cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5547464
title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans

description: To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in <em>Caenorhabditis elegans,</em> neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal <em>hsf-1</em> is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.
DOI: 10.5281/zenodo.5519410
title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans

description: To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in <em>Caenorhabditis elegans,</em> neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal <em>hsf-1</em> is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.
DOI: 10.34740/kaggle/dsv/2675414
title: UNET Lung Segmentation Weights for Chest X Rays
DOI: 10.5517/ccdc.csd.cc28y64l
title: CCDC 2113429: Experimental Crystal Structure Determination

description: Related Article: Ferdinand Belaj, Kristin Kogler, Jörg A. Schachner, Nadia C. Mösch-Zanetti|2021|CSD Communication|||
DOI: 10.21227/53mq-g936
title: Identification of Beehive Piping Audio Signals

description: We introduce a novel dataset of bee piping audio signals which was built by collecting 44 different recordings which were published by various beekeepers on the YouTube platform.Each recording has a duration varying from 2 to 13 seconds and is annotated according to the beekeeper comment respectively as Tooting or Quacking.We extracted the audio using ``YouTube soundtrack extraction'' from 14 distinct videos from which the signal is stored without a loss of quality into a WAVE file with a sampling frequency of F_s=22.05 kHz and a sample precision of 16 bits.After removing the silent frames, the resulting dataset contains 36 tooting and 8 quacking signals which correspond to a duration of 145 seconds for tooting and 60 seconds for quacking (total 205 seconds).For copyright reasons, we only made publicly available the short-time Fourier transforms matrices and the timbre descriptors computed using a matlab implementation of the timbre toolbox proposed by Peeters et al. in 2011.A more detailed description of the dataset containing the links of the original youtube videos can be found
DOI: 10.6084/m9.figshare.14937795
title: JAGF4 and JAGF5 population dataset of tomato plant

description: Many studies showed that few degrees above tomato optimum growth temperature threshold can lead to serious loss in production. Therefore, the development of innovative strategies to obtain tomato cultivars with improved yield under high temperature conditions is a main goal both for basic genetic studies and breeding activities. In this paper, a JAGF4 segregating population was phenotypically evaluated for quantitative and qualitative traits under heat stress conditions. Moreover, a genotyping by sequencing (GBS) approach has been employed for building up genomic selection (GS) models both for yield and soluble solid content (SCC). A good prediction accuracy for the two analyzed traits (0.729 for yield production and 0.715 for SCC) was obtained. The predicted models improved the genetic gain of selection in the next breeding cycles, suggesting that GS approach is a promising strategy to accelerate breeding for heat tolerance in tomato.
DOI: 10.5281/zenodo.5547573
title: Offering ART refill through community health workers versus clinic-based follow-up after home-based same-day ART initiation in rural Lesotho: The VIBRA cluster-randomised clinical trial

description: These are pseudo-anonymised data from the VIBRA randomized trial: "Offering ART refill through community health workers versus clinic-based follow-up after home-based same-day ART initiation in rural Lesotho: The VIBRA cluster-randomised clinical trial". The data dictionary explains the data available in the dataset. Between August 2018 and May 2019, 257 eligible individuals from 117 consenting villages were enrolled from two districts of Lesotho, and followed up for a maximum of 15 months. The protocol was published, doi: 10.1186/s13063-019-3510-5
DOI: 10.5281/zenodo.5547572
title: Offering ART refill through community health workers versus clinic-based follow-up after home-based same-day ART initiation in rural Lesotho: The VIBRA cluster-randomised clinical trial

description: These are pseudo-anonymised data from the VIBRA randomized trial: "Offering ART refill through community health workers versus clinic-based follow-up after home-based same-day ART initiation in rural Lesotho: The VIBRA cluster-randomised clinical trial". The data dictionary explains the data available in the dataset. Between August 2018 and May 2019, 257 eligible individuals from 117 consenting villages were enrolled from two districts of Lesotho, and followed up for a maximum of 15 months. The protocol was published, doi: 10.1186/s13063-019-3510-5
DOI: 10.34740/kaggle/dsv/2675534
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.5281/zenodo.5547453
title: DataOnFigure1

