cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8638058
title: Supplementary Material for: 2019 European Thyroid Association Guidelines on the Management of Thyroid Dysfunction following Immune Reconstitution Therapy

description: Thyroid dysfunction (TD) frequently occurs as an autoimmune complication of immune reconstitution therapy (IRT), especially in individuals with multiple sclerosis treated with alemtuzumab, a pan-lymphocyte depleting drug with subsequent recovery of immune cell numbers. Less frequently, TD is triggered by highly active antiretroviral therapy (HAART) in patients infected with human immunodeficiency virus (HIV), or patients undergoing bone-marrow/hematopoietic-stem-cell transplantation (BMT/HSCT). In both alemtuzumab-induced TD and HIV/HAART patients, the commonest disorder is Graves’ disease (GD), followed by hypothyroidism and thyroiditis; Graves’ orbitopathy is observed in some GD patients. On the contrary, GD is rare post-BMT/HSCT, where hypothyroidism predominates probably as a consequence of the associated radiation damage. In alemtuzumab-induced TD, the autoantibodies against the thyrotropin receptor (TRAb) play a major role, and 2 main aspects distinguish this condition from the spontaneous form: (1) up to 20% of GD cases exhibit a fluctuating course, with alternating phases of hyper- and hypothyroidism, due to the coexistence of TRAb with stimulating and blocking function; (2) TRAb are also positive in about 70% of hypothyroid patients, with blocking TRAb responsible for nearly half of the cases. The present guidelines will provide up-to-date recommendations and suggestions dedicated to all phases of IRT-induced TD: (1) screening before IRT (recommendations 1–3); (2) monitoring during/after IRT (recommendations 4–7); (3) management of TD post-IRT (recommendations 8–17). The clinical management of IRT-induced TD, and in particular GD, can be challenging. In these guidelines, we propose a summary algorithm which has particular utility for nonspecialist physicians and which is tailored toward management of alemtuzumab-induced TD. However, we recommend prompt referral to specialist endocrinology services following diagnosis of any IRT-induced TD diagnosis, and in particular for pregnant women and those considering pregnancy.
DOI: 10.6084/m9.figshare.8638058.v1
title: Supplementary Material for: 2019 European Thyroid Association Guidelines on the Management of Thyroid Dysfunction following Immune Reconstitution Therapy

description: Thyroid dysfunction (TD) frequently occurs as an autoimmune complication of immune reconstitution therapy (IRT), especially in individuals with multiple sclerosis treated with alemtuzumab, a pan-lymphocyte depleting drug with subsequent recovery of immune cell numbers. Less frequently, TD is triggered by highly active antiretroviral therapy (HAART) in patients infected with human immunodeficiency virus (HIV), or patients undergoing bone-marrow/hematopoietic-stem-cell transplantation (BMT/HSCT). In both alemtuzumab-induced TD and HIV/HAART patients, the commonest disorder is Graves’ disease (GD), followed by hypothyroidism and thyroiditis; Graves’ orbitopathy is observed in some GD patients. On the contrary, GD is rare post-BMT/HSCT, where hypothyroidism predominates probably as a consequence of the associated radiation damage. In alemtuzumab-induced TD, the autoantibodies against the thyrotropin receptor (TRAb) play a major role, and 2 main aspects distinguish this condition from the spontaneous form: (1) up to 20% of GD cases exhibit a fluctuating course, with alternating phases of hyper- and hypothyroidism, due to the coexistence of TRAb with stimulating and blocking function; (2) TRAb are also positive in about 70% of hypothyroid patients, with blocking TRAb responsible for nearly half of the cases. The present guidelines will provide up-to-date recommendations and suggestions dedicated to all phases of IRT-induced TD: (1) screening before IRT (recommendations 1–3); (2) monitoring during/after IRT (recommendations 4–7); (3) management of TD post-IRT (recommendations 8–17). The clinical management of IRT-induced TD, and in particular GD, can be challenging. In these guidelines, we propose a summary algorithm which has particular utility for nonspecialist physicians and which is tailored toward management of alemtuzumab-induced TD. However, we recommend prompt referral to specialist endocrinology services following diagnosis of any IRT-induced TD diagnosis, and in particular for pregnant women and those considering pregnancy.
DOI: 10.6084/m9.figshare.8637974
title: Evidence for non-marine Jurassic to earliest Cretaceous sediments in the pre-breakup section of the Mentelle Basin, southwestern Australia

