cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17982460
title: Additional file 8 of Integrative profiling of Epstein–Barr virus transcriptome using a multiplatform approach

description: Additional file 8. Coding potential and BLAST analysis of alternatively spliced transcripts. For the analysis of the coding potential we used the CPAT tool.
DOI: 10.6084/m9.figshare.17982460.v1
title: Additional file 8 of Integrative profiling of Epstein–Barr virus transcriptome using a multiplatform approach

description: Additional file 8. Coding potential and BLAST analysis of alternatively spliced transcripts. For the analysis of the coding potential we used the CPAT tool.
DOI: 10.6084/m9.figshare.17982487
title: Additional file 1 of End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach

description: Additional file 1 The REPRODUCE-ME ontology. A supplemental document containing the REPRODUCE-ME ontology in OWL format (reproduce-me.owl) is available for this manuscript.
DOI: 10.6084/m9.figshare.17982487.v1
title: Additional file 1 of End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach

description: Additional file 1 The REPRODUCE-ME ontology. A supplemental document containing the REPRODUCE-ME ontology in OWL format (reproduce-me.owl) is available for this manuscript.
DOI: 10.6084/m9.figshare.17982508
title: Additional file 2 of The new frontline: exploring the links between moral distress, moral resilience and mental health in healthcare workers during the COVID-19 pandemic

description: Additional file 2.
DOI: 10.6084/m9.figshare.17982508.v1
title: Additional file 2 of The new frontline: exploring the links between moral distress, moral resilience and mental health in healthcare workers during the COVID-19 pandemic

description: Additional file 2.
DOI: 10.6084/m9.figshare.17982523
title: Additional file 1 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 1. 5′ UTR analysed. The data on the 2088 genes used for the analysis in Fig. 1 and Additional file 6: Fig. S1, including the 5′ UTR sequences used.
DOI: 10.6084/m9.figshare.17982523.v1
title: Additional file 1 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 1. 5′ UTR analysed. The data on the 2088 genes used for the analysis in Fig. 1 and Additional file 6: Fig. S1, including the 5′ UTR sequences used.
DOI: 10.6084/m9.figshare.17982526
title: Additional file 2 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 2. P16 sequence. The plasmid sequence for P16 used to generate new constructs.
DOI: 10.6084/m9.figshare.17982526.v1
title: Additional file 2 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 2. P16 sequence. The plasmid sequence for P16 used to generate new constructs.
DOI: 10.6084/m9.figshare.17982529
title: Additional file 3 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 3. 5′ UTR sequences. The sequences of all the 5′ UTR sequences evaluated in this manuscript.
DOI: 10.6084/m9.figshare.17982529.v1
title: Additional file 3 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 3. 5′ UTR sequences. The sequences of all the 5′ UTR sequences evaluated in this manuscript.
DOI: 10.6084/m9.figshare.17982532
title: Additional file 4 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 4: Fig. data. All the raw and processed data used to generate the Figures in this manuscript.
DOI: 10.6084/m9.figshare.17982532.v1
title: Additional file 4 of Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

description: Additional file 4: Fig. data. All the raw and processed data used to generate the Figures in this manuscript.
DOI: 10.6084/m9.figshare.17982634
title: Additional file 3 of The experiences, needs and barriers of people with impairments related to usability and accessibility of digital health solutions, levels of involvement in the design process and strategies for participatory and universal design: a scoping review

description: Additional file 3.
DOI: 10.6084/m9.figshare.17982634.v1
title: Additional file 3 of The experiences, needs and barriers of people with impairments related to usability and accessibility of digital health solutions, levels of involvement in the design process and strategies for participatory and universal design: a scoping review

description: Additional file 3.
DOI: 10.6084/m9.figshare.17982638
title: Additional file 2 of The effectiveness of supervision strategies to improve health care provider practices in low- and middle-income countries: secondary analysis of a systematic review

description: Additional file 2: Characteristics of included studies.
DOI: 10.6084/m9.figshare.17982638.v1
title: Additional file 2 of The effectiveness of supervision strategies to improve health care provider practices in low- and middle-income countries: secondary analysis of a systematic review

