cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7925/drs1.duchas_5104600
title: Old Song

description: Story collected by a student at Clonback, Aughnacliffe school (Cloonback, Co. Longford) from informant Mrs Ann Connell.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Seán Mac Ionnraic.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.7925/drs1.duchas_5104601
title: Feats of Strength

description: Story collected by Annie Larkin, a student at Géag (C.), Baile na Muc school (Gaigue, Co. Longford) from informant John J. Larkin.
description: Collected as part of the Schools' Folklore scheme, 1937-1938, under the supervision of teacher Máire Ní Mhurchadha.
description: Supported by funding from the Department of Arts, Heritage and the Gaeltacht (Ireland), University College Dublin, and the National Folklore Foundation (Fondúireacht Bhéaloideas Éireann), 2014-2016.
DOI: 10.6084/m9.figshare.13684573
title: Additional file 8 of Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep

description: Additional file 8 Table S8. Primers used in the qRT-PCR analysis.
DOI: 10.6084/m9.figshare.21547379.v1
title: Additional file 1 of Congenital coronary artery-left ventricular multiple micro-fistulas and hypertrophic cardiomyopathy: a case report and literature review

description: Additional file 1: Video 1 Left coronary angiography in right anterior oblique 30° + cranial 20°2. Video 2 Left coronary angiography in right anterior oblique 30° + caudal 20°.
DOI: 10.6084/m9.figshare.21547382
title: Additional file 2 of Congenital coronary artery-left ventricular multiple micro-fistulas and hypertrophic cardiomyopathy: a case report and literature review

description: Additional file 2: Table1
DOI: 10.6084/m9.figshare.16306020.v1
title: Additional file 1 of Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes

description: Additional file 1. Table S1: Clinical parameters. Table S2: Primers for generating amplicons for targeted bisulfite-sequencing. Table S3: MEST, H19, XIST and DDX4 methylation values obtained by DBS for the testicular sperm samples. Table S4: WGBS statistics. Quality control parameters were based on QualiMap and MethylDackel reports. Table S5: WGBS methylation values for the 50 imprinting controls regions. Table S6: High-confidence TGC unmethylated regions. Table S7: High-confidence TGC low-methylated regions. Table S8: WGBS methylation values for the 1329 DMRs. Table S9: Annotations for the 271 CTR-CZ DMRs. Table S10: DMR-associated genes. Table S11: Differentially expressed DMR-associated genes using tradeSeq. Table S12: Differentially expressed DMR-associated genes using MAST.
DOI: 10.5281/zenodo.10628268
title: A multi-ancestry cerebral cortex transcriptome-wide association study identifies genes associated with smoking behaviors
DOI: 10.5281/zenodo.10628269
title: A multi-ancestry cerebral cortex transcriptome-wide association study identifies genes associated with smoking behaviors
DOI: 10.6084/m9.figshare.21547379
title: Additional file 1 of Congenital coronary artery-left ventricular multiple micro-fistulas and hypertrophic cardiomyopathy: a case report and literature review

description: Additional file 1: Video 1 Left coronary angiography in right anterior oblique 30° + cranial 20°2. Video 2 Left coronary angiography in right anterior oblique 30° + caudal 20°.
DOI: 10.6084/m9.figshare.23665132.v1
title: Additional file 2 of A new compact adenine base editor generated through deletion of HNH and REC2 domain of SpCas9

description: Additional file 2. All data generated or analyzed during this study are included in this published article and its supplementary information file 2.
DOI: 10.6084/m9.figshare.13159182
title: Additional file 7 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 7: Supplementary Table S7. Pathways enriched from RNA-seq analysis
DOI: 10.6084/m9.figshare.13159161
title: Additional file 2 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 2: Supplementary Table S2. SNV list
DOI: 10.6084/m9.figshare.13159158.v1
title: Additional file 1 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 1: Supplementary Table S1. list of gene fusion events and their sequences, and the oligos used and products detected by RT-PCR.
DOI: 10.6084/m9.figshare.13159170.v1
title: Additional file 4 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 4: Supplementary Table S4. LMS_deleted_gene list in 0.95 confidence level
DOI: 10.6084/m9.figshare.13159158
title: Additional file 1 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 1: Supplementary Table S1. list of gene fusion events and their sequences, and the oligos used and products detected by RT-PCR.
DOI: 10.6084/m9.figshare.13159167
title: Additional file 3 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 3: Supplementary Table S3. LMS_amplified_gene list in 0.95 confidence level
DOI: 10.6084/m9.figshare.13159170
title: Additional file 4 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 4: Supplementary Table S4. LMS_deleted_gene list in 0.95 confidence level
DOI: 10.6084/m9.figshare.13159176
title: Additional file 6 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 6: Supplementary Table S6. RNA expression from RNA-seq analysis
DOI: 10.6084/m9.figshare.13684763.v1
title: Additional file 5 of Global transcriptomic analysis reveals Lnc-ADAMTS9 exerting an essential role in myogenesis through modulating the ERK signaling pathway