description: The Mentelle Basin, located off the southwestern continental Australian margin, is an under-explored deep-water basin that developed during the breakup of eastern Gondwana in the Middle Jurassic through to the Early Cretaceous. There is a high degree of uncertainty in stratigraphic interpretations of the basin owing to the lack of well and seismic data in the region. As a consequence, there has been a heavy reliance on data from the neighbouring Perth Basin to infer the geological history of the Mentelle Basin. During Expedition 369 of the International Ocean Discovery Program, a single hole was drilled with a rotary core bit to 517.10 m below seafloor at Site U1515 on the continental slope in the eastern Mentelle Basin. The aim was to sample and date the inferred Permian to Jurassic pre-breakup strata. The presence of palynomorphs including <i>Murospora florida</i> and <i>Retitriletes watherooensis</i> in the fluvio-lacustrine succession below the Valanginian breakup unconformity indicates a Jurassic to earliest Cretaceous age for the upper part of the pre-rift sedimentary succession. Notable characteristics of this succession include intervals with high percentages of total organic carbon (up to 44 wt%) and high hydrogen index values (Type I source rocks) associated with an increase in <i>Botryococcus</i> and other freshwater algae that accumulated in shallow lakes and waterlogged floodplains. A possible example of dinoturbation was also noted in this core. The discovery of Jurassic to earliest Cretaceous pre-breakup strata at Site U1515 suggests that Jurassic rifting was not constrained to the western depocentre of the Mentelle Basin, but also extended to a number of depocentres in the eastern Mentelle Basin. This has significant implications for the understanding of the regional tectonic history and the Mentelle Basin’s petroleum potential.Pre-breakup strata sampled in the eastern Mentelle Basin for the first time by IODP Expedition 369Upper Jurassic–Lower Cretaceous non-marine strata below the Valanginian UnconformityHigh TOC’s, high abundances of <i>Botryococcus</i> algae in a few horizons and a possible example of dinoturbationJurassic rifting not constrained to the western Mentelle Basin, but to depocentres in the east Pre-breakup strata sampled in the eastern Mentelle Basin for the first time by IODP Expedition 369 Upper Jurassic–Lower Cretaceous non-marine strata below the Valanginian Unconformity High TOC’s, high abundances of <i>Botryococcus</i> algae in a few horizons and a possible example of dinoturbation Jurassic rifting not constrained to the western Mentelle Basin, but to depocentres in the east
DOI: 10.6084/m9.figshare.8637974.v2
title: Evidence for non-marine Jurassic to earliest Cretaceous sediments in the pre-breakup section of the Mentelle Basin, southwestern Australia

description: The Mentelle Basin, located off the southwestern continental Australian margin, is an under-explored deep-water basin that developed during the breakup of eastern Gondwana in the Middle Jurassic through to the Early Cretaceous. There is a high degree of uncertainty in stratigraphic interpretations of the basin owing to the lack of well and seismic data in the region. As a consequence, there has been a heavy reliance on data from the neighbouring Perth Basin to infer the geological history of the Mentelle Basin. During Expedition 369 of the International Ocean Discovery Program, a single hole was drilled with a rotary core bit to 517.10 m below seafloor at Site U1515 on the continental slope in the eastern Mentelle Basin. The aim was to sample and date the inferred Permian to Jurassic pre-breakup strata. The presence of palynomorphs including <i>Murospora florida</i> and <i>Retitriletes watherooensis</i> in the fluvio-lacustrine succession below the Valanginian breakup unconformity indicates a Jurassic to earliest Cretaceous age for the upper part of the pre-rift sedimentary succession. Notable characteristics of this succession include intervals with high percentages of total organic carbon (up to 44 wt%) and high hydrogen index values (Type I source rocks) associated with an increase in <i>Botryococcus</i> and other freshwater algae that accumulated in shallow lakes and waterlogged floodplains. A possible example of dinoturbation was also noted in this core. The discovery of Jurassic to earliest Cretaceous pre-breakup strata at Site U1515 suggests that Jurassic rifting was not constrained to the western depocentre of the Mentelle Basin, but also extended to a number of depocentres in the eastern Mentelle Basin. This has significant implications for the understanding of the regional tectonic history and the Mentelle Basin’s petroleum potential.Pre-breakup strata sampled in the eastern Mentelle Basin for the first time by IODP Expedition 369Upper Jurassic–Lower Cretaceous non-marine strata below the Valanginian UnconformityHigh TOC’s, high abundances of <i>Botryococcus</i> algae in a few horizons and a possible example of dinoturbationJurassic rifting not constrained to the western Mentelle Basin, but to depocentres in the east Pre-breakup strata sampled in the eastern Mentelle Basin for the first time by IODP Expedition 369 Upper Jurassic–Lower Cretaceous non-marine strata below the Valanginian Unconformity High TOC’s, high abundances of <i>Botryococcus</i> algae in a few horizons and a possible example of dinoturbation Jurassic rifting not constrained to the western Mentelle Basin, but to depocentres in the east
DOI: 10.6084/m9.figshare.8637974.v1
title: Evidence for non-marine Jurassic to earliest Cretaceous sediments in the pre-breakup section of the Mentelle Basin, southwestern Australia