description: Additional file 2: Characteristics of included studies.
DOI: 10.6084/m9.figshare.17982643
title: Additional file 1 of Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial

description: Additional file 1. Results for zero-inflated negative binomial regression of species abundance on treatment received (Table S1) and time since treatment (Table S2).
DOI: 10.6084/m9.figshare.17982643.v1
title: Additional file 1 of Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial

description: Additional file 1. Results for zero-inflated negative binomial regression of species abundance on treatment received (Table S1) and time since treatment (Table S2).
DOI: 10.5281/zenodo.5826465
title: Global Soil Moisture-Air Temperature Interactions from Linear and Nonlinear Granger Causalities

description: These datasets were generated to assess linear and nonlinear Granger causalities in the submitted manuscript, Global Soil Moisture-Air Temperature Interactions from Linear and Nonlinear Granger Causalities by Bhatti et al. submitted to AGU-GRL. Nonlinear GC here is achieved with the Kernel Granger causality by Marinazzo et al. (2008). The data was used to develop theoretical experiments that help validate the strengths and limitations of both the linear Granger causality and the Kernel Granger causality before applying to real world datasets
description: The manuscript is yet to be peer reviewed. Therefore, the data should be used with caution as review comments could require some changes in the experiment setup.
DOI: 10.5281/zenodo.5826464
title: Global Soil Moisture-Air Temperature Interactions from Linear and Nonlinear Granger Causalities

description: These datasets were generated to assess linear and nonlinear Granger causalities in the submitted manuscript, Global Soil Moisture-Air Temperature Interactions from Linear and Nonlinear Granger Causalities by Bhatti et al. submitted to AGU-GRL. Nonlinear GC here is achieved with the Kernel Granger causality by Marinazzo et al. (2008). The data was used to develop theoretical experiments that help validate the strengths and limitations of both the linear Granger causality and the Kernel Granger causality before applying to real world datasets
description: The manuscript is yet to be peer reviewed. Therefore, the data should be used with caution as review comments could require some changes in the experiment setup.
DOI: 10.6084/m9.figshare.17982707
title: Additional file 1 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 1. Detailed information on the clinical samples and the corresponding sequence variants. Clinical samples were processed in three different sample batches. While the primer set used for the first batch proved highly successful, the fraction of BPV-specific reads in some of the samples was low, indicating significant off-target amplification. The higher specificity of the V2 primer set significantly increased the fraction of BPV-specific reads.
DOI: 10.6084/m9.figshare.17982707.v1
title: Additional file 1 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 1. Detailed information on the clinical samples and the corresponding sequence variants. Clinical samples were processed in three different sample batches. While the primer set used for the first batch proved highly successful, the fraction of BPV-specific reads in some of the samples was low, indicating significant off-target amplification. The higher specificity of the V2 primer set significantly increased the fraction of BPV-specific reads.
DOI: 10.6084/m9.figshare.17982713