description: Additional file 5: Table S3. List of 755 DEGs between adipogenic and myogenic precursors derived from pig skeletal muscle. Table S4. List of GO terms based on 755 DEGs between adipogenic and myogenic percursors derived from pig skeletal muscle. Table S5. List of KEGG terms based on 755 DEGs between adipogenic and myogenic percursors derived from pig skeletal muscle.
DOI: 10.6084/m9.figshare.23665132
title: Additional file 2 of A new compact adenine base editor generated through deletion of HNH and REC2 domain of SpCas9

description: Additional file 2. All data generated or analyzed during this study are included in this published article and its supplementary information file 2.
DOI: 10.6084/m9.figshare.13159176.v1
title: Additional file 6 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 6: Supplementary Table S6. RNA expression from RNA-seq analysis
DOI: 10.6084/m9.figshare.13159182.v1
title: Additional file 7 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 7: Supplementary Table S7. Pathways enriched from RNA-seq analysis
DOI: 10.6084/m9.figshare.16829218.v1
title: Additional file 6 of Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage

description: Additional file 6. Dataset S4 Sequences of extracted TALE homeodomain (63 amino acids) from molluscan species.
DOI: 10.6084/m9.figshare.16829359
title: Additional file 5 of The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

description: Additional file 5: Table S10. Metabolites detected in the fecal metabolomes of QML group (n = 3) and YS group (n = 3).
DOI: 10.6084/m9.figshare.16829200
title: Additional file 2 of Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage

description: Additional file 2: Table S1. Results of Blast searches. Table S2. Lists and annotations of TALE genes used in this study. Table S3. Primers for gene isolation.
DOI: 10.6084/m9.figshare.8966213
title: Telomerase activation in small intestinal neuroendocrine tumours is associated with aberrant <i>TERT</i> promoter methylation, but not hot-spot mutations

description: Telomere maintenance is a critical requirement for enabling replicative immortality and tumour development. Here, telomerase expression and activity, telomere length (TL) and potential regulatory factors that can underlie telomerase machinery alterations in small intestinal neuroendocrine tumours (SI-NETs) were analyzed. Telomerase activity assessed by TRAP assay was increased in SI-NETs compared to normal ileum (<i>P</i> &lt; 0.001). The telomerase reverse transcriptase gene (<i>TERT</i>) was over-expressed in SI-NETs vs. normal ileal samples (<i>P</i> = 0.01). Furthermore, relative TL assessed by qPCR was found shorter in tumours compared with normal ileum (<i>P</i> = 0.02) and in distant metastasis samples compared to primary tumours and local metastases (<i>P</i>= 0.02). <i>TERT</i> promoter hotspot mutations were not present and <i>TERT</i> copy number gain was only observed in 3/70 tumour samples. <i>TERT</i> or chromosome 18 copy number alterations were not associated with telomerase expression and activity or TL. However, hypermethylation of <i>TERT</i> promoter in Region B – in the proximity of the transcription start site – was inversely correlated with <i>TERT</i> expression and telomerase activity and positively correlated with TL. Global LINE1 methylation was positively correlated with <i>TERT</i> promoter Region B methylation and was inversely correlated with telomerase activity, <i>TERT</i> expression and the upstream Region A methylation. The results show that telomerase activation, <i>TERT</i> expression and shorter telomeres are commonly found in SI-NETs. Aberrant DNA methylation of <i>TERT</i> promoter and of LINE1 can be implicated in abnormal regulation of <i>TERT</i> in SI-NETs.
DOI: 10.6084/m9.figshare.8966213.v1
title: Telomerase activation in small intestinal neuroendocrine tumours is associated with aberrant <i>TERT</i> promoter methylation, but not hot-spot mutations

