cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11072818
title: iGEM: a model system for team science and innovation

description: This dataset is extracted from the international Genetically Engineered Machine (iGEM) competition between years 2008 and 2018, and can be used as a model system for studying team science and innovation. It is described at length in this article.

The dataset encompass detailed records from the iGEM competition, capturing various aspects of team participation and achievements. Specifically, the Team Information dataset (teams_table.csv) provides insights into team characteristics and achievements, including medal status and region of origin. User Information (users_table.csv) offers a look into individual participants, detailing their roles in the team. Awards Information (awards_table.csv) and Medal Criteria (medals_criteria.csv) lay out the awards teams have garnered and the standards for medal attainment. The BioBricks Information (biobricks_table.csv) corresponds to the BioBrick sequences associated with each team, while Wiki Edits (wikis_table.csv) tracks the changes made by users on their team's (wiki) lab notebook. Finally, the Collaboration Network (collaboration_network.csv) corresponds to the weighted directed inter-team collaboration network collected using team mentions across team wikis.

In addition to the structured dataframes above, we provide in team_wikis_full_text.zip the full texts of the wiki pages from the digital laboratory notebooks collaboratively edited by iGEM teams in the forms of wiki instances. There is a folder for each year from 2008-2018 and within which there are individual folders for each team. Each team folder has a file denoting the pagelist and two files for each page. One file is the html content, and the other the text content, extracted using the "KeepEverythingExtractor" option in the boilerpipe.extract library for processing and removing boilerplate content after webscraping.
DOI: 10.5281/zenodo.11654383
title: Long pulse surface NMR

description: Data set for the paper: Feasibility of surface nuclear magnetic resonance with absurdly long excitation pulses
DOI: 10.5281/zenodo.12726686
title: Spatiotemporal Upscaling of Sparse Air-Sea pCO2 Data via Physics-Informed Transfer Learning

description: Global measurements of ocean pCO2 are critical to monitor and understand changes in the global carbon cycle. However, pCO2 observations remain sparse as they are mostly collected on opportunistic ship tracks. Several approaches, especially based on machine learning, have been used to upscale and extrapolate sparse point data to dense global estimates based on globally available input features. However, those estimates tend to exhibit spatially heterogeneous performance. As a result, we propose a physics-informed transfer learning workflow to generate dense pCO2 estimates. The model is initially trained on synthetic Earth system model data, and then adjusted (using transfer learning) to the actual sparse SOCAT observational data, thus leveraging both the spatial and temporal correlation pre-learned on physically-informed Earth system ensembles. Compared to the benchmark upscaling of SOCAT point-wise data on baseline models, our transfer learning methodology shows a major improvement of up to 30-52%. Our strategy thus presents a new monthly global pCO2 estimates that spans for 35 years between 1982 and 2017.
DOI: 10.5281/zenodo.13279718
title: Deep Learning Neural Network Development for the Classification of Bacteriocin Sequences Produced by Lactic Acid Bacteria

description: This project contains the following underlying data:

      Software-Related Files

               ·         BacLABNet_script.ipynb (Deep Learning Neural Network for classification of Bacteriocin Sequences) 

               ·         embed_proteins.py (Recurrent Neural Network to obtained the embedding vectors)

               ·         model_I22.h5 (This file contains the trained weights of the trained model)

               ·         model_I22.json (This file contains the structure of the trained model)

               ·         rnn_gru.pt (Initial weights of the Recurrent Neural Network to obtain embedding vectors)

               ·         List_kmers.csv (List of 5-mers and 7-mers obtained from dataset after it filtered sequences shorter than 50 aa and                           longer than 2000 aa)

             

      Files Used for Training, Testing, and Validation of the Neural Network

               ·         data_nonBacLAB.csv (25000 nonBacLAB amino acid sequences retrieved from Uniprot)

               ·         data_BacLAB.csv (24964 BacLAB amino acid sequences retrieved from Uniprot)

     

       Additional Files

                ·         data_BacLAB_and_nonBacLAB.csv (Combination of sequences from data_BacLAB.csv and data_nonBacLAB.csv)

                 ·         all k.mers list.xlsx (Table of all k-mers obtained for k=3,5,7,15,20)

 

Note: Codes are additionally available on GitHub. 