description: The Mentelle Basin, located off the southwestern continental Australian margin, is an under-explored deep-water basin that developed during the breakup of eastern Gondwana in the Middle Jurassic through to the Early Cretaceous. There is a high degree of uncertainty in stratigraphic interpretations of the basin owing to the lack of well and seismic data in the region. As a consequence, there has been a heavy reliance on data from the neighbouring Perth Basin to infer the geological history of the Mentelle Basin. During Expedition 369 of the International Ocean Discovery Program, a single hole was drilled with a rotary core bit to 517.10 m below seafloor at Site U1515 on the continental slope in the eastern Mentelle Basin. The aim was to sample and date the inferred Permian to Jurassic pre-breakup strata. The presence of palynomorphs including <i>Murospora florida</i> and <i>Retitriletes watherooensis</i> in the fluvio-lacustrine succession below the Valanginian breakup unconformity indicates a Jurassic to earliest Cretaceous age for the upper part of the pre-rift sedimentary succession. Notable characteristics of this succession include intervals with high percentages of total organic carbon (up to 44 wt%) and high hydrogen index values (Type I source rocks) associated with an increase in <i>Botryococcus</i> and other freshwater algae that accumulated in shallow lakes and waterlogged floodplains. A possible example of dinoturbation was also noted in this core. The discovery of Jurassic to earliest Cretaceous pre-breakup strata at Site U1515 suggests that Jurassic rifting was not constrained to the western depocentre of the Mentelle Basin, but also extended to a number of depocentres in the eastern Mentelle Basin. This has significant implications for the understanding of the regional tectonic history and the Mentelle Basin’s petroleum potential.Pre-breakup strata sampled in the eastern Mentelle Basin for the first time by IODP Expedition 369Upper Jurassic–Lower Cretaceous non-marine strata below the Valanginian UnconformityHigh TOC’s, high abundances of <i>Botryococcus</i> algae in a few horizons and a possible example of dinoturbationJurassic rifting not constrained to the western Mentelle Basin, but to depocentres in the east Pre-breakup strata sampled in the eastern Mentelle Basin for the first time by IODP Expedition 369 Upper Jurassic–Lower Cretaceous non-marine strata below the Valanginian Unconformity High TOC’s, high abundances of <i>Botryococcus</i> algae in a few horizons and a possible example of dinoturbation Jurassic rifting not constrained to the western Mentelle Basin, but to depocentres in the east
DOI: 10.6084/m9.figshare.8637911
title: Additional file 7: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S5. Primer sequences used for expression analysis (qRT-PCR) of the mouse (Additional file 4: Figure S1) and chicken genes (Fig. 3 and Additional file 5: Figure S2) (XLSX 33 kb)
DOI: 10.6084/m9.figshare.8637911.v1
title: Additional file 7: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S5. Primer sequences used for expression analysis (qRT-PCR) of the mouse (Additional file 4: Figure S1) and chicken genes (Fig. 3 and Additional file 5: Figure S2) (XLSX 33 kb)
DOI: 10.6084/m9.figshare.8637905