description: Telomere maintenance is a critical requirement for enabling replicative immortality and tumour development. Here, telomerase expression and activity, telomere length (TL) and potential regulatory factors that can underlie telomerase machinery alterations in small intestinal neuroendocrine tumours (SI-NETs) were analyzed. Telomerase activity assessed by TRAP assay was increased in SI-NETs compared to normal ileum (<i>P</i> &lt; 0.001). The telomerase reverse transcriptase gene (<i>TERT</i>) was over-expressed in SI-NETs vs. normal ileal samples (<i>P</i> = 0.01). Furthermore, relative TL assessed by qPCR was found shorter in tumours compared with normal ileum (<i>P</i> = 0.02) and in distant metastasis samples compared to primary tumours and local metastases (<i>P</i>= 0.02). <i>TERT</i> promoter hotspot mutations were not present and <i>TERT</i> copy number gain was only observed in 3/70 tumour samples. <i>TERT</i> or chromosome 18 copy number alterations were not associated with telomerase expression and activity or TL. However, hypermethylation of <i>TERT</i> promoter in Region B – in the proximity of the transcription start site – was inversely correlated with <i>TERT</i> expression and telomerase activity and positively correlated with TL. Global LINE1 methylation was positively correlated with <i>TERT</i> promoter Region B methylation and was inversely correlated with telomerase activity, <i>TERT</i> expression and the upstream Region A methylation. The results show that telomerase activation, <i>TERT</i> expression and shorter telomeres are commonly found in SI-NETs. Aberrant DNA methylation of <i>TERT</i> promoter and of LINE1 can be implicated in abnormal regulation of <i>TERT</i> in SI-NETs.
DOI: 10.6084/m9.figshare.16829209.v1
title: Additional file 4 of Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage

description: Additional file 4. Dataset S2 Sequences of homeodomain (63 amino acids) from bilaterians for phylogenetic analysis of Fig. S1.
DOI: 10.6084/m9.figshare.16829215.v1
title: Additional file 5 of Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage

description: Additional file 5. Dataset S3 Sequences of SPILE genes in molluscs for Fig. S3-7.
DOI: 10.6084/m9.figshare.16829362
title: Additional file 6 of The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

description: Additional file 6: Table S11. Metabolites detected in the fecal metabolomes of HN_f2 group (n = 3) and XH_f1 group (n = 3).
DOI: 10.6084/m9.figshare.13159167.v1
title: Additional file 3 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 3: Supplementary Table S3. LMS_amplified_gene list in 0.95 confidence level
DOI: 10.6084/m9.figshare.16829305
title: Additional file 1 of Occurrence and molecular characterization of Cryptosporidium spp., Giardia duodenalis, Enterocytozoon bieneusi, and Blastocystis sp. in captive wild animals in zoos in Henan, China

description: Additional file 1: Table S1. Specimens from wildlife at six zoos in Henan, China examined in this study.
DOI: 10.6084/m9.figshare.13159161.v1
title: Additional file 2 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 2: Supplementary Table S2. SNV list
DOI: 10.6084/m9.figshare.13159173.v1
title: Additional file 5 of Integrated genomic and transcriptomic analysis revealed mutation patterns of de-differentiated liposarcoma and leiomyosarcoma

description: Additional file 5:. Supplementary Table S5. DDLPS_ amplified_gene list in 0.95 confidence level
DOI: 10.6084/m9.figshare.16829359.v1
title: Additional file 5 of The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

description: Additional file 5: Table S10. Metabolites detected in the fecal metabolomes of QML group (n = 3) and YS group (n = 3).
DOI: 10.6084/m9.figshare.16829356
title: Additional file 4 of The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

description: Additional file 4: Table S9. Information on 263 predicted KEGG pathways (level 3) present in all the eight groups.
DOI: 10.6084/m9.figshare.16829365
title: Additional file 7 of The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

description: Additional file 7: Table S12. Information on 154 metabolites identified in all the samples (n = 12).
DOI: 10.6084/m9.figshare.16829398.v1
title: Additional file 2 of DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation

description: Additional file 2. Contains supplementary tables S1-S13.
DOI: 10.6084/m9.figshare.16829203.v1
title: Additional file 3 of Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage

description: Additional file 3. Dataset S1 Sequences of TALE genes from mussel transcriptome assembly.
DOI: 10.7281/t1wd3xhm/xlxy4n
title: Contraction of SMLC.zip

description: This zip file contains images taken of SMLCs after subjection to carbachol and atropine.
DOI: 10.5281/zenodo.7525681
title: Gene/Protein BridgeDb ID Mapping Database (Ensembl 107)

description: Ensembl 107 derived ID mapping databases for use with BridgeDb. The scripts used to create these databases based on Ensembl BioMart can be found at https://github.com/bridgedb/create-bridgedb-genedb. This work was funded by the FAIRplus project (grant agreement no 802750) and NWO Open Science Fund (grant no 203.001.121).
DOI: 10.5281/zenodo.7775118
title: Gene/Protein BridgeDb ID Mapping Database (Ensembl 107)

description: Ensembl 107 derived ID mapping databases for use with BridgeDb.<br> This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio). The scripts used to create these databases based on Ensembl BioMart can be found at https://github.com/bridgedb/create-bridgedb-genedb.
DOI: 10.5281/zenodo.7525680
title: Gene/Protein BridgeDb ID Mapping Database (Ensembl 107)