Data are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication)(http://creativecommons.org/publicdomain/zero/1.0/)
DOI: 10.5281/zenodo.13793352
title: Code for 'Revealing the Local Time Structure of the Alfven Radius and travel times in Jupiter's magnetosphere'
DOI: 10.5281/zenodo.7670784
title: Smart City Tracker: A living archive of smart city prevalence

description: An interactive platform where users can track and explore local governments' smart city implementation in the United States.
DOI: 10.5281/zenodo.7790448
title: Brazilian Starter Data Kit Update to Support the Paper "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage"

description: This dataset presents updates on the Brazilian starter data kit, considering current load profile data and specific renewable energy sources production, using public data from official Brazilian power system agents. The dataset contains the input data and respective files to run OSeMOSYS and Flextool, including the utility-scale storage model. Additionally, this dataset contains the results of the study "Integrated Long-Term Expansion Planning and Short-Term Operation Assessment for Decarbonisation Pathways in Brazil Considering Utility-Scale Storage". This study evaluates the increase in variable renewable energy in Brazil and its integration with Storage systems.
DOI: 10.5281/zenodo.8368477
title: Hyperspectral Oblique Plane Microscopy - microparticles

description: Processed spectra data for microparticle classification and raw hyperspectral images from mixture of microparticles
DOI: 10.5883/bold:aai3227
title: Overview of Barcode Index Number - BOLD:AAI3227

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aai3230
title: Barcode Index Number BOLD:AAI3230

description: A cluster of barcode records associated with a Barcode Index Number(BIN). Each cluster is a proxy for a named or unnamed species. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.11609688
title: FACTORS AFFECTING THE ADOPTION OF BIG DATA ANALYTICS IN COMPANIES

description: ABSTRACT With the total quantity of data doubling every two years, the low price of computing and data storage, make Big Data analytics (BDA) adoption desirable for companies, as a tool to get competitive advantage. Given the availability of free software, why have some companies failed to adopt these techniques? To answer this question, we extend the unified theory of technology adoption and use of technology model (UTAUT) adapted for the BDA context, adding two variables: resistance to use and perceived risk. We used the level of implementation of these techniques to divide companies into users and non-users of BDA. The structural models were evaluated by partial least squares (PLS). The results show the importance of good infrastructure exceeds the difficulties companies face in implementing it. While companies planning to use Big Data expect strong results, current users are more skeptical about its performance.
DOI: 10.7910/dvn/on9xnd/ptmccv
title: NAVCO 1.3 Codebook List.pdf

description: NAVCO 1.3 Codebook and Variable Descriptions
DOI: 10.12770/070818f6-6520-49e4-bafd-9d4d0609bf7d
title: Site d'émissions de fluides, Mayotte, zone Fer à Cheval (C. Scalabrin, 2021)

description: Site d'émissions de fluides, Mayotte, zone Fer à Cheval (C. Scalabrin, 2021). Ce jeu de données présente les sites d'émission de fluides sous-marins détectés en acoustique active dans la zone du Fer à Cheval au large de Mayotte de mai 2019 à septembre 2021.
DOI: 10.14459/2022mp1686390
title: broccoli: Beautiful Robot C++ Code Library

description: Broccoli is a generic C++ header-only library for common algorithms used in robotics. It puts special emphasis on real-time capability, speed, and portability to real-time operating systems. The main motivation behind the development of broccoli is code reuse between robotic projects at the Chair of Applied Mechanics, TUM. Some parts of broccoli originate from the source code of the Lola Humanoid Robot project. Broccoli is not a complete robotics ecosystem (such as ROS); instead it is meant to provide a set of independently usable modules for rapid prototyping in robotic research projects. This work was supported by the German Research Foundation (DFG). Release v3.1.0
DOI: 10.15468/dl.9hpbrb
title: Occurrence Download

description: A dataset containing 229 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis racemus (Lynch, 1980)"
 ]
}

