cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0108670.10fu
title: SH0108670.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.13145/bacdive116794.20251217.10
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive116795.20241212.9.2
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.15468/dl.mze4k3
title: Occurrence Download

description: A dataset containing 99628 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trichophorum cespitosum (L.) Hartm.",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2010",
 "HasCoordinate is true"
 ]
}

 The dataset includes 99628 records from 331 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006276-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/2gme27
title: UCM Fossil Vertebrate Specimens (Arctos)

description: The UCM Fossil Vertebrate Collection contains nearly a hundred thousand cataloged fossil vertebrate specimens. This collection is the culmination of over 100 years of collecting from around the world and contains fossils that range in age from the Devonian through the Quaternary Periods. Its strengths are in Cretaceous marine vertebrates and Late Mesozoic-Cenozoic fossil mammals from the Rocky Mountain region.
DOI: 10.15468/dl.fuep28
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pinna rugosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Occurrence evidence)",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is one of (Absent)"
 ]
 }
 }
 ]
}

 The dataset includes 113 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005248-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5ewp89
title: Occurrence Download

description: A dataset containing 1911 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus rubra",
 "HasCoordinate is true",
 "Country is Denmark"
 ]
}

 The dataset includes 1911 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005249-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tgh7qf
title: Occurrence Download

description: A dataset containing 1698 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Quercus rubra",
 "HasCoordinate is true",
 "Country is Sweden"
 ]
}

 The dataset includes 1698 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005250-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30305644
title: Supplementary Material for: RNA-editing enzyme ADAR1 attenuates rheumatoid arthritis via regulating fibroblast-like synoviocytes-derived exosomal circFTO

description: Rheumatoid arthritis (RA) is a chronic debilitating autoimmune disorder and a predominant cause of potentially treatable functional disability. Adenosine deaminase acting on RNA 1 (ADAR1), as an RNA-editing enzyme, can regulate circular RNAs (circRNAs) and fibroblast-like synoviocytes (FLSs)-derived exosomal circFTO has been proposed as a contributor to RA. This study was dedicated to elaborate the role of ADAR1 in RA and the association between ADAR1 and circFTO. RT-qPCR examined circFTO, fat mass and obesity-associated protein (FTO), DExH-box helicase 9 (DHX9), ADAR1 and Quaking (QKI) expressions in RA-FLSs and human fibroblast-like synoviocytes (HFLSs), and circFTO expression in RA-FLSs- or HFLSs-derived exosomes. In severe combined immunodeficiency (SCID) mice engrafted with human cartilage and rheumatoid synovium tissue (SCID-HuRAg), the in vivo imaging technique was adopted to track the distribution and migration of RA-FLSs and HFLSs. H&E staining and Safranin-O staining measured the severity of RA and engrafted cartilage degradation. Immunohistochemistry assessed the expression of inflammation-, anabolic- and catabolic-related genes. Also, RT-qPCR examined the expressions of circFTO, miR-548a-3p, heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1), anabolic- and catabolic-related genes. ADAR1 was lowly expressed in RA-FLSs and ADAR1 silencing reduced circFTO expression in RA-FLSs-derived exosomes. In vivo, RA-FLSs were widely distributed and the migration capability was enhanced compared with HFLSs. ADAR1 overexpression efficiently decreased arthritis severity, attenuated cartilage degradation and inflammatory response in SCID-HuRAg mice injected with RA-FLSs. Besides, ADAR1 could decrease circFTO and hnRNPA2B1 expressions while elevating miR-548a-3p expression, particularly in SCID-HuRAg mice injected with RA-FLSs. To summarize, our findings identify ADAR1 as a potential treatment target for RA at least partially via regulating circFTO.
DOI: 10.6084/m9.figshare.30305644.v1
title: Supplementary Material for: RNA-editing enzyme ADAR1 attenuates rheumatoid arthritis via regulating fibroblast-like synoviocytes-derived exosomal circFTO