description: Ensembl 107 derived ID mapping databases for use with BridgeDb.<br> This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio). The scripts used to create these databases based on Ensembl BioMart can be found at https://github.com/bridgedb/create-bridgedb-genedb.
DOI: 10.5281/zenodo.7789774
title: Heterogeneous environmental seascape across a biogeographic break influences the thermal physiology and tolerances to ocean acidification in an ecosystem engineer

description: Dataset for the metabolic rates of limpets under two different pCO2/pH conditions MR are in O2 mg h−1g−1
DOI: 10.5281/zenodo.7789773
title: Heterogeneous environmental seascape across a biogeographic break influences the thermal physiology and tolerances to ocean acidification in an ecosystem engineer

description: Dataset for the metabolic rates of limpets under two different pCO2/pH conditions MR are in O2 mg h−1g−1
DOI: 10.7281/t1/yxvvml/h6s8tu
title: Raw data for thiophene and edot polymers Li et al. JACS 2017.zip

description: These data were used to derive the figures in the manuscript and the supporting information.
DOI: 10.7281/t1/wbr06u/ahdce8
title: backup_data_for_NO2_sensor_Li_et_al_ACS_AMI_2017.zip

description: These data were used to derive Table 1 and Figures 4-6 in the manuscript.  The data also support the limit of detection calculation and present the lack of effect of NO2 on the absorbance spectra and an attempt to promote reversibility of the sensing by adding guanine to the polymers.
DOI: 10.5281/zenodo.7789780
title: M&A 2023 ROA

description: Mergers&Acquisitions 2023 ROA
DOI: 10.5281/zenodo.7789781
title: M&A 2023 ROA

description: Mergers&Acquisitions 2023 ROA
DOI: 10.5066/p9jpvpgv
title: Everglades Vulnerability Analysis (EVA) modeling scripts and output

description: The Everglades Vulnerability Analysis (EVA) is a series of connected Bayesian networks that models the landscape-scale response of indicators of Everglades ecosystem health to changes in hydrology and salinity on the landscape. Using the uncertainty built into each network, it also produces surfaces of vulnerability in relation to user-defined ‘ideal’ outcomes. This dataset includes the code used to build the modules and generate outputs of module outcome probabilities and landscape vulnerability.
DOI: 10.5281/zenodo.6821244
title: Beyond sequence similarity: cross-phyla protein annotation by structural prediction and alignment

description: <strong>Background:</strong> Annotating protein function is a major goal in molecular biology, yet experimentally determined knowledge is often limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer function, however this approach loses predictive power with longer evolutionary distances. Here we propose a pipeline for the functional annotation of proteins using structural similarity, exploiting the fact that protein structures are directly linked to function and can be more conserved than protein sequences. <strong>Results:</strong> We propose a pipeline of openly available tools for the functional annotation of proteins via structural similarity (MorF: <strong>Mor</strong>pholog <strong>F</strong>inder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in &gt;90% cases, and annotates an additional 50% of the proteome beyond standard sequence-based methods. Using this, we uncover new functions for sponge cell types, including extensive FGF, TGF and Ephrin signalling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls. <strong>Conclusions:</strong> Our work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this to be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.
description: {"references": ["Ruperti, Fabian and Papadopoulos, Nikolaos, et al. (2022). Data related to https://doi.org/10.1101/2022.07.05.498892"]}
DOI: 10.6084/m9.figshare.22445212
title: Well-fed or nearly dead? Using quantitative PCR to detect dietary stress in Daphnia pulex.

description: Nutrition is at the center of interactions between organisms and their environment. During this time of unprecedented anthropogenic environmental change, biological indicators of nutritional changes and their effects on ecosystems are crucial if we are to understand and mitigate these changes. In this study, we developed a qPCR assay to examine nutritional responsiveness of ten genes identified as potential indicators of nutritional state in the freshwater zooplankton <em>Daphnia pulex</em>. We grew animals in six ecologically relevant treatments: nutrient replete, low carbon (food), low phosphorus, low nitrogen, low calcium, and high Cyanobacteria. We selected ten nutrient sensitive genes, two per limiting nutrient, and two reference genes from an RNA sequencing dataset. We found that using the nutrient-specific pairs of genes for single nutrient limitation assays showed mixed results with some treatments (calcium, nitrogen, carbon) with high levels of treatment discrimination, but gene responses designed for other treatments (phosphorus and Cyanobacteria) showed little to no treatment discrimination. However, when we used all ten genes as a single nutritional state assay, we could discriminate between our six nutritional states with high levels of accuracy. These results represent a compelling proof of concept for the use of gene-based nutritional biomarkers, paving the way for the use of genetically based nutritional state biomarkers in the study of ecology