 The dataset includes 229 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039256-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25500/edata.bham.00001152
title: Diagnostic performance of ultrasound vs. ultrasound-guided FNAc in thyroid nodules: data from the ElaTION trial
DOI: 10.5063/f12j69b2
title: Data and code: Phenology varies with phylogeny but not by trophic level with climate change

description: Changes in the timing of species life history events, or phenologies, are widely associated with recent increases in temperatures globally. Understanding how these changes alter the synchrony of species interactions is of particular concern, given the potential for increasing asynchrony to alter community structures. Previous meta-analyses have found contrasting trends in how the phenologies of varying groups of species have changed and whether there is increasing phenological asynchrony. These studies differ in their species composition, types of interactions, and their use of single species time-series versus paired species data. We constructed a database of long-term time-series data from diverse phenological events. Using a Bayesian phylogenetic model, we tested for trends in phenological shifts across trophic levels and lineages, and the potential effects on synchrony. While on average we found species to have advanced in the timing of their phenological events, we did not observe any relative differences across groups of species, or consistent changes in synchrony across suites of interactions. The results of this study provide greater insight into the scope of variation of phenological changes and the continued challenges of predicting the direction and consequences of shifting phenologies in ecological communities.
DOI: 10.5067/viirs/vnp46a3.001
title: VIIRS/NPP Lunar BRDF-Adjusted Nighttime Lights Monthly L3 Global 15 arc-second Linear Lat Lon Grid
DOI: 10.5281/zenodo.4478251
title: The growth of COVID-19 scientific literature: A forecast analysis of different daily time series in specific settings

description: Submitted to The ISSI 2021 Conference. The conference is organised by KU Leuven in close collaboration with the university of Antwerp under the auspices of ISSI – the International Society for Informetrics and Scientometrics (http://www.issi-society.org/). We present a forecasting analysis on the growth of scientific literature related to COVID-19 expected for 2021. Considering the paramount scientific and financial efforts made by the research community to find solutions to end the COVID-19 pandemic, an unprecedented volume of scientific outputs is being produced. This questions the capacity of scientists, politicians and citizens to maintain infrastructure, digest content and take scientifically informed decisions. A crucial aspect is to make predictions to prepare for such a large corpus of scientific literature. Here we base our predictions on the ARIMA model and use two different data sources: the Dimensions and World Health Organization COVID-19 databases. These two sources have the particularity of including in the metadata information on the date in which papers were indexed. We present global predictions, plus predictions in three specific settings: by type of access (Open Access), by NLM source (PubMed and PMC), and by domain-specific repository (SSRN and MedRxiv). We conclude by discussing our findings.
DOI: 10.5281/zenodo.5602178
title: MetaFunc Databases: Kaiju database

description: MetaFunc is a computational pipeline that can take input reads and pass it through a pipeline that will then analyse host genes from the reads on one side, and microbiome taxonomies and gene ontology annotations on the other, and finally allowing for microbe-host gene correlations. This dataset contains databases used for analysing the microbiome component of the pipeline. Full description of the pipeline can be found at https://metafunc.readthedocs.io/en/latest/#.
description: Funding: Maurice and Phyllis Paykel Trust Gut Cancer Foundation (NZ), with support from the Hugh Green Foundation Colorectal Surgical Society of Australia and New Zealand (CSSANZ) The Health Research Council of New Zealand
description: {"references": ["Menzel, P., Ng, K.L., Krogh, A., 2016. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications 7, 11257. https://doi.org/10.1038/ncomms11257"]}
DOI: 10.5281/zenodo.7035874
title: Symbiodiniaceae dynamics in Pocillopora spp. during the 2015 to 2016 El Nino

description: Cleaned code after reviews
DOI: 10.5281/zenodo.8043971
title: in vivo characterization of research antibodies for Moesin, CD44, Midkine, and sFRP-1

description: in vivo characterization of research antibodies for Moesin, CD44, Midkine, and sFRP-1 in mouse brain homogenate from 9 month old WT and 5xFAD mice.
DOI: 10.5883/bold:aai3231
title: Overview of Barcode Index Number - BOLD:AAI3231

