cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14404406
title: Additional file 5 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 5 Results of GO/pathway term network analysis (ClueGO) associated with down-regulated differentially expressed genes (DEGs) of the Warm & Normoxic (WN) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.5281/zenodo.4682374
title: Materials: Requirements Engineering for Machine Learning: A Systematic Mapping Study

description: Machine learning (ML) has become a core feature for today's real-world applications, making it a trending topic for the software engineering community. Requirements Engineering (RE) is no stranger to this and its main conferences have included workshops aiming at discussing RE in the context of ML. However, current research on the intersection between RE and ML mainly focuses on using ML techniques to support RE activities rather than on exploring how RE can improve the development of ML-based systems. This paper concerns a systematic mapping study aiming at characterizing the publication landscape of RE for ML-based systems, outlining research contributions and contemporary gaps for future research. In total, we identified 35 studies that met our inclusion criteria. We found several different types of contributions, in the form of analyses, approaches, checklists and guidelines, quality models, and taxonomies. We discuss gaps by mapping these contributions against the RE topics to which they were contributing and their type of empirical evaluation. We also identified quality characteristics that are particularly relevant for the ML context (e.g., data quality, explainability, fairness, safety, and transparency). Main reported challenges are related to the lack of validated RE techniques, the fragmented and incomplete understanding of NFRs for ML, and difficulties in handling customer expectations. There is a need for future research on the topic to reveal best practices and to propose and investigate approaches that are suitable to be used in practice.
DOI: 10.5281/zenodo.4682373
title: Materials: Requirements Engineering for Machine Learning: A Systematic Mapping Study

description: Machine learning (ML) has become a core feature for today's real-world applications, making it a trending topic for the software engineering community. Requirements Engineering (RE) is no stranger to this and its main conferences have included workshops aiming at discussing RE in the context of ML. However, current research on the intersection between RE and ML mainly focuses on using ML techniques to support RE activities rather than on exploring how RE can improve the development of ML-based systems. This paper concerns a systematic mapping study aiming at characterizing the publication landscape of RE for ML-based systems, outlining research contributions and contemporary gaps for future research. In total, we identified 35 studies that met our inclusion criteria. We found several different types of contributions, in the form of analyses, approaches, checklists and guidelines, quality models, and taxonomies. We discuss gaps by mapping these contributions against the RE topics to which they were contributing and their type of empirical evaluation. We also identified quality characteristics that are particularly relevant for the ML context (e.g., data quality, explainability, fairness, safety, and transparency). Main reported challenges are related to the lack of validated RE techniques, the fragmented and incomplete understanding of NFRs for ML, and difficulties in handling customer expectations. There is a need for future research on the topic to reveal best practices and to propose and investigate approaches that are suitable to be used in practice.
DOI: 10.5281/zenodo.4682379
title: On the Discoverability of npm Package Vulnerabilities in Node.js Projects

description: This package contains the scripts used for our approach in the manuscript "On the Discoverability of npm Package Vulnerabilities in Node.js Projects." For more information on how to understand the folder structure, please read the README.md.
DOI: 10.5281/zenodo.4682400
title: On the Discoverability of npm Package Vulnerabilities in Node.js Projects

description: This package contains the scripts used for our approach in the manuscript "On the Discoverability of npm Package Vulnerabilities in Node.js Projects." For more information on how to understand the folder structure, please read the README.md.
DOI: 10.6084/m9.figshare.14403962
title: gview-all-5CC408DE772C5D536F76BFEF6073B258.zip

description: Blast Atlas alignment of pESI-like plasmids assambled from illumina sequences of whole genomes of Salmonella Infantis isolated from poultry samples in Ecuador
DOI: 10.6084/m9.figshare.14403962.v1
title: gview-all-5CC408DE772C5D536F76BFEF6073B258.zip

description: Blast Atlas alignment of pESI-like plasmids assambled from illumina sequences of whole genomes of Salmonella Infantis isolated from poultry samples in Ecuador
DOI: 10.6084/m9.figshare.14404447
title: Additional file 2 of A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants

description: Additional file 2: Table S1. GEO accession numbers for all the datasets analysed.
DOI: 10.6084/m9.figshare.14404450
title: Additional file 3 of A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants

description: Additional file 3: Table S2. Name, coordinates (Hg38) and PSI mean value and standard error for the 25 exons of the basal B-specific signature in Basal A and Basal B cancer cells and patients. The difference in splicing levels between basal B and basal A is shown as deltaPSI.
DOI: 10.6084/m9.figshare.14404450.v1
title: Additional file 3 of A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants

description: Additional file 3: Table S2. Name, coordinates (Hg38) and PSI mean value and standard error for the 25 exons of the basal B-specific signature in Basal A and Basal B cancer cells and patients. The difference in splicing levels between basal B and basal A is shown as deltaPSI.
DOI: 10.6084/m9.figshare.14404447.v1
title: Additional file 2 of A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants

description: Additional file 2: Table S1. GEO accession numbers for all the datasets analysed.
DOI: 10.6084/m9.figshare.14403971
title: Supplementary materials of paper "Antifungal mechanism of Bacillus amyloliquefaciens strain GKT04 against Fusarium wilt revealed using genomic and transcriptomic analysis"

description: Description on the transciptomic data of Bacillus amyloliquefaciens GKT04, a strain isolated from banana root, which showed high inhibitory activity against FOC4.
DOI: 10.6084/m9.figshare.14403971.v1
title: Supplementary materials of paper "Antifungal mechanism of Bacillus amyloliquefaciens strain GKT04 against Fusarium wilt revealed using genomic and transcriptomic analysis"

description: Description on the transciptomic data of Bacillus amyloliquefaciens GKT04, a strain isolated from banana root, which showed high inhibitory activity against FOC4.
DOI: 10.6084/m9.figshare.14404400.v1
title: Additional file 3 of The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

description: Additional file 3 Results of GO/pathway term network analysis (ClueGO) associated with up-regulated differentially expressed genes (DEGs) of the Warm & Normoxic (WN) treatment group. Listed are the significantly enriched Gene Ontology (GO) terms, and KEGG or Reactome pathways (hypergeometric test p
DOI: 10.6084/m9.figshare.14404370.v1
title: Additional file 5 of Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus)

description: Additional file 5: Table S1. Primers sequences used in the study. AP4 (1 and 2) are for the detection of Pir-VP genes. Vpir A is for the detection of Pir-A gene while Vpir B is for the amplification of Pir-B gene. Length represents the length of the amplicon generated by each pair of primers. Table S2. ILI’s genome protein annotation using Prokka against the NCBI’s database. Table S3. ILI’s large plasmid proteins predicted by Prokka against the NCBI’s database with their corresponding functions and ID. The number of ASVs detected per sample is plotted on the axis of Observed OTUs. Function is assigned when hits with an e-value &lt; 1e- 06 were obtained. Table S4. Genomes used to for genomic similarity analysis. The genomic identity between ILI and the selected genome is shown in the last column of the table. Table S5. GenBank accession numbers and genomic characteristics of genomes used for the phylogenetic reconstruction of the ILI strain. Table S6. DDH, ANIb and TETRA values. In silico DNA-DNA hybridization (DDH) was calculated only between the ILI strain and the other evaluated strains. ANIb and TETRA were calculated for all possible comparisons. A heatmap representation of the values can be observed on Figure 3. Table S7. Virulence factors identified in the secretion systems of the strain V. diabolicus ILI. They were compared with the genomes of the V. parahaemolyticus RIMD 2210633 strain, the V. parahaemolyticus NCKU TN S02 strain, the V. parahaemolyticus BA94C2 strain and the V. diabolicus FDA 105 strain. The table includes the respective name of the genes for each genome, the gene product, the percent identity, and the percent coverage. Comparisons based on percentage of identity and coverage included are shown in key color.
DOI: 10.6084/m9.figshare.14403983.v1
title: Additional file 13 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

description: Additional file 12: Table S6. Primer sequences specific to each crAss-like phage strains detected following sequencing of subject ID: 924 faeces post fermentation.
DOI: 10.6084/m9.figshare.14403980.v1
title: Additional file 12 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

description: Additional file 11: Table S5. Partial and complete genomic contigs of crAss-like phages. (XLS 9 kb)
DOI: 10.6084/m9.figshare.14403974.v1
title: Additional file 10 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

description: Additional file 9: Table S4. Summary of ΦcrAss001 and ΦcrAss002 characteristics.
DOI: 10.6084/m9.figshare.14403980
title: Additional file 12 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

description: Additional file 11: Table S5. Partial and complete genomic contigs of crAss-like phages. (XLS 9 kb)
DOI: 10.6084/m9.figshare.14403977
title: Additional file 11 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

description: Additional file 10: Sequences of non-redundant contigs in FASTA format.
DOI: 10.6084/m9.figshare.14403974
title: Additional file 10 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

description: Additional file 9: Table S4. Summary of ΦcrAss001 and ΦcrAss002 characteristics.
DOI: 10.5281/zenodo.4681883
title: Posts about GME in Wallstreetbets and GME stock prices 2020-21