description: Dataset for publication "Combining life cycle sustainability assessment with agent-based modeling and techno-economic analysis to support an integrated assessment of chemical recycling contribution to UN Sustainable Development Goals" in the Journal of Industrial Ecology
DOI: 10.34740/kaggle/dsv/2675550
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.5547644
title: Data release: Parameterised population models of transient non-Gaussian noise in the LIGO gravitational-wave detectors

description: This contains the data release associated to "Parameterised population models of transient non-Gaussian noise in the LIGO gravitational-wave detectors". We provide the figures, machine-readable json summary files associated to Tables I-IV, and the scripts used to produce the hyperparameter inference.
DOI: 10.5281/zenodo.5532578
title: A comprehensive evaluation of module detection methods for gene expression data

description: <strong>A critical step in the analysis of large genome-wide gene expression datasets is the use of module detection methods to group genes into co-expression modules. Because of limitations of classical clustering methods, numerous alternative module detection methods have been proposed, which improve upon clustering by handling co-expression in only a subset of samples, modeling the regulatory network, or allowing overlap between modules. In this study we use known regulatory networks to do a comprehensive and robust evaluation of these different methods. Overall, decomposition methods outperform all other strategies, while we could not find any clear advantages of biclustering and network-inference based approaches. Using our evaluation workflow, we also investigate several practical aspects of module detection, such as parameter estimation and the use of alternative similarity measures, and conclude with recommendations for the further development of these methods.</strong>
description: Changes since V1: - Added the baselines, which were missing in the first version - Added a new E. coli dataset (https://github.com/SBRG/precise2/tree/b58057a42cc620985ce92df7ff51cfdb9260860c/data/precise2) - Added a much needed update of the RegulonDB database (RegulonDB 10.9, 06/29/2021) - Added results from the top methods
DOI: 10.5281/zenodo.1157937
title: A comprehensive evaluation of module detection methods for gene expression data

description: <strong>A critical step in the analysis of large genome-wide gene expression datasets is the use of module detection methods to group genes into co-expression modules. Because of limitations of classical clustering methods, numerous alternative module detection methods have been proposed, which improve upon clustering by handling co-expression in only a subset of samples, modeling the regulatory network, or allowing overlap between modules. In this study we use known regulatory networks to do a comprehensive and robust evaluation of these different methods. Overall, decomposition methods outperform all other strategies, while we could not find any clear advantages of biclustering and network-inference based approaches. Using our evaluation workflow, we also investigate several practical aspects of module detection, such as parameter estimation and the use of alternative similarity measures, and conclude with recommendations for the further development of these methods.</strong>
description: Changes since V1: - Added the baselines, which were missing in the first version - Added a new E. coli dataset (https://github.com/SBRG/precise2/tree/b58057a42cc620985ce92df7ff51cfdb9260860c/data/precise2) - Added a much needed update of the RegulonDB database (RegulonDB 10.9, 06/29/2021) - Added results from the top methods
DOI: 10.5517/ccdc.csd.cc2337fx
title: CCDC 1939528: Experimental Crystal Structure Determination

description: Related Article: Ming-Hao Du, Xiu-Ying Zheng, Xiang-Jian Kong, La-Sheng Long, Lan-Sun Zheng|2020|Matter|3|1334|doi:10.1016/j.matt.2020.06.020
DOI: 10.5517/ccdc.csd.cc26c660
title: CCDC 2036551: Experimental Crystal Structure Determination

description: Related Article: H.A. Aisa, L. Izotova, A. Karimov, E. Botirov, A. Mamadrahimov, B. Ibragimov|2020|Acta Crystallogr.,Sect.E:Cryst.Commun.|76|1748|doi:10.1107/S2056989020013596
DOI: 10.17632/n6zk3dp8fy.1
title: Assessment of Prevalence of Counterfeit Drugs in Developing Countries

description: This data is raw data generated from respondents across developing countries on counterfeit drugs and the major contributors to the prevalence of this act in their country.
DOI: 10.17632/bgps766mxp.1
title: DATASET S2: ORFs prediction from the transcriptomic profile of the cockle Cerastoderma edule exposed to seasonal dinophysistoxins outbreaks.

