cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4813082
title: In silico saturation mutagenesis of cancer genes

description: Source data and code needed to reproduce figures and pipeline associated to this study:

In silico saturation mutagenesis of cancer genesFerran Muiños, Francisco Martinez-Jimenez, Oriol Pich, Abel Gonzalez-Perez, Nuria Lopez-BigasDOI: 10.1038/s41586-021-03771-1URL: https://www.nature.com/articles/s41586-021-03771-1

Repo to reproduce all the figures of the paper: https://github.com/bbglab/boostdm-analyses

Repo to reproduce the training and prediction pipeline of the paper: https://github.com/bbglab/boostdm-pipeline
DOI: 10.6084/m9.figshare.c.3721585_d23.v1
title: Additional file 7: of 
                     Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana

description: Gene ontology (GO) terms within biological processes that are significantly enriched amongst genes up-regulated in the expression profiling. Results of the GO enrichment analysis for up-regulated genes. (XLSX 328 kb)
DOI: 10.6084/m9.figshare.c.3721585_d23
title: Additional file 7: of 
                     Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana

description: Gene ontology (GO) terms within biological processes that are significantly enriched amongst genes up-regulated in the expression profiling. Results of the GO enrichment analysis for up-regulated genes. (XLSX 328 kb)
DOI: 10.17866/rd.salford.28035425
title: IoT Research and Innovation Lab - Smart Home System (IRIL-SHS)

description: Smart cities, businesses, workplaces, and even residences have all been converged by the Internet of Things (IoT). The types and characteristics of these devices vary depending on the industry 4.0 and have rapidly increased recently, especially in smart homes. These gadgets can expose users to serious cyber dangers because of a variety of computing constraints and vulnerabilities in the security-by-design concept. The smart home network testbed setup presented in this study is used to evaluate and validate the protection of the smart cyber-physical system. The context-aware threat intelligence and response model identifies the states of the aligned smart devices to distinguish between real-world typical and attack scenarios. It then dynamically writes specific rules for protection against potential cyber threats. The context-aware model is trained on the IoT Research and Innovation Lab - Smart Home System (IRIL-SHS) testbed dataset. The labelled dataset is utilized to create a random forest model, which is subsequently used to train and test the context-aware threat intelligence SHS model's effectiveness and performance. Finally, the model's logic is used to gain rules to be included in Suricata signatures and the firewall rulesets for the response system. Significant values of the measuring parameters were found in the results. The presented model can be used for the real-time security of smart home cyber-physical systems and develops a vision of security challenges for Industry 4.0.
DOI: 10.6084/m9.figshare.c.3721705_d6
title: Additional file 15 of Preservation affinity in consensus modules among stages of HIV-1 progression

description: List of the genes involved in the non–preserved category–1 meta-modules: “green” and “blue”. (XLSX 22.7 kb)
DOI: 10.6084/m9.figshare.c.3721705_d7.v1
title: Additional file 1 of Preservation affinity in consensus modules among stages of HIV-1 progression

description: List of genes expressed in different stages of HIVâ  1 infection. (XLSX 95.7 kb)
DOI: 10.6084/m9.figshare.c.3721705_d7
title: Additional file 1 of Preservation affinity in consensus modules among stages of HIV-1 progression

description: List of genes expressed in different stages of HIVâ  1 infection. (XLSX 95.7 kb)
DOI: 10.6084/m9.figshare.c.3721705_d8.v1
title: Additional file 2 of Preservation affinity in consensus modules among stages of HIV-1 progression

description: List of genes exclusively expressed in different stages of HIVâ  1 infection. (XLSX 21.1 kb)
DOI: 10.6084/m9.figshare.c.3721705_d8
title: Additional file 2 of Preservation affinity in consensus modules among stages of HIV-1 progression

description: List of genes exclusively expressed in different stages of HIVâ  1 infection. (XLSX 21.1 kb)
DOI: 10.6084/m9.figshare.c.3721705_d11.v1
title: Additional file 5 of Preservation affinity in consensus modules among stages of HIV-1 progression

description: List of acute stage genes involved in category-1 (acuteâ  chronic stage Pair) consensus module formation. (XLSX 23.0 kb)
DOI: 10.15468/dl.n79k65
title: Occurrence Download

description: A dataset containing 661 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argentina sphyraena Linnaeus, 1758",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 661 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038858-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3723010_d1.v1
title: Additional file 1: Supplemental Table. of Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients

description: Table S1: Patients data (RNA-Seq). (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3723010_d1
title: Additional file 1: Supplemental Table. of Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients

description: Table S1: Patients data (RNA-Seq). (XLSX 49 kb)
DOI: 10.15468/dl.54yps7
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Marasmiellus paspali (Petch) Singer, 1955"
 ]
}