description: Temporally restricted access, for more information please contact with (rgvaliente at alumni.uoc.es). Dataset 1: Posts_GME_Wallstreetbets_2020-21 Posts en r/Wallstreetbets hechos durante el último año que mencionan a GME en su título, fecha y número de comentarios.<br> Columnas: Created_on Fecha, Title (título del post), Number_of_comments (número de comentarios).<br> Fuente: Reddit, la web en la que se crearon estos posts. Dataset 2: Stock_prices_GME_2020-21 Evolución diaria del precio de las acciones de GME durante el último año.<br> Columnas: High (máximo del día), Low (mínimo del día),Open (precio de la acción al abrir el mercado),Close (precio de la acción al cierre del mercado),Volume (volumen de acciones),Adj Close (precio de la acción ajustado por dividendos), Day_diff (diferencia entre apertura y cierre)<br> Fuente: Yahoo Finances, un agregador de precios de acciones.
DOI: 10.5281/zenodo.4681882
title: Posts about GME in Wallstreetbets and GME stock prices 2020-21

description: Temporally restricted access, for more information please contact with (rgvaliente at alumni.uoc.es). Dataset 1: Posts_GME_Wallstreetbets_2020-21 Posts en r/Wallstreetbets hechos durante el último año que mencionan a GME en su título, fecha y número de comentarios.<br> Columnas: Created_on Fecha, Title (título del post), Number_of_comments (número de comentarios).<br> Fuente: Reddit, la web en la que se crearon estos posts. Dataset 2: Stock_prices_GME_2020-21 Evolución diaria del precio de las acciones de GME durante el último año.<br> Columnas: High (máximo del día), Low (mínimo del día),Open (precio de la acción al abrir el mercado),Close (precio de la acción al cierre del mercado),Volume (volumen de acciones),Adj Close (precio de la acción ajustado por dividendos), Day_diff (diferencia entre apertura y cierre)<br> Fuente: Yahoo Finances, un agregador de precios de acciones.
DOI: 10.5281/zenodo.4682270
title: MOM6 Input dataset for SmartSim ML EKE Experiment

description: The Input dataset used for the MOM6 model augmented with a machine learning surrogate for the prediction of eddy kinetic energy.
DOI: 10.5281/zenodo.4682269
title: MOM6 Input dataset for SmartSim ML EKE Experiment

description: The Input dataset used for the MOM6 model augmented with a machine learning surrogate for the prediction of eddy kinetic energy.
DOI: 10.6084/m9.figshare.14404883
title: Supplementary Material for: Protective and Anti-Aging Effects of 5 Cosmeceutical Peptide Mixtures on Hydrogen Peroxide-Induced Premature Senescence in Human Skin Fibroblasts

description: Skin aging usually leads to the excessive deterioration of the dermal extracellular matrix, loss of antimicrobial function, loss of skin barrier function, and a series of inflammatory processes. Bioactive peptides have been widely used in cosmetics due to their protective effects on skin and efficient absorption. Combination of different peptides may lead to synergistic or antagonistic effects, so different formulas need to be designed and tested properly. In this study, 5 functional cosmeceutical peptides were tested on their individual and mixed activities to detect a suitable anti-aging and protective formula from our experiments. After the individual activity test, the optimal concentration is 200 μg/mL of carnosine for the superoxide dismutase (SOD) activity, 200 μg/mL of GHK peptide for the hydroxyproline (HYP) content activity, 100 μg/mL of acetyl tetrapeptide-5 for the angiotensin-converting enzyme 1 activity, 400 μg/mL of hexapeptide-11 for the HYP content activity, and 400 μg/mL of acetyl hexapeptide-3 for the catecholamine content activity. According to the optimal concentration of these 5 cosmeceutical peptides, 6 formulations of peptide mixtures were designed and tested for their anti-aging activities and protective effects against hydrogen peroxide-induced premature senescence in human skin fibroblasts. One of the cosmeceutical peptide mixtures (carnosine + acetyl tetrapeptide-5 + hexapeptide-11 + acetyl hexapeptide-3) significantly reduced the intracellular malondialdehyde and hydroxyl free radical contents and increased the HYP and human elastin contents as well as the enzymatic activities of SOD and glutathione peroxidase. Our study suggests that this formula of cosmeceutical peptide mixtures could be a promising agent for use in anti-aging and protective cosmetics.
DOI: 10.7931/kjtp-mn13
title: Home range use and habitat selection of Auckland Island Pigs
DOI: 10.6084/m9.figshare.12630665.v1
title: Interference Effects of Phonological Similarity in Word Production

description: This item include the behavioral data of the four experiments which explore the influence of phonolgocai/orthographical similarity on langauge production. It also include the matlab code which simulate the behavioral results with an incremental learning mechanism.
DOI: 10.6084/m9.figshare.12630665
title: Interference Effects of Phonological Similarity in Word Production

description: This item include the behavioral data of the four experiments which explore the influence of phonolgocai/orthographical similarity on langauge production. It also include the matlab code which simulate the behavioral results with an incremental learning mechanism.
DOI: 10.6084/m9.figshare.12630665.v3
title: Interference Effects of Phonological Similarity in Word Production