description: Resulting .fasta and .gff files corresponding to the Open Reading Frames (ORFs) prediction obtained from the de novo transcriptome assembly and clustering analyses in the article: Transcriptomic profile of the cockle Cerastoderma edule exposed to seasonal dinophysistoxins outbreaks. Domínguez-Pérez, D. et al., 2021.

Ce_assembly_unique_CDS.fasta: The corresponding nucleotide .fasta file of the Protein Coding Sequences (CDS) obtained by six-frame translation with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene.

Ce_assembly_unique_proteins.fasta: The resulting amino acid .fasta file of the Protein Coding Sequences (CDS) obtained by six-frame translation with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene.

Ce_assembly_unique_ORFs.gff: The corresponding .gff file of the Protein Coding Sequences (CDS) obtained by six-frame translation with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene.

predict_coding_regions_results_assembled_transcripts_clustering.pdf: Summary of the ORFs prediction with TransDecoder v5.5.0., considering a minimum length of 100 amino acids for open reading frames (ORFs), homology to known proteins via Pfam searches, and the best/longest isoform per gene.

predict_coding_regions_summary_assembled_transcripts_clustering.pdf: The figure depicts the summary and relative representation of complete, partial and internal ORFs obtained from the de novo transcriptome assembly of C. edule.
DOI: 10.17632/vkw2jcmmzt.1
title: DATASET S1: Transcriptomic profile of the cockle Cerastoderma edule exposed to seasonal dinophysistoxins outbreaks.

description: Resulting .fasta and .gff files obtained from de novo transcriptome assembly and clustering analyses in the article: Transcriptomic profile of the cockle Cerastoderma edule exposed to seasonal dinophysistoxins outbreaks. Domínguez-Pérez, D. et al., 2021.

Ce_assembly_unique.fasta: The de novo transcriptome assembly of C. edule before submission to NCBI, obtained with Trinity v2.10.0 by combining four samples (gills and digestive glands without DTSs and exposed) into a single transcriptome.

C.edule_assembly_submitted_ncbi.fasta: The de novo transcriptome assembly submitted NCBI (registered with the BioProject ID: PRJNA739261 (http://www.ncbi.nlm.nih.gov/bioproject/739261). It is noteworthy, a total of 147 transcripts with length below 200 bp were removed during NCBI submission. 

Ce_assembly_unique_supertranscript.fasta: The corresponding supertranscript file constructed from the de novo transcriptome assembly of C. edule.

Ce_assembly_unique.gff: The corresponding .gff file obtained from the de novo transcriptome assembly of C. edule.

transcript_to_gene_map.txt: The corresponding transcripts-to-gene-mapping file obtained from the de novo transcriptome assembly of C. edule, and used for clustering analyses.

rna_seq_de_novo_assembly_trinity_output.pdf: The resulting output file containing the statistics summary of the de novo transcriptome assembly of C. edule.