description: Rheumatoid arthritis (RA) is a chronic debilitating autoimmune disorder and a predominant cause of potentially treatable functional disability. Adenosine deaminase acting on RNA 1 (ADAR1), as an RNA-editing enzyme, can regulate circular RNAs (circRNAs) and fibroblast-like synoviocytes (FLSs)-derived exosomal circFTO has been proposed as a contributor to RA. This study was dedicated to elaborate the role of ADAR1 in RA and the association between ADAR1 and circFTO. RT-qPCR examined circFTO, fat mass and obesity-associated protein (FTO), DExH-box helicase 9 (DHX9), ADAR1 and Quaking (QKI) expressions in RA-FLSs and human fibroblast-like synoviocytes (HFLSs), and circFTO expression in RA-FLSs- or HFLSs-derived exosomes. In severe combined immunodeficiency (SCID) mice engrafted with human cartilage and rheumatoid synovium tissue (SCID-HuRAg), the in vivo imaging technique was adopted to track the distribution and migration of RA-FLSs and HFLSs. H&E staining and Safranin-O staining measured the severity of RA and engrafted cartilage degradation. Immunohistochemistry assessed the expression of inflammation-, anabolic- and catabolic-related genes. Also, RT-qPCR examined the expressions of circFTO, miR-548a-3p, heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1), anabolic- and catabolic-related genes. ADAR1 was lowly expressed in RA-FLSs and ADAR1 silencing reduced circFTO expression in RA-FLSs-derived exosomes. In vivo, RA-FLSs were widely distributed and the migration capability was enhanced compared with HFLSs. ADAR1 overexpression efficiently decreased arthritis severity, attenuated cartilage degradation and inflammatory response in SCID-HuRAg mice injected with RA-FLSs. Besides, ADAR1 could decrease circFTO and hnRNPA2B1 expressions while elevating miR-548a-3p expression, particularly in SCID-HuRAg mice injected with RA-FLSs. To summarize, our findings identify ADAR1 as a potential treatment target for RA at least partially via regulating circFTO.
DOI: 10.6084/m9.figshare.30305647
title: Supplementary Material for: Breathing dysfunction as a meaningful and measurable aspect of health in Rett Syndrome: A caregiver's perspective

description: Introduction: Incorporating outcome measures that assess the most impactful symptoms is a priority for clinical trials. We qualitatively examined whether caregivers of individuals with Rett Syndrome deemed breathing dysfunction as a meaningful and measurable aspect of health. Methods: We conducted semi-structured interviews (N = 13) with caregivers of individuals with Rett syndrome followed by thematic analysis grounded in theory to examine themes. Results: Themes and sub-themes for experiences with breathing dysfunction emerged: (1) meaningfulness; (2) impact; and (3) connecting with other symptoms. Two themes for preferences for digitally measuring breathing dysfunction emerged: (1) conditional willingness; and (2) benefits of digital measurement. Conclusion: Caregivers reported that breathing dysfunction was meaningful and measurable and had significant impacts on their child’s lives as well as theirs and their families. This study lays the groundwork for guiding the development of novel measures and outcomes within future clinical trials managing breathing dysfunction.
DOI: 10.6084/m9.figshare.30305647.v1
title: Supplementary Material for: Breathing dysfunction as a meaningful and measurable aspect of health in Rett Syndrome: A caregiver's perspective

description: Introduction: Incorporating outcome measures that assess the most impactful symptoms is a priority for clinical trials. We qualitatively examined whether caregivers of individuals with Rett Syndrome deemed breathing dysfunction as a meaningful and measurable aspect of health. Methods: We conducted semi-structured interviews (N = 13) with caregivers of individuals with Rett syndrome followed by thematic analysis grounded in theory to examine themes. Results: Themes and sub-themes for experiences with breathing dysfunction emerged: (1) meaningfulness; (2) impact; and (3) connecting with other symptoms. Two themes for preferences for digitally measuring breathing dysfunction emerged: (1) conditional willingness; and (2) benefits of digital measurement. Conclusion: Caregivers reported that breathing dysfunction was meaningful and measurable and had significant impacts on their child’s lives as well as theirs and their families. This study lays the groundwork for guiding the development of novel measures and outcomes within future clinical trials managing breathing dysfunction.
DOI: 10.6084/m9.figshare.30305650
title: Supplementary Material for: Paroxysmal Kinesigenic Dyskinesia caused by 16p11.2 microdeletion: A Case Report

