co-author on the paper) . 1. Phylogenetic distance data sets between all fish species in the US. 2. Morphological traits dataset that list 10 traits information of fish species. 3. Occurrence dataset that list occurrence information of fish species in HUC8 regions of the US There is one dataset that lists exotic species in the US. The entries for exotic species are removed from about datasets before analysis.
DOI: 10.14278/rodare.2086
title: Data publication: A network-based approach to identifying correlations between phylogeny, morphological traits and occurrence of fish species in US river basins.

description: There are three primary datasets used in this work.These were obtained from Dr. Guohuan Su (co-author on the paper) . 1. Phylogenetic distance data sets between all fish species in the US. 2. Morphological traits dataset that list 10 traits information of fish species. 3. Occurrence dataset that list occurrence information of fish species in HUC8 regions of the US There is one dataset that lists exotic species in the US. The entries for exotic species are removed from about datasets before analysis.
DOI: 10.25625/glhhhu/odzvm3
title: Ergebnisbericht der ersten Studie.docx

description: :unav
DOI: 10.25625/glhhhu
title: Ergebnisbericht Studie 1

description: Ergebnisbericht Studie 1
DOI: 10.25625/6rw46b/2elptb
title: Befragungsergebnisse_LokalesInformationsverhalten.docx

description: :unav
DOI: 10.25625/6rw46b/dsxkdd
title: Mastermatrix_V30_131021_Land.xlsx

description: :unav
DOI: 10.5683/sp2/9xvonu
title: LAPOP: Uruguay 2010

description: The Latin American Public Opinion Project (LAPOP) is an academic institution hosted by Vanderbilt University that began with the study of democratic values in Costa Rica, but today carries out surveys in much of Latin America, Canada, the United States, and the Caribbean. In 2004, LAPOP established the AmericasBarometer as multi-country, regularly conducted survey of democratic values and behaviors in the Americas, and the first round included voting-age respondents from 11 countries. LAPOP collected opinions on major problems facing the country and community, threats to security, attitudes towards the country's political system, and trust in government institutions. Also measured were respondents' participation in community organizations, attitudes towards government critics, voting behavior, confidence in local government, and the prevalence of crime. Demographic information collected includes nationality, ethnicity, native language, age, gender, education level, occupation, religion, and whether the respondent lives in an urban or rural area.
DOI: 10.25625/6rw46b/tpmbbi
title: Stichprobengröße_Einzelsegmente.xlsx

description: :unav
DOI: 10.25625/6rw46b/dnhm1w
title: Mastermatrix_V30_131021_Gesamt.xlsx

description: :unav
DOI: 10.25625/6rw46b/btq26f
title: Ergebnispräsentation.pptx

description: :unav
DOI: 10.25625/6rw46b/qznsfk
title: Mastermatrix_V30_131021_Stadt.xlsx

description: :unav
DOI: 10.25625/6rw46b
title: Nutzerbefragung

description: Analyse und Ergebnisse der quantiativen Nutzerbefragung
DOI: 10.5281/zenodo.5770455
title: Dataset for AlphaDesign: A de novo protein design framework based on AlphaFold

description: This dataset consists of output data from the work reported in: Jendrusch, M., Korbel, J. O., & Sadiq, S. K. (2021). AlphaDesign: A de novo protein design framework based on AlphaFold. bioRxiv.
DOI: 10.5281/zenodo.5770456
title: Dataset for AlphaDesign: A de novo protein design framework based on AlphaFold

description: This dataset consists of output data from the work reported in: Jendrusch, M., Korbel, J. O., & Sadiq, S. K. (2021). AlphaDesign: A de novo protein design framework based on AlphaFold. bioRxiv.
DOI: 10.5281/zenodo.4548256
title: Dataset for the paper, Single nucleotide polymorphism induces divergent dynamic patterns in CYP3A5: a microsecond scale biomolecular simulation of variants identified in Sub-Saharan African populations

description: The dataset contains data files from the molecular dynamics simulation from different variants of CYP3A5. Instructions are described in `README.md` file to reproduce the analysis and run the jupyter notebook.
DOI: 10.5281/zenodo.4548257
title: Dataset for the paper, Single nucleotide polymorphism induces divergent dynamic patterns in CYP3A5: a microsecond scale biomolecular simulation of variants identified in Sub-Saharan African populations

description: The dataset contains data files from the molecular dynamics simulation from different variants of CYP3A5. Instructions are described in `README.md` file to reproduce the analysis and run the jupyter notebook.
DOI: 10.5281/zenodo.4643780
title: Helical protein phi/psi angle dataset