description: This item include the behavioral data of the four experiments which explore the influence of phonolgocai/orthographical similarity on langauge production. It also include the matlab code which simulate the behavioral results with an incremental learning mechanism.
DOI: 10.6084/m9.figshare.12630665.v2
title: Interference Effects of Phonological Similarity in Word Production

description: This item include the behavioral data of the four experiments which explore the influence of phonolgocai/orthographical similarity on langauge production. It also include the matlab code which simulate the behavioral results with an incremental learning mechanism.
DOI: 10.6084/m9.figshare.14403977.v1
title: Additional file 11 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

description: Additional file 10: Sequences of non-redundant contigs in FASTA format.
DOI: 10.6085/aa/marine_ltm.21.1
title: (:unkn)
DOI: 10.6085/aa/marine_ltm.22.1
title: (:unkn)
DOI: 10.6085/aa/marine_ltm.20.1
title: MARINe: Intertidal: MARINe Long-Term Monitoring Surveys: Publication Data: Latitudinal variation in long-term stability of North American rocky intertidal communities

description: This metadata record documents the Photo Plot and Temperature data for the Multi-Agency Rocky Intertidal Network (MARINe) Long-Term Monitoring surveys. These surveys are done throughout the year at sites ranging from Southeast Alaska to Southern California. The photo plot data are a subset of our full dataset available at https://doi.org/10.6085/AA/marine_ltm.12.4. Temperature measurements were collected using one of the following temperature loggers from Onset Computer Corp: TBI32-05+37, UTBI-001, UA-002-64, MX2201, MX2203). For a comprehensive dataset, please contact the data set owner(s). For more information about the data described in this metadata record, please visit pacificrockyintertidal.org.
DOI: 10.5281/zenodo.4682224
title: example perturbation free energy data

description: example perturbation free energy data used to show the usage of the simulation update scheme feature of the SMArt toolkit - available at https://github.com/drazen-petrov/SMArt data contains: GROMACS format: perturbation of a histone tail H3K4 lysine trimethylation mark bound to the Sp100C PHD finger
DOI: 10.5281/zenodo.4682223
title: example perturbation free energy data

description: example perturbation free energy data used to show the usage of the simulation update scheme feature of the SMArt toolkit - available at https://github.com/drazen-petrov/SMArt data contains: GROMACS format: perturbation of a histone tail H3K4 lysine trimethylation mark bound to the Sp100C PHD finger
DOI: 10.5281/zenodo.4682615
title: Flower surface wax chemicals in green gram help to stimulate oviposition in Spilosoma obliqua Walker (Lepidoptera: Arctiidae) within short distances

description: <strong>SUPPLEMENTARY MATERIAL</strong> <strong>Flower surface wax chemicals in green gram help to stimulate oviposition in <em>Spilosoma obliqua </em>Walker (Lepidoptera: Arctiidae) within short distances</strong>
DOI: 10.22011/strenda_db.fr1z67
title: Disease Variants of Human Δ1-Pyrroline-5-Carboxylate Reductase 2 (PYCR2)

description: Pyrroline-5-carboxylate reductase 2 (P5C reductase 2) (P5CR 2), Q96C36, null
DOI: 10.6084/m9.figshare.14405333
title: Supplementary Material for: Variable Learning Curve of Basic Rigid Bronchoscopy in Trainees

description: <b><i>Background:</i></b> Despite increased use of rigid bronchoscopy (RB) for therapeutic indications and recommendations from professional societies to use performance-based competency, an assessment tool has not been utilized to measure the competency of trainees to perform RB in clinical settings. <b><i>Objectives:</i></b> The aim of the study was to evaluate a previously developed assessment tool – <i>Rigid Bronchoscopy Tool for Assessment of Skills and Competence</i> (RIGID-TASC) – for determining the RB learning curve of interventional pulmonary (IP) trainees in the clinical setting and explore the variability of learning curve of trainees. <b><i>Methods:</i></b> IP fellows at 4 institutions were enrolled. After preclinical simulation training, all RBs performed in patients were scored by faculty using RIGID-TASC until competency threshold was achieved. Competency threshold was defined as unassisted RB intubation and navigation through the central airways on 3 consecutive patients at the first attempt with a minimum score of 89. A regression-based model was devised to construct and compare the learning curves. <b><i>Results:</i></b> Twelve IP fellows performed 178 RBs. Trainees reached the competency threshold between 5 and 24 RBs, with a median of 15 RBs (95% CI, 6–21). There were differences among trainees in learning curve parameters including starting point, slope, and inflection point, as demonstrated by the curve-fitting model. Subtasks that required the highest number of procedures (median = 10) to gain competency included ability to intubate at the first attempt and intubation time of &lt;60 s. <b><i>Conclusions:</i></b> Trainees acquire RB skills at a variable pace, and RIGID-TASC can be used to assess learning curve of IP trainees in clinical settings.