title: Additional file 6: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S4. List of GOs (BP GOTERM) corresponding to the 379 fly genes according to DAVID Functional Annotation Tool, with Fold Enrichment (column E) and Bonferroni P-value (column F). (XLSX 60 kb)
DOI: 10.6084/m9.figshare.8637905.v1
title: Additional file 6: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S4. List of GOs (BP GOTERM) corresponding to the 379 fly genes according to DAVID Functional Annotation Tool, with Fold Enrichment (column E) and Bonferroni P-value (column F). (XLSX 60 kb)
DOI: 10.6084/m9.figshare.8637887
title: Additional file 3: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S3A. List of the 28 fly genes (columns B-F), whose mouse orthologs (68) are enriched in testis (G-L). Chicken (M-R) and zebrafish (S-X) orthologs were retrieved with Biomart tool, and their syntenic position and tissular expression were analysed. Mutant phenotype was indicated in fly (E), and when available in mouse (L) and zebrafish (X). Table S3B. Lines 1 to 11: mouse/chicken orthology links of the testicular genes described in Table S3A Lines 12 to 21: mouse/zebrafish orthology links of the testicular genes described in Table S3A. (ZIP 50 kb)
DOI: 10.6084/m9.figshare.8637887.v1
title: Additional file 3: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S3A. List of the 28 fly genes (columns B-F), whose mouse orthologs (68) are enriched in testis (G-L). Chicken (M-R) and zebrafish (S-X) orthologs were retrieved with Biomart tool, and their syntenic position and tissular expression were analysed. Mutant phenotype was indicated in fly (E), and when available in mouse (L) and zebrafish (X). Table S3B. Lines 1 to 11: mouse/chicken orthology links of the testicular genes described in Table S3A Lines 12 to 21: mouse/zebrafish orthology links of the testicular genes described in Table S3A. (ZIP 50 kb)
DOI: 10.6084/m9.figshare.8637881
title: Additional file 2: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S2. FLY genes without ortholog in chordates. These genes are extracted from (Additional file 1: Table S1) for more readability. In blue: genes having a tree in Ensembl (release 88) In orange: genes with no tree in Ensembl (release 88) but in EnsemblMetazoa (release 88). (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8637872
title: Additional file 1: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S1. Columns B to I: fly genes List of the 379 Drosophila genes with male reproductive phenotype when mutated (A-F) and their paralogs (G-I). Columns J to BL: mouse genes. The mouse orthologs of the 379 fly genes are listed (columns J-M) and for each of them their expression in adult mice organs (according to Unigene EST profile) is provided (for calculation of their relative testis/ovary expression: columns BG-BL). (XLSX 691 kb)
DOI: 10.6084/m9.figshare.8637881.v1
title: Additional file 2: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S2. FLY genes without ortholog in chordates. These genes are extracted from (Additional file 1: Table S1) for more readability. In blue: genes having a tree in Ensembl (release 88) In orange: genes with no tree in Ensembl (release 88) but in EnsemblMetazoa (release 88). (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8637872.v1
title: Additional file 1: of An evolutionary approach to recover genes predominantly expressed in the testes of the zebrafish, chicken and mouse