 The dataset includes 13 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038860-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3723010_d2.v1
title: Additional file 2: Supplemental Datasets S1-S10. of Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients

description: Dataset S1: Complete RNA-Seq data. Dataset S2: EdgeR results. Dataset S3: Signature A expression data. Dataset S4: Signature B expression data. Dataset S5: Cluster I expression data. Dataset S6: Cluster II expression data. Dataset S7: Cluster III expression data. Dataset S8: Common cluster I / signature A genes. Dataset S9: Common cluster III / signature B genes. Dataset S10: PRECOG z-scores for signature A and B genes. (XLSX 6898 kb)
DOI: 10.57754/fdat.gx69f-9gs26
title: Gedichtkorpus Shakespeare / Cummings / Dickinson

description: The corpus consists of the poems "He fumbles at your soul", "next to of course god america I", and "Shall I compare thee to a summer's day" by Dickinson, Cummings and Shakespeare respectively, and is the basis of an analysis of the relation of notions of meaning in literary studies to the notion of meaning in formal semantics. Applying the tools from intensional semantics to the problem of finding meanings of fictional texts leads us to observe a new kind of intensional environment.
description: Research carried out in work package A02 of the SFB 833.
DOI: 10.6084/m9.figshare.c.3723010_d2
title: Additional file 2: Supplemental Datasets S1-S10. of Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients

description: Dataset S1: Complete RNA-Seq data. Dataset S2: EdgeR results. Dataset S3: Signature A expression data. Dataset S4: Signature B expression data. Dataset S5: Cluster I expression data. Dataset S6: Cluster II expression data. Dataset S7: Cluster III expression data. Dataset S8: Common cluster I / signature A genes. Dataset S9: Common cluster III / signature B genes. Dataset S10: PRECOG z-scores for signature A and B genes. (XLSX 6898 kb)
DOI: 10.6084/m9.figshare.c.3723112_d11.v1
title: Additional file 1: of An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)

description: Morphological character matrix of Amphidiscophora in Nexus format. (NEX 2.05 KB)
DOI: 10.6084/m9.figshare.c.3723103_d12.v1
title: Additional file 4: Table S3. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: Classification of genes according to their enriched expression in endocrine, acinar, or ductal cells. Expression levels were compared for each gene between endocrine, acinar, and ductal cells (pair-wise comparison with DEseq2). Classification was performed using the cut-off values of fold change &gt; 4 and adjusted P &lt; 0.05. The enrichment is given for each gene as Log2 of fold change and with the adjusted P value. (XLSX 2192 kb)
DOI: 10.6084/m9.figshare.c.3723103_d12
title: Additional file 4: Table S3. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: Classification of genes according to their enriched expression in endocrine, acinar, or ductal cells. Expression levels were compared for each gene between endocrine, acinar, and ductal cells (pair-wise comparison with DEseq2). Classification was performed using the cut-off values of fold change &gt; 4 and adjusted P &lt; 0.05. The enrichment is given for each gene as Log2 of fold change and with the adjusted P value. (XLSX 2192 kb)
DOI: 10.6084/m9.figshare.c.3723103_d13.v1
title: Additional file 5: Table S4. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: Genes presenting conserved endocrine expression. The ZMH excel page shows the genes with endocrine-enriched expression in zebrafish, mice and human. The ZM, ZH and HM excel pages show genes with endocrine-enriched expression in two species (ZM: zebrafish and mice; ZH: zebrafish and human; HM: human and mice). The tables give the expression mean in endocrine cells (Normalized counts) and the enrichment (FC: fold change) in the three species. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.c.3723112_d11
title: Additional file 1: of An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida)