description: Paroxysmal Kinesigenic Dyskinesia (PKD) is a rare movement disorder which can present a diagnostic challenge. We present a case with video examples, of an uncommon cause of PKD. A 16 year old male presented with abrupt onset, brief episodes of right sided head version, usually accompanied by extension of the left and rarely right arm. He experienced proceeding bilateral sensory disturbance in his legs. His twin brother was diagnosed with focal seizures. There were no neurodevelopmental concerns. Sudden movement preceded stereotypical episodes. MRI brain was unremarkable. Home video and video EEG was utilised to reach a clinical diagnosis. The clinical phenotype of (PKD) was recognised and he was treated with low dose carbamazepine. Next-generation sequencing showed no pathogenic variant in gene panels for dystonia or channelopathies, including the common genes associated with PKD such as PRRT2 mutations. Subsequent microarray testing demonstrated a pathogenic 599kb gene deletion on the 16p11.2 region, which includes the PRRT2 gene, confirming the diagnosis of PKD. PKD is an important diagnosis to consider due to the potential delay in diagnosis, genetic implications, and treatment responsiveness. Video recordings are valuable diagnostic tools. When suspecting PKD, screening for PRRT2 variants as well as 16p11.2 microdeletions should be considered.
DOI: 10.6084/m9.figshare.30305650.v1
title: Supplementary Material for: Paroxysmal Kinesigenic Dyskinesia caused by 16p11.2 microdeletion: A Case Report

description: Paroxysmal Kinesigenic Dyskinesia (PKD) is a rare movement disorder which can present a diagnostic challenge. We present a case with video examples, of an uncommon cause of PKD. A 16 year old male presented with abrupt onset, brief episodes of right sided head version, usually accompanied by extension of the left and rarely right arm. He experienced proceeding bilateral sensory disturbance in his legs. His twin brother was diagnosed with focal seizures. There were no neurodevelopmental concerns. Sudden movement preceded stereotypical episodes. MRI brain was unremarkable. Home video and video EEG was utilised to reach a clinical diagnosis. The clinical phenotype of (PKD) was recognised and he was treated with low dose carbamazepine. Next-generation sequencing showed no pathogenic variant in gene panels for dystonia or channelopathies, including the common genes associated with PKD such as PRRT2 mutations. Subsequent microarray testing demonstrated a pathogenic 599kb gene deletion on the 16p11.2 region, which includes the PRRT2 gene, confirming the diagnosis of PKD. PKD is an important diagnosis to consider due to the potential delay in diagnosis, genetic implications, and treatment responsiveness. Video recordings are valuable diagnostic tools. When suspecting PKD, screening for PRRT2 variants as well as 16p11.2 microdeletions should be considered.
DOI: 10.6084/m9.figshare.30305653
title: Supplementary Material for: Adverse Event Monitoring with Imaging: Prognostic Significance in Atezolizumab Plus Bevacizumab Therapy for Unresectable Hepatocellular Carcinoma

description: Background/Aim: Immune checkpoint inhibitors (ICIs) have emerged as the first-line systemic therapy for unresectable hepatocellular carcinoma (HCC). Emerging evidence suggests that immune-related adverse events (irAEs) may be associated with improved ICI efficacy. This study evaluated the impact of adverse events during atezolizumab plus bevacizumab therapy on clinical outcomes in patients with unresectable HCC.
Methods: This retrospective study included consecutive patients receiving first-line atezolizumab plus bevacizumab for unresectable HCC. IrAEs and bevacizumab-related adverse events were assessed using the National Cancer Institute's Common Terminology Criteria for Adverse Events (version 5.0). Imaging studies conducted during treatment were reviewed to identify asymptomatic, imaging-detected adverse events. Overall survival (OS) was the primary endpoint and was analyzed using time-dependent Cox regression. The secondary endpoint was the disease control rate (DCR).
Results: Among the 198 enrolled patients, 12 had imaging-detected irAEs without symptoms (asymptomatic AE group), whereas 56 experienced clinical symptoms of irAEs (n=28), bevacizumab-related adverse events (n=19) or both (n=9) (symptomatic AE group). The OS rates at 6, 12, 18, and 24 months were 100.0%, 82.5%, 82.5%, and 82.5%, respectively, in the asymptomatic AE group; 89.1%, 64.1%, 41.7%, and 40.5%, respectively, in the symptomatic AE group; and 72.3%, 48.3%, 31.3%, and 19.4%, respectively, for the non-AE group. Compared with the non-AE group, both the asymptomatic and symptomatic AE groups showed significantly improved OS in the inverse probability of treatment weighting-adjusted time-dependent Cox regression analysis (P=0.02). The DCR was significantly greater in the asymptomatic AE group (100.0%) and the symptomatic AE group (91.8%) than in the non-AE group (60.0%) (P&lt;0.001).
Conclusion: Adverse events during atezolizumab plus bevacizumab therapy are associated with improved OS and treatment response in unresectable HCC patients. Asymptomatic imaging-detected irAEs may serve as prognostic factors, highlighting the value of proactive imaging in patient management.
DOI: 10.6084/m9.figshare.30305653.v1
title: Supplementary Material for: Adverse Event Monitoring with Imaging: Prognostic Significance in Atezolizumab Plus Bevacizumab Therapy for Unresectable Hepatocellular Carcinoma