Ce_assembly_unique_clustering.fasta: The resulting clustering .fasta file from the de novo transcriptome assembly of C.edule, using CD-HIT 4.8.1, setting 0.9 as the Sequence Identity Threshold.

cluster_distribution_[assembled_transcripts].pdf: The figure shows the clusters distribution of the assembled transcripts.

clustering_results_assembled_transcripts.pdf: Summary of the clustering analyses using CD-HIT 4.8.1.
DOI: 10.17632/6z6rpf9w8z.1
title: DATASET S3: Data used for the differential expression analyses in the article: Transcriptomic profile of the cockle Cerastoderma edule exposed to seasonal dinophysistoxins outbreaks. Domínguez-Pérez, D. et al., 2021.

description: 47496_isoforms.box: 47,496 ORFs encoded by 33,665 genes in .box format exported by the 
OmicsBox v1.4.11, formerly used to retrieve all the related isoforms for differential expression analyses.

relative_counts_per_category_[counts_isoforms].pdf: Relative counts per isoform/transcript obtained for isoform/gene-level quantification.

counts_genes.box and counts_isoforms.box: The resulting count tables in .box format exported by OmicsBox v1.4.11, corresponding to the expression estimated at gene-level and isoform-level, respectively. 

omicsbox_count_table_genes.txt and omicsbox_count_table_isoforms.txt: The resulting count tables in .text format exported by OmicsBox v1.4.11, corresponding to the expression estimated at gene-level and isoform-level, respectively. 

ce_dge_vs_ce_dgc.box and ce_ge_vs_ce_gc.box: Results of the differential expression analyses in .box format exported by OmicsBox v1.4.11, corresponding to the pairwise comparison between exposed samples to dinophysistoxins and control obtained from the digestive gland (ce_dge_vs_ce_dgc.box) and gills (ce_ge_vs_ce_gc) of the cockle C. edule.

pairwise_differential_expression_wr_ce_dge_vs_ce_dgc.pdf: Summary file of the differential expression analyses from the digestive gland of the cockle C. edule. The pairwise comparison was performed between samples exposed to dinophysistoxins and control (without DSTs), using NOISeq v2.30.0, with 5 technical replicates simulated per sample and p-value 0.01.

pairwise_differential_expression_wr_ce_ge_vs_ce_gc.pdf: Summary file of the differential expression analyses from the gills of the cockle C. edule. The pairwise comparison was performed between samples exposed to dinophysistoxins and control (without DSTs), using NOISeq v2.30.0, with 5 technical replicates simulated per sample and p-value 0.01.

normalized_counts_ce_dge_vs_ce_dgc.txt: Normalized counts obtained from the differential expression analyses from the digestive gland of the cockle C. edule. The pairwise comparison was performed between samples exposed to dinophysistoxins and control (without DSTs), using NOISeq v2.30.0, with 5 technical replicates simulated per sample and p-value 0.01.

normalized_counts_ce_ge_vs_ce_gc.txt: Normalized counts obtained from the differential expression analyses from the gills of the cockle C. edule. The pairwise comparison was performed between samples exposed to dinophysistoxins and control (without DSTs), using NOISeq v2.30.0, with 5 technical replicates simulated per sample and p-value 0.01.
DOI: 10.17632/5yp5ncm2vp.1
title: DATASET S4: Data used for the enrichment analyses in the article: Transcriptomic profile of the cockle Cerastoderma edule exposed to seasonal dinophysistoxins outbreaks. Domínguez-Pérez, D. et al., 2021.

description: 47496_genes.box and 47496_genes.annot: 47,496 ORFs encoded by 33,665 genes in .box format exported by the OmicsBox v1.4.11, which contain embedded all the annotations used for the enrichment analyses (Fisher's exact test, FDR <0.05).

test_set_16_common_DEGs_up_exposed: List of 16 common DEGs with a similar up-regulated pattern identified in both condition exposed to DSTs, used as test set in the enrichment analyses.

test_set_189_common_DEGs_down_exposed: List of 189 common DEGs with a similar down-regulated pattern identified in both condition exposed to DSTs, used as test set in the enrichment analyses.

test_set_185_unique_DEGs_up_Ce_DGe_vs_Ce_DGc: List of 185 unique up-regulated DEGs identified in the digestive gland (Ce_DGe_vs_Ce_DGc), used as test set in the enrichment analyses.

test_set_168_unique_DEGs_down_Ce_DGe_vs_Ce_DGc: List of 168 unique down-regulated DEGs identified in the digestive gland (Ce_DGe_vs_Ce_DGc), used as test set in the enrichment analyses.