description: Table S1. Columns B to I: fly genes List of the 379 Drosophila genes with male reproductive phenotype when mutated (A-F) and their paralogs (G-I). Columns J to BL: mouse genes. The mouse orthologs of the 379 fly genes are listed (columns J-M) and for each of them their expression in adult mice organs (according to Unigene EST profile) is provided (for calculation of their relative testis/ovary expression: columns BG-BL). (XLSX 691 kb)
DOI: 10.6084/m9.figshare.8637857
title: Additional file 10: of Active eukaryotes in drinking water distribution systems of ground and surface waterworks

description: Metadata file of samples (Table S12.) and DNA/RNA pairs (Table S13.) (XLSX 50 kb)
DOI: 10.6084/m9.figshare.8637857.v1
title: Additional file 10: of Active eukaryotes in drinking water distribution systems of ground and surface waterworks

description: Metadata file of samples (Table S12.) and DNA/RNA pairs (Table S13.) (XLSX 50 kb)
DOI: 10.6084/m9.figshare.8637797
title: MOESM1 of Detection of genomic regions underlying resistance to gastrointestinal parasites in Australian sheep

description: Additional file 1: Table S1. List of candidate genes and the biological pathways they belong to.
DOI: 10.6084/m9.figshare.8637797.v1
title: MOESM1 of Detection of genomic regions underlying resistance to gastrointestinal parasites in Australian sheep

description: Additional file 1: Table S1. List of candidate genes and the biological pathways they belong to.
DOI: 10.6084/m9.figshare.8637776
title: MOESM1 of The autophagy protein ATG9A promotes HIV-1 infectivity

description: Additional file 1: Table S1. Identification of HIV-1 and SIV Nef interactors by the TAP-MS protocol outlined in Fig. 1b. Initial datasets were filtered against the experimental control of the empty vector. The “IPI” column provides the International Protein Index identification code referring to the name of the protein in the “User input” column. The “unique peptide” column indicates the number of distinct peptides used to identify the protein whereas the “total peptide” column indicates the total number of identified peptides matched for the protein. Raw data were filtered against the CRAPome database and several values were generated. The experiment appeared (ExpAP) ratio indicates the number of times that protein appeared in a control experiment divided by the total number of experiments analyzed. The column “ExpAP calculated” provides the value of the calculated ratio from the “ExpAP” column. The average spectral count (Ave SC) is the average number of peptides in the experiments where the protein appeared. Max SC is the highest number of peptides found in a single experiment. By multiplying AveSC and ExpAP, we obtained an estimate of both the number of times the protein was identified in a negative control and its abundance when it was identified.
DOI: 10.6084/m9.figshare.8637776.v1
title: MOESM1 of The autophagy protein ATG9A promotes HIV-1 infectivity

description: Additional file 1: Table S1. Identification of HIV-1 and SIV Nef interactors by the TAP-MS protocol outlined in Fig. 1b. Initial datasets were filtered against the experimental control of the empty vector. The “IPI” column provides the International Protein Index identification code referring to the name of the protein in the “User input” column. The “unique peptide” column indicates the number of distinct peptides used to identify the protein whereas the “total peptide” column indicates the total number of identified peptides matched for the protein. Raw data were filtered against the CRAPome database and several values were generated. The experiment appeared (ExpAP) ratio indicates the number of times that protein appeared in a control experiment divided by the total number of experiments analyzed. The column “ExpAP calculated” provides the value of the calculated ratio from the “ExpAP” column. The average spectral count (Ave SC) is the average number of peptides in the experiments where the protein appeared. Max SC is the highest number of peptides found in a single experiment. By multiplying AveSC and ExpAP, we obtained an estimate of both the number of times the protein was identified in a negative control and its abundance when it was identified.
DOI: 10.6084/m9.figshare.8637725
title: Additional file 2: of Regulation of nursing professionals in Cambodia and Vietnam: a review of the evolution and key influences

description: Chronologies of nursing regulatory development in Vietnam. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8637725.v1
title: Additional file 2: of Regulation of nursing professionals in Cambodia and Vietnam: a review of the evolution and key influences

description: Chronologies of nursing regulatory development in Vietnam. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8637716
title: Additional file 1: of Regulation of nursing professionals in Cambodia and Vietnam: a review of the evolution and key influences

description: Chronologies of nursing regulatory development in Cambodia. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8637716.v1
title: Additional file 1: of Regulation of nursing professionals in Cambodia and Vietnam: a review of the evolution and key influences

description: Chronologies of nursing regulatory development in Cambodia. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8637575
title: Additional file 5: of iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis

description: Preliminary analysis report generated automatically by the iMAP to provide a summary of conserved taxonomy assigned to OTUs and the initial analysis of OTUs and taxa data. The preliminary analysis report was automatically saved in the “reports” folder as “report4_preliminary_analysis.html”. (HTML 20379 kb)
DOI: 10.6084/m9.figshare.8637575.v1
title: Additional file 5: of iMAP: an integrated bioinformatics and visualization pipeline for microbiome data analysis

description: Preliminary analysis report generated automatically by the iMAP to provide a summary of conserved taxonomy assigned to OTUs and the initial analysis of OTUs and taxa data. The preliminary analysis report was automatically saved in the “reports” folder as “report4_preliminary_analysis.html”. (HTML 20379 kb)