title: Additional file 2 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 2. Overview of all used primer sets for the amplification of complete BPV genomes. The primer set used in batch 1 (V1) consisted of ten overlapping amplicons, divided across two pools, that spanned the complete BPV genome. These primers were degenerated at multiple positions to allow them to amplify nearly all members of the species Deltapapillomavirus 4, including types 1, 2 and 13. To increase target-specificity, reducing the fraction of non-usable data and allowing more samples to be run on the same flow cell, a second version of the primer set was designed (V2). The number of amplicons in this second set was reduced to eight and their specificity was limited to BPV-1 and BPV-2, allowing the degree of degeneracy to be lowered considerably. Because two of the genomes from batch 2 contained a large deletion, disrupting one of the primer sites and leading to amplicon dropout, an alternative primer was designed for one of the amplicons. This slightly modified primer set (V3) was used to amplify a final batch of 30 samples.
DOI: 10.6084/m9.figshare.17982713.v1
title: Additional file 2 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 2. Overview of all used primer sets for the amplification of complete BPV genomes. The primer set used in batch 1 (V1) consisted of ten overlapping amplicons, divided across two pools, that spanned the complete BPV genome. These primers were degenerated at multiple positions to allow them to amplify nearly all members of the species Deltapapillomavirus 4, including types 1, 2 and 13. To increase target-specificity, reducing the fraction of non-usable data and allowing more samples to be run on the same flow cell, a second version of the primer set was designed (V2). The number of amplicons in this second set was reduced to eight and their specificity was limited to BPV-1 and BPV-2, allowing the degree of degeneracy to be lowered considerably. Because two of the genomes from batch 2 contained a large deletion, disrupting one of the primer sites and leading to amplicon dropout, an alternative primer was designed for one of the amplicons. This slightly modified primer set (V3) was used to amplify a final batch of 30 samples.
DOI: 10.6084/m9.figshare.17982719
title: Additional file 3 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 3. A complete overview of the genome organization, highlighting all BPV-1 mutations compared to the corresponding reference sequence. Overall, more than 120 unique substitutions were observed in the BPV-1 genomes, with some being present in all our sequences. One of these samples (batch 1, sample 3) contained multiple sequence variants: 1R3b with reference and 1R3a with mutant E5. Interestingly, several major deletions in the BPV-1 genomes were only present in part of the sequencing data, and the non-deleted variant could be detected in parallel.
DOI: 10.6084/m9.figshare.17982719.v1
title: Additional file 3 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 3. A complete overview of the genome organization, highlighting all BPV-1 mutations compared to the corresponding reference sequence. Overall, more than 120 unique substitutions were observed in the BPV-1 genomes, with some being present in all our sequences. One of these samples (batch 1, sample 3) contained multiple sequence variants: 1R3b with reference and 1R3a with mutant E5. Interestingly, several major deletions in the BPV-1 genomes were only present in part of the sequencing data, and the non-deleted variant could be detected in parallel.
DOI: 10.6084/m9.figshare.17982725.v1
title: Additional file 4 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 4. A complete overview of the genome organization, highlighting all BPV-2 mutations compared to the corresponding reference sequence. We managed to retrieve 53 complete genomes, 5 corresponding to BPV-2. Due to the low sample load for this type, no conclusion could be made regarding sequence variation for sarcoid-derived BPV-2 sequences.
DOI: 10.6084/m9.figshare.17982725
title: Additional file 4 of New approach for genomic characterisation of equine sarcoid-derived BPV-1/-2 using nanopore-based sequencing