test_set_80_unique_DEGs_up_Ce_Ge_vs_Ce_Gc: List of 80 unique up-regulated DEGs identified in the gills (Ce_Ge_vs_Ce_Gc), used as test set in the enrichment analyses.

test_set_456_unique_DEGs_down_Ce_Ge_vs_Ce_Gc: List of 456 unique down-regulated DEGs identified in the gills (Ce_Ge_vs_Ce_Gc), used as test set in the enrichment analyses.

enriched_graph_189_common_DEGs_down_exposed: Enriched graphs resulting from the enrichment analyses (one-tailed Fisher's exact test, FDR <0.05), using the list of 189 common DEGs as test set (file: test_set_189_common_DEGs_down_exposed).

enriched_graph_168_unique_DEGs_down_Ce_DGe_vs_Ce_DGc: Enriched graph resulting from the enrichment analyses (one-tailed Fisher's exact test, FDR <0.05), using the list of 168 unique down-regulated DEGs as test set (file: test_set_168_unique_DEGs_down_Ce_DGe_vs_Ce_DGc).

enriched_graph_456_unique_DEGs_down_Ce_Ge_vs_Ce_Gc: Enriched graph resulting from the enrichment analyses (one-tailed Fisher's exact test, FDR <0.05), using the list of 456 unique down-regulated DEGs as test set (file: test_set_456_unique_DEGs_down_Ce_Ge_vs_Ce_Gc).
DOI: 10.17632/m58j89hsp9.1
title: Conceitos, concepções, correntes e teorias utilizadas sobre participação social em saúde: um protocolo de revisão de escopo

description: Uma gama de definições pode ser encontrada na literatura, a  exemplo da Organização Mundial de Saúde que apresenta a participação em saúde como processos de reflexão coletiva por meio dos quais a população elabora dados ou informações significativas na área da saúde e, a partir delas, dialoga no processo decisório por meio de mecanismos participativos, de maneira colaborativa com as instituições responsáveis por elas e engajando-as no planejamento e posterior implementação dessas decisões(1-6). Contudo, não há um termo abrangente acordado para diferentes fenômenos que podem constituir a definição de participação em saúde. 
Uma revisão de escopo é o tipo de estudo adequado para mapear conceitos e terminologia que são aplicados em um contexto específico(1,2). Isso é particularmente útil quando o tópico não é suficientemente restrito para permitir uma revisão sistemática da literatura e quando as evidências têm formatos e qualidades heterogêneas(2). 
Aliada a escassos recursos e tempo para tomada de decisão em políticas públicas, a Organização Mundial da Saúde tem promovido cada vez mais a disseminação de métodos de revisão rápida (4). Embora sua abordagem metodológica e conceitual ainda seja ampla, a revisão rápida é atualmente definida como uma forma de conhecimento síntese que acelera o processo de realização de uma revisão sistemática tradicional através da simplificação ou omissão de uma variedade de métodos com o objetivo de produzir evidências em termos de recursos de forma eficiente(2). 
Este estudo busca mapear os conceitos, concepções, correntes e teorias utilizados sobre participação social em saúde utilizadas pelos países das Américas e Caribe no século XXI. Tais resultados podem subsidiar a melhoria dos processos de trabalho que envolvam participação social. Ainda, a revisão de escopo proposta fornecerá um ponto de partida essencial para pesquisas futuras de construção de teorias.
DOI: 10.17632/kwb97szmc5.1
title: Literature used for updating the Reasons for Concern 2021

description: Literature used in expert elicitation for updating the assessment of the Reasons for Concern 2021, WGII AR6 Chapter 16 Key risks across sectors and regions. The list is in addition to that cited in Chapter 16 Key risks across sectors and regions,  and mentioned in the Chapter 16 Supplementary Material, In IPCC WGII AR6 Final Draft.