description: Background/Aim: Immune checkpoint inhibitors (ICIs) have emerged as the first-line systemic therapy for unresectable hepatocellular carcinoma (HCC). Emerging evidence suggests that immune-related adverse events (irAEs) may be associated with improved ICI efficacy. This study evaluated the impact of adverse events during atezolizumab plus bevacizumab therapy on clinical outcomes in patients with unresectable HCC.
Methods: This retrospective study included consecutive patients receiving first-line atezolizumab plus bevacizumab for unresectable HCC. IrAEs and bevacizumab-related adverse events were assessed using the National Cancer Institute's Common Terminology Criteria for Adverse Events (version 5.0). Imaging studies conducted during treatment were reviewed to identify asymptomatic, imaging-detected adverse events. Overall survival (OS) was the primary endpoint and was analyzed using time-dependent Cox regression. The secondary endpoint was the disease control rate (DCR).
Results: Among the 198 enrolled patients, 12 had imaging-detected irAEs without symptoms (asymptomatic AE group), whereas 56 experienced clinical symptoms of irAEs (n=28), bevacizumab-related adverse events (n=19) or both (n=9) (symptomatic AE group). The OS rates at 6, 12, 18, and 24 months were 100.0%, 82.5%, 82.5%, and 82.5%, respectively, in the asymptomatic AE group; 89.1%, 64.1%, 41.7%, and 40.5%, respectively, in the symptomatic AE group; and 72.3%, 48.3%, 31.3%, and 19.4%, respectively, for the non-AE group. Compared with the non-AE group, both the asymptomatic and symptomatic AE groups showed significantly improved OS in the inverse probability of treatment weighting-adjusted time-dependent Cox regression analysis (P=0.02). The DCR was significantly greater in the asymptomatic AE group (100.0%) and the symptomatic AE group (91.8%) than in the non-AE group (60.0%) (P&lt;0.001).
Conclusion: Adverse events during atezolizumab plus bevacizumab therapy are associated with improved OS and treatment response in unresectable HCC patients. Asymptomatic imaging-detected irAEs may serve as prognostic factors, highlighting the value of proactive imaging in patient management.
DOI: 10.6084/m9.figshare.c.3627302_d1.v1
title: Additional file 3: Table S2. of Infectious hematopoietic necrosis virus (IHNV) persistence in Sockeye Salmon: influence on brain transcriptome and subsequent response to the viral mimic poly(I:C)

description: Fold change (FC ≤ 1.5) list and GO enrichment analysis of probes affected by IHNV status.
DOI: 10.25378/janelia.24246616
title: Manual organelle segmentations (crop97) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized breast cancer cell (jrc_sum159-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><br><br>- <b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<br><br><b>Annotation description</b>: Dense segmentations of nucleus in jrc_sum159-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<br><br><b>Annotation ID</b>: crop97<br><br><b>Primary Annotator</b>: Aubrey Weigel<br><br><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<br><br><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<br><br><b>Annotated voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 0.8 x 0.8 x 0.8 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 26823 x 3831 x 23351 (x, y, z)<br><br><b>Classes annotated</b>: nucleus<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop97<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-1<br><br><b>Source (EM) voxel size (nm)</b>: 4 x 4 x 4.56 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 64 x 11.2 x 34.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.13114352<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-1<br><br><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<br><br><b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<br><br><b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.
DOI: 10.25378/janelia.24246616.v1
title: Manual organelle segmentations (crop97) in near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of immortalized breast cancer cell (jrc_sum159-1)

description: <b>This acquisition is part of the CellMap 2024 Segmentation Challenge</b><br><br>- <b>Challenge DOI:</b> https://doi.org/10.25378/janelia.c.7456966<br><br>- <b>Challenge Website:</b> https://cellmapchallenge.janelia.org/<br><br><b>Annotation description</b>: Dense segmentations of nucleus in jrc_sum159-1 using Amira 3D 2021.1, Classic Segmentation Workroom and the 'Using Amira to manually segment organelles in vEM for machine learning V.3' annotation protocol.<br><br><b>Annotation ID</b>: crop97<br><br><b>Primary Annotator</b>: Aubrey Weigel<br><