description: Additional file 4. A complete overview of the genome organization, highlighting all BPV-2 mutations compared to the corresponding reference sequence. We managed to retrieve 53 complete genomes, 5 corresponding to BPV-2. Due to the low sample load for this type, no conclusion could be made regarding sequence variation for sarcoid-derived BPV-2 sequences.
DOI: 10.6084/m9.figshare.17982802
title: Additional file 1 of Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs

description: Additional file 1.
DOI: 10.6084/m9.figshare.17982802.v1
title: Additional file 1 of Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs

description: Additional file 1.
DOI: 10.6084/m9.figshare.17982842
title: Additional file 6 of PHD finger protein 20-like protein 1 (PHF20L1) in ovarian cancer: from its overexpression in tissue to its upregulation by the ascites microenvironment

description: Additional file 6: Table S1. General data of the patients whose tissues were used in this study.
DOI: 10.6084/m9.figshare.17982842.v1
title: Additional file 6 of PHD finger protein 20-like protein 1 (PHF20L1) in ovarian cancer: from its overexpression in tissue to its upregulation by the ascites microenvironment

description: Additional file 6: Table S1. General data of the patients whose tissues were used in this study.
DOI: 10.6084/m9.figshare.17982889.v1
title: Additional file 2 of Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism

description: Additional file 1: Supplementary methods and Supplementary Figures. Figure S1. tp53 mutant GITs are aberrantly infiltrated by increased numbers of neutrophils and exhibit hyperimmune responses similar to those induced by DSS treatment. Figure S2. Overview of the experimental procedure and comparisons of gross anatomy between the wild type and tp 53 mutants. Figure S3. The increased number of Alcian blue-positive goblet cells in tp53 mutants are due to Gram (-) bacteria. Figure S4. Gamma-proteobacteria class is enriched in the GITs of tp53 mutants. Figure S5. Aeromonas spp., Citrobacter spp., and Pseudomonas spp. are enriched in the tp53 mutant GITs. Figure S6. E. coli does not induce the increase of Alcian blue-positive goblet cells. Figure S7. Photobacterium damselae DreWT1 isolated from GITs of WT does not induce the increase of NFκB-EGFP activity. Figure S8. Endogenous Aeromonas spp. as well as Pseudomonas spp. and Citrobacter spp. were isolated from tp53 mutants in AMB agar plate culture. Figure S9. tp53 mutation alters metabolic pathways in GITs. Figure S10. SCFA levels show no differences between WT and tp53 mutants. Figure S11. Oseltamivir treatment does not alter free sialic acid levels of the host. Figure S12. Neu5Gc, but not Neu5Ac is utilized as a carbon source by Aeromonas jandaei TP531 for its growth. Figure S13. Elevated inflammation elicited by exogenous addition of mCherry-tagged A. jandaei TP531 in tp53 mutants is abolished by limiting available sialic acids with oseltamivir. Figure S14. Neu5Gc supplementation elevates intestinal inflammation but does barely promote Aeromonas blooming. Figure S15. Neu5Ac supplementation elevates intestinal inflammation in a microbiota-dependent manner, but does not promote blooming of Aeromonas spp.. Figure S16. Citrobacter spp. may outcompete Aeronomas spp. when Neu5Gc and Neu5Ac are supplemented as carbon sources. Figure S17. Monoassociation with A. jandaei TP531 does not induce the lethality and the increase of Alcian blue-positive goblet cells. Figure S18. A proposed working model illustrates dysbiosis and intestinal inflammation by tp53 mutation via imbalanced sialometabolism and a potential therapeutic intervention.
DOI: 10.6084/m9.figshare.17982889
title: Additional file 2 of Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism

description: Additional file 1: Supplementary methods and Supplementary Figures. Figure S1. tp53 mutant GITs are aberrantly infiltrated by increased numbers of neutrophils and exhibit hyperimmune responses similar to those induced by DSS treatment. Figure S2. Overview of the experimental procedure and comparisons of gross anatomy between the wild type and tp 53 mutants. Figure S3. The increased number of Alcian blue-positive goblet cells in tp53 mutants are due to Gram (-) bacteria. Figure S4. Gamma-proteobacteria class is enriched in the GITs of tp53 mutants. Figure S5. Aeromonas spp., Citrobacter spp., and Pseudomonas spp. are enriched in the tp53 mutant GITs. Figure S6. E. coli does not induce the increase of Alcian blue-positive goblet cells. Figure S7. Photobacterium damselae DreWT1 isolated from GITs of WT does not induce the increase of NFκB-EGFP activity. Figure S8. Endogenous Aeromonas spp. as well as Pseudomonas spp. and Citrobacter spp. were isolated from tp53 mutants in AMB agar plate culture. Figure S9. tp53 mutation alters metabolic pathways in GITs. Figure S10. SCFA levels show no differences between WT and tp53 mutants. Figure S11. Oseltamivir treatment does not alter free sialic acid levels of the host. Figure S12. Neu5Gc, but not Neu5Ac is utilized as a carbon source by Aeromonas jandaei TP531 for its growth. Figure S13. Elevated inflammation elicited by exogenous addition of mCherry-tagged A. jandaei TP531 in tp53 mutants is abolished by limiting available sialic acids with oseltamivir. Figure S14. Neu5Gc supplementation elevates intestinal inflammation but does barely promote Aeromonas blooming. Figure S15. Neu5Ac supplementation elevates intestinal inflammation in a microbiota-dependent manner, but does not promote blooming of Aeromonas spp.. Figure S16. Citrobacter spp. may outcompete Aeronomas spp. when Neu5Gc and Neu5Ac are supplemented as carbon sources. Figure S17. Monoassociation with A. jandaei TP531 does not induce the lethality and the increase of Alcian blue-positive goblet cells. Figure S18. A proposed working model illustrates dysbiosis and intestinal inflammation by tp53 mutation via imbalanced sialometabolism and a potential therapeutic intervention.
DOI: 10.6084/m9.figshare.17982892
title: Additional file 3 of Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism

description: Additional file 2. Lists of differentially expressed genes (DEGs) of the gastrointestinal tracts (GITs) from WT vs. tp53 mutants or CR vs. GF conditions at 7 dpf.
DOI: 10.6084/m9.figshare.17982892.v1
title: Additional file 3 of Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism

description: Additional file 2. Lists of differentially expressed genes (DEGs) of the gastrointestinal tracts (GITs) from WT vs. tp53 mutants or CR vs. GF conditions at 7 dpf.
DOI: 10.6084/m9.figshare.17982964
title: Additional file 1 of Multivariate analysis of pedicle screw invasion of the proximal facet joint after lumbar surgery

description: Additional file 1.
DOI: 10.6084/m9.figshare.17982964.v1
title: Additional file 1 of Multivariate analysis of pedicle screw invasion of the proximal facet joint after lumbar surgery

description: Additional file 1.
DOI: 10.6084/m9.figshare.17983012
title: Additional file 1 of Regional heterogeneity and unexpectedly high abundance of Cooperia punctata in beef cattle at a northern latitude revealed by ITS-2 rDNA nemabiome metabarcoding

description: Additional file 1: Figure S1. Gastrointestinal nematode species proportions determined by ITS-2 rDNA nemabiome metabarcoding of herd-level third-stage larval pools prepared from fecal samples of calves from 40 western Canadian cow-calf operations. Numbers from 1–40 on the x-axis identify the individual herds of each province. Except for herds 9, 14, 25, and 34, nemabiome metabarcoding was undertaken on duplicate or triplicate (R1, R2, R3) aliquots of 250 larvae per herd.
DOI: 10.6084/m9.figshare.17983012.v1
title: Additional file 1 of Regional heterogeneity and unexpectedly high abundance of Cooperia punctata in beef cattle at a northern latitude revealed by ITS-2 rDNA nemabiome metabarcoding

description: Additional file 1: Figure S1. Gastrointestinal nematode species proportions determined by ITS-2 rDNA nemabiome metabarcoding of herd-level third-stage larval pools prepared from fecal samples of calves from 40 western Canadian cow-calf operations. Numbers from 1–40 on the x-axis identify the individual herds of each province. Except for herds 9, 14, 25, and 34, nemabiome metabarcoding was undertaken on duplicate or triplicate (R1, R2, R3) aliquots of 250 larvae per herd.
DOI: 10.6084/m9.figshare.17983013
title: Additional file 1 of Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections

description: Additional file 1 Supplementary Tables 1- 12b. Supplementary tables_final.
DOI: 10.6084/m9.figshare.17983013.v1
title: Additional file 1 of Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections

description: Additional file 1 Supplementary Tables 1- 12b. Supplementary tables_final.
DOI: 10.5517/ccdc.csd.cc29brl0
title: CCDC 2125502: Experimental Crystal Structure Determination

description: Related Article: Olivier Blacque, Chunfang Jiang, Heinz Berke|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc29bsq5
title: CCDC 2125537: Experimental Crystal Structure Determination

description: Related Article: Olivier Blacque, Chunfang Jiang, Heinz Berke|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc29bswb
title: CCDC 2125542: Experimental Crystal Structure Determination

description: Related Article: Olivier Blacque, Chunfang Jiang, Heinz Berke|2021|CSD Communication|||
DOI: 10.5517/ccdc.csd.cc29bt9s
title: CCDC 2125555: Experimental Crystal Structure Determination

description: Related Article: Olivier Blacque, Chunfang Jiang, Heinz Berke|2021|CSD Communication|||