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.25711047.v1
title: LAI and GPP simulations for the study "Evaluation of leaf phenology of different vegetation types from local to hemispheric scale in CLM"

description: This dataset contains leaf area index (LAI) and gross primary productivity (GPP) data from GSWP3 forced Community Land Model versions 5.0 and 4.5 (CLM5.0 BGC and CLM4.5 BGC) simulations for each natural plant functional type (PFT). It was used in the analysis presented in Li et al., "Evaluation of leaf phenology of different vegetation types from local to hemispheric scale in CLM". The manuscript is currently under review at <i>Journal of Geophysical Research: Biogeosciences</i>. A preprint is available at 10.22541/essoar.168298711.15374345/v1. Please cite the published paper when it becomes available.<br>The PFTs included are:1. NETt: needleleaf evergreen temperate tree;2. NETb: needleleaf evergreen boreal tree;3. NDTb: needleleaf deciduous boreal tree;4. BETtrop: broadleaf evergreen tropical;5. BETt: broadleaf evergreen temperate tree;6. BDTtrop: broadleaf deciduous tropical tree;7. BDTt: broadleaf deciduous temperate tree;8. BDTb: broadleaf deciduous boreal tree;9. BES: broadleaf evergreen temperate shrub;10. BDSt: broadleaf deciduous temperate shrub;11. BDSb: broadleaf deciduous boreal shrub;12. C3a: C3 arctic grass;13. C3: C3 non-arctic grass;14. C4: C4 grass.
DOI: 10.6084/m9.figshare.25955851.v1
title: Data for [First Late Cambrian Paleomagnetic Results from the Oulongbuluke Terrane, Northern Tibetan Plateau: Implications for the Paleogeography of the Proto-Tethys Ocean]

description: Data for [First Late Cambrian Paleomagnetic Results from the Oulongbuluke Terrane, Northern Tibetan Plateau: Implications for the Paleogeography of the Proto-Tethys Ocean]
DOI: 10.6084/m9.figshare.26819323
title: Sustainability of catch-and-release fishing under climate change

description: This archive contains the model code and input for the simulation experiments, as well as their output data, published in: Ayllón, Blasco Hernanz, Nicola, Elvira, Almodóvar. 2024. Mediterranean brown trout catch-and-release recreational fisheries might not be sustainable under concurrent climate warming and hydrological change. Hydrobiologia.The archive consists of:1. One zip file containing the NetLogo code and all files needed to run the simulations: NetLogo extensions required by the software (six folders), input files to define the stream reach and perform the hydraulic modelling (two text files and two csv files), input files defining the temperature and flow time series for each of the three environmental scenarios simulated (three text files), one input file defining the setup of fishing scenarios (one text file), and a file defining the values of parameters that are not set up in the software’s interface (one nls file).2. One RData file containing the outputs of each simulation experiment performed in data frame format. A data frame with the experimental setup is also included.
DOI: 10.6084/m9.figshare.26954725
title: Supplementary Material for: Towards centrality evaluation of yearning symptoms for Prolonged Grief Disorder: a cross-cultural approach