description: Morphological character matrix of Amphidiscophora in Nexus format. (NEX 2.05 KB)
DOI: 10.6084/m9.figshare.c.3723103_d13
title: Additional file 5: Table S4. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: Genes presenting conserved endocrine expression. The ZMH excel page shows the genes with endocrine-enriched expression in zebrafish, mice and human. The ZM, ZH and HM excel pages show genes with endocrine-enriched expression in two species (ZM: zebrafish and mice; ZH: zebrafish and human; HM: human and mice). The tables give the expression mean in endocrine cells (Normalized counts) and the enrichment (FC: fold change) in the three species. (XLSX 123 kb)
DOI: 10.6084/m9.figshare.c.3723103_d15.v1
title: Additional file 7: Table S5. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: Genes presenting conserved exocrine expression. The ZMH excel page shows the genes with exocrine-enriched expression in zebrafish, mice and human. The ZM, ZH and HM excel pages show genes with endocrine-enriched expression in two species (ZM: zebrafish and mice; ZH: zebrafish and human; HM: human and mice). The tables give the expression mean in endocrine cells (Normalized counts) and the enrichment (FC: fold change) in the three species. (XLSX 101 kb)
DOI: 10.6084/m9.figshare.c.3723103_d16.v1
title: Additional file 8: Table S6. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: List of endocrine-enriched genes with an expression level above 100 counts in embryonic endocrine cells at 27 hpf. List of 911 genes with endocrine-enriched expression in adult and showing an expression level above 100 Normalized counts. Gene expression is provided for the three replicates (selection of pancreatic cells at 27 hpf from Tg(pax6:GFP)) as well as the mean expression level. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.c.3723103_d15
title: Additional file 7: Table S5. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: Genes presenting conserved exocrine expression. The ZMH excel page shows the genes with exocrine-enriched expression in zebrafish, mice and human. The ZM, ZH and HM excel pages show genes with endocrine-enriched expression in two species (ZM: zebrafish and mice; ZH: zebrafish and human; HM: human and mice). The tables give the expression mean in endocrine cells (Normalized counts) and the enrichment (FC: fold change) in the three species. (XLSX 101 kb)
DOI: 10.6084/m9.figshare.c.3723103_d16
title: Additional file 8: Table S6. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: List of endocrine-enriched genes with an expression level above 100 counts in embryonic endocrine cells at 27 hpf. List of 911 genes with endocrine-enriched expression in adult and showing an expression level above 100 Normalized counts. Gene expression is provided for the three replicates (selection of pancreatic cells at 27 hpf from Tg(pax6:GFP)) as well as the mean expression level. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.c.3723103_d17.v1
title: Additional file 9: Table S7. of Transcriptome analysis of pancreatic cells across distant species highlights novel important regulator genes

description: Classification of endocrine-enriched genes according to their expression in alpha, beta, and delta endocrine cells. Gene expression ratio was calculated for all pair-wise comparison (alpha versus beta: A&B; beta versus delta: B&D and alpha versus delta: A&D). The enrichment is given as Log2 fold change with the adjust value. Classification was done using the cut-off threshold of Log2 fold change &gt; 2 and adjusted P &lt; 0.05. (XLSX 265 kb)
DOI: 10.6084/m9.figshare.c.3723820_d1.v1
title: Additional file 10 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Module and pathway enrichments for variable and invariable gene sets (Fisherâ  s exact test q â ¤ 0.25). (CSV 7 kb)
DOI: 10.6084/m9.figshare.c.3723766_d16.v1
title: Additional file 24: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Table of immuneâ  fibrotic axis consensus genes. (TSV 27 kb)
DOI: 10.6084/m9.figshare.c.3723820_d1
title: Additional file 10 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Module and pathway enrichments for variable and invariable gene sets (Fisherâ  s exact test q â ¤ 0.25). (CSV 7 kb)
DOI: 10.57754/fdat.1syzb-6mb88
title: Gedichtkorpus Emily Dickinson

description: The corpus of poems by Emily Dickinson forms the basis of annotation and analysis in the project "Interpreability in Context". The poems are available upon request.
description: Research carried out in work package A02 of the SFB 833.
DOI: 10.6084/m9.figshare.c.3723766_d16
title: Additional file 24: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Table of immuneâ  fibrotic axis consensus genes. (TSV 27 kb)
DOI: 10.6084/m9.figshare.c.3723766_d17.v1
title: Additional file 25: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Node attribute file for lung network (Fig.Â 3). (TXT 17 kb)
DOI: 10.6084/m9.figshare.c.3723766_d17
title: Additional file 25: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Node attribute file for lung network (Fig.Â 3). (TXT 17 kb)
DOI: 10.6084/m9.figshare.c.3723766_d18.v1
title: Additional file 26: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Edge list for lung network (Fig.Â 3). (TXT 27 kb)
DOI: 10.6084/m9.figshare.c.3723829_d1.v1
title: Additional file 10: of Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity

description: Table S5. DEGs expressed in both root and leaf tissues and their predicted function. Only significantly (p, FDRâ
DOI: 10.6084/m9.figshare.c.3723766_d18
title: Additional file 26: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Edge list for lung network (Fig.Â 3). (TXT 27 kb)
DOI: 10.6084/m9.figshare.c.3723820_d2.v1
title: Additional file 11 of Proteobacteria explain significant functional variability in the human gut microbiome

description: Module and pathway enrichments for variable/high-PD and invariable/low-PD gene sets (Fisherâ  s exact test qâ ¤0.25). (CSV 2 kb)
DOI: 10.6084/m9.figshare.c.3723766_d19.v1
title: Additional file 27: of A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis

description: Node attribute file for differential lung network (Fig.Â 4). (TXT 4 kb)
DOI: 10.15468/dl.eh64z3
title: Occurrence Download

description: A dataset containing 565 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argyropelecus aculeatus Valenciennes, 1850",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1900",
 "CoordinateUncertaintyInMeters is less than or equal to 10000"
 ]
}

 The dataset includes 565 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038861-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14283869
title: UCI Adult (Version 2) - Artificial Prevalence Protocol (APP) Test Indices

description: Dataset
Adult


# data points
45,222


# non-sensitive features (preprocessed)
95


sensitive attribute
sex


S = 1
Male


Pr(S=1)
0.675


target variable
income/class


Y = ⊕
>$50,000


Pr(Y=⊕)
0.248




The UCI Adult dataset is loaded using fetch_openml from scikit-learn (version 2). To ensure reproducibility, the dataset is split into three equal subsets using stratified sampling based on the joint distribution of (S, Y) and a random seed of 0.