description: This is a dataset of only helical protein structures' Φ and Ψ angles. Please refer to this GiHub repository and this paper to understand how this dataset was generated and how it was used to perform <em>de novo </em>protein backbone design.
DOI: 10.5281/zenodo.4643781
title: Helical protein phi/psi angle dataset

description: This is a dataset of only helical protein structures' Φ and Ψ angles. Please refer to this GiHub repository and this paper to understand how this dataset was generated and how it was used to perform <em>de novo </em>protein backbone design.
DOI: 10.5281/zenodo.4293817
title: Assessing SIRAH's Capability to Simulate Intrinsically Disordered Proteins and Peptides

description: This dataset contains the structures, topologies, and trajectory files of coarse-grained molecular dynamics simulations of five Intrinsically Disordered Proteins (IDPs). We explored the dynamics of α-synuclein (randomly generated conformers), p31-43(PDB is: 6QAX), PaaA2 antitoxin (PDB id:3ZBE), Amyloid-beta 1-40 (PDB id: 2FLM), and Insulin C-peptide (PDB id: 1T0C) using the SIRAH force field running with the Gromacs 18.4 under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Briefly, simulations were performed in triplicate for 5 μs at 300 K and 1 atm in the NPT ensemble. We used a time-step of 20 fs, a direct cutoff for non-bonded interactions of 1.2 nm, and Particle Mesh Ewald summation for long-range electrostatics. For α-synuclein and p31-43, initial conformations were obtained from models built on arbitrary conformations and heated up to 340 K. For PaaA2 antitoxin, Amyloid-beta 1-40, and Proinsulin C-peptide, three different NMR conformers were arbitrarily selected. The information is divided into five tar files containing each system's data (only protein coordinates are reported). Additionally, the Sirah Tools' tcl script with macros for selections and analyses is also included. Please visit http://www.sirahff.com for step-by-step tutorials on running and analyzing CG simulations with SIRAH. To take a quick look at the trajectories: 1- Untar the tar file of interest 2- Open the trajectory on VMD using the command line: vmd "your_protein".psf "your_protein".xtc -e sirah_vmdtk.tcl <br> Note that using the tcl script you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset contains simulations associated to a manuscript with the same title and by the same authors. For questions, kindly contact Florencia Klein (fklein@pasteur.edu.uy), Exequiel Barrera (ebarrera@pasteur.edu.uy), or Sergio Pantano (spantano@pasteur.edu.uy).
DOI: 10.5281/zenodo.4293818
title: Assessing SIRAH's Capability to Simulate Intrinsically Disordered Proteins and Peptides

description: This dataset contains the structures, topologies, and trajectory files of coarse-grained molecular dynamics simulations of five Intrinsically Disordered Proteins (IDPs). We explored the dynamics of α-synuclein (randomly generated conformers), p31-43(PDB is: 6QAX), PaaA2 antitoxin (PDB id:3ZBE), Amyloid-beta 1-40 (PDB id: 2FLM), and Insulin C-peptide (PDB id: 1T0C) using the SIRAH force field running with the Gromacs 18.4 under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Briefly, simulations were performed in triplicate for 5 μs at 300 K and 1 atm in the NPT ensemble. We used a time-step of 20 fs, a direct cutoff for non-bonded interactions of 1.2 nm, and Particle Mesh Ewald summation for long-range electrostatics. For α-synuclein and p31-43, initial conformations were obtained from models built on arbitrary conformations and heated up to 340 K. For PaaA2 antitoxin, Amyloid-beta 1-40, and Proinsulin C-peptide, three different NMR conformers were arbitrarily selected. The information is divided into five tar files containing each system's data (only protein coordinates are reported). Additionally, the Sirah Tools' tcl script with macros for selections and analyses is also included. Please visit http://www.sirahff.com for step-by-step tutorials on running and analyzing CG simulations with SIRAH. To take a quick look at the trajectories: 1- Untar the tar file of interest 2- Open the trajectory on VMD using the command line: vmd "your_protein".psf "your_protein".xtc -e sirah_vmdtk.tcl <br> Note that using the tcl script you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset contains simulations associated to a manuscript with the same title and by the same authors. For questions, kindly contact Florencia Klein (fklein@pasteur.edu.uy), Exequiel Barrera (ebarrera@pasteur.edu.uy), or Sergio Pantano (spantano@pasteur.edu.uy).