description: Background: The new ICD-11 diagnosis of Prolonged Grief Disorder (PGD) is characterized by the prominent role of yearning as hallmark symptom. A secondary analysis of eight international datasets on PGD was conducted to evaluate this assumption. Additionally, cross-cultural comparison explored whether the centrality of yearning differs across world regions. 
Methods: Primary studies originated from German-speaking countries (n = 4 samples), other European countries and Israel (n = 3 samples), as well as China (n = 1 samples). Different PGD measures were used, including yearning and longing as symptoms. For the centrality assessment of yearning, PGD symptoms were ranked by their factor loadings from confirma-tory factor analyses (CFA), followed by statistical testing to determine significant differences between yearning and other symptoms of PGD in their factor loading estimates. Subsequently, ranking positions of yearning in three world regions (German-speaking, Other Europe-Israel, and China) were compared. Finally, proxy thresholds for individuals at high-risk states for PGD were defined for the different datasets, and sensitivity-specificity analyses of yearn-ing were performed. 
Results: Yearning was ranked high in five out of 12 models tested. In the German-speaking region, it was predominantly ranked among the most central symptoms; in the Other Europe-Israel region as well as China it tended to fall into the middle or lower rankings of symptom cen-trality. Sensitivity values were consistently high, while specificity values indicated moderate levels. 
Discussion: In line with previous research on the general outcomes of grief, the present study showed that yearning may be subject to a culture-specific distribution. Other central symptoms such as feeling as if a part of oneself died have also been shown to potentially play a central role in PGD across world regions. On the other hand, the sensitivity-specificity analyses revealed that yearning can be considered a significant (diagnostically highly sensi-tive) symptom for individuals in high-risk states for PGD, although it has only moderate spec-ificity (i.e., its absence does not necessarily indicate individuals experiencing normative grief). Nonetheless, a culture-sensitive approach to psychopathology should consider the cul-tural differences in the centrality of this symptom group. More research is needed to better understand the role of yearning and its determinants across world regions.
DOI: 10.6084/m9.figshare.27060091
title: Supplementary Material for: Microbial Isolates and Antimicrobial Resistance Patterns in Adults with Inborn Errors of Immunity: A Retrospective Longitudinal Analysis of Sputum Cultures

description: Introduction: Individuals with inborn errors of immunity (IEI) are at increased risk of respiratory infection and frequently receive prolonged broad-spectrum antibiotics, leading to antibiotic resistance. To identify respiratory pathogens and antibiotic resistance patterns in IEI patients.
Methods: We retrospectively studied 36 IEI patients with positive bacterial growth in sputum cultures between 2014 and 2023. Data covered hospitalizations, respiratory infections, yearly antibiotic prescriptions, past sputum cultures, and antibiotic sensitivities. Patients with primary ciliary dyskinesia (PCD) and bronchiectasis served as a control group.
Results: A total of 314 sputum cultures were analyzed from patients with IEI, alongside 585 cultures from individuals with PCD, and 113 cultures from patients with bronchiectasis. Patients with IEI had a median age of 23.5 years, with 61% male. The study compared the differences in bacterial isolates from sputum cultures and antibiotic resistance between patients with IEI and the control groups. The most common bacterial isolates across all groups were Haemophilus influenzae (159 isolates in IEI vs. 314 in PCD and 26 in bronchiectasis), Pseudomonas aeruginosa, and Streptococcus pneumoniae. In IEI patients, 992 symptomatic respiratory exacerbations and 43 pneumonia-related hospitalizations were recorded. Notably, Haemophilus influenzae in IEI patients showed high resistance rates to cefuroxime (82%), amoxicillin/clavulanic acid (66%), trimethoprim/sulfamethoxazole (59%), and ampicillin/sulbactam (49%). Pseudomonas aeruginosa in IEI patients displayed significant resistance to ciprofloxacin (85%), ceftazidime (42%), and aminoglycosides (23-33%). Additionally, all Streptococcus pneumoniae isolates in IEI patients were tetracycline-resistant, with high resistance rates to penicillin, clindamycin, and erythromycin. It's essential to highlight the substantial resistance of common pathogens to oral antibiotics. In contrast, the control groups exhibited lower resistance rates across all bacterial isolates.
Conclusion: Antimicrobial resistance is a growing concern among vulnerable IEI patients. We suggest conducting similar investigations in other regions to address this issue. The findings should inform future infection management guidelines for IEIs.
DOI: 10.5883/bold:aai3237
title: Overview of Barcode Index Number - BOLD:AAI3237

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aai3239
title: Overview of Barcode Index Number - BOLD:AAI3239

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aai3240
title: Barcode Index Number BOLD:AAI3240

description: A cluster of barcode records associated with a Barcode Index Number(BIN). Each cluster is a proxy for a named or unnamed species. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5883/bold:aai3249
title: Overview of Barcode Index Number - BOLD:AAI3249

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.