The indices stored in adult_D1.indices, adult_D2.indices, and adult_D3.indices refer to the original dataset's instances after any instances containing missing values have been removed. The indices in adult_D3_protocol.indices correspond to the instances in the LabelledCollection constructed using the indices from adult_D3.indices.

Categorical features are converted to dummy variables, and numerical features are standardised using a standard scaler.




Feature Type
Features


Categorical
workclass, education, marital-status, occupation, race, native-country


Numerical
age, capital-gain, capital-loss, hours-per-week






 

The Artificial Prevalence Protocol (APP) is applied to vary the distribution of the sensitive attribute across 11 prevalence values: Pr(s|⊖) ∈ {0.0, 0.1, ..., 0.9, 1.0}. To minimise variance in the evaluation results, 500 samples are drawn repeatedly under the protocol. This entire process is repeated 10 times, consistently using a random seed of 0 for reproducibility.


This work has been funded by the QuaDaSh project “Finanziato dall’Unione europea- Next Generation EU, Missione 4 Componente 2 CUP B53D23026250001”
DOI: 10.5281/zenodo.14283870
title: UCI Adult (Version 2) - Artificial Prevalence Protocol (APP) Test Indices

description: Dataset
Adult


# data points
45,222


# non-sensitive features (preprocessed)
95


sensitive attribute
sex


S = 1
Male


Pr(S=1)
0.675


target variable
income/class


Y = ⊕
>$50,000


Pr(Y=⊕)
0.248




The UCI Adult dataset is loaded using fetch_openml from scikit-learn (version 2). To ensure reproducibility, the dataset is split into three equal subsets using stratified sampling based on the joint distribution of (S, Y) and a random seed of 0.

The indices stored in adult_D1.indices, adult_D2.indices, and adult_D3.indices refer to the original dataset's instances after any instances containing missing values have been removed. The indices in adult_D3_protocol.indices correspond to the instances in the LabelledCollection constructed using the indices from adult_D3.indices.

Categorical features are converted to dummy variables, and numerical features are standardised using a standard scaler.




Feature Type
Features


Categorical
workclass, education, marital-status, occupation, race, native-country


Numerical
age, capital-gain, capital-loss, hours-per-week






 

The Artificial Prevalence Protocol (APP) is applied to vary the distribution of the sensitive attribute across 11 prevalence values: Pr(s|⊖) ∈ {0.0, 0.1, ..., 0.9, 1.0}. To minimise variance in the evaluation results, 500 samples are drawn repeatedly under the protocol. This entire process is repeated 10 times, consistently using a random seed of 0 for reproducibility.


This work has been funded by the QuaDaSh project “Finanziato dall’Unione europea- Next Generation EU, Missione 4 Componente 2 CUP B53D23026250001”
DOI: 10.15468/dl.9u8az7
title: Occurrence Download

description: A dataset listing the 1057 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "Geometry POLYGON((-74.29644 4.63873,-74.23609 4.64007,-74.20532 4.65007,-74.1972 4.70482,-74.24608 4.71502,-74.26515 4.71631,-74.29199 4.71631,-74.29644 4.63873))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 1057 records were derived from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038838-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/mwpjdb
title: Badanie trwałości zmęczeniowej złącza spawanego

description: In the course of the conducted work, the geometry of specimens intended for ultrasonic fatigue testing was developed. The design was tailored to allow for the extraction of samples from at least three different depths of the weld. Tests were carried out to determine fundamental design data, such as material parameters and mechanical properties of the specimens. Subsequently, fatigue tests under gigacyclic conditions were performed for butt-weld joints, enabling a detailed determination of their fatigue life and the acquisition of data essential for further analyses and the development of durability models.
DOI: 10.57754/fdat.2y8xv-n4h64
title: Gedichtkorpus Dickinson / Donne / Shakespeare II

description: The second corpus of poems by Dickinson, Donne, Shakespeare consists of the poems `You said that I "was great"´, `When in disgrace with fortune and men's eyes´, and Batter my heart´ used for an article on problems of ambiguity for translation.
description: Research carried out in work package A02 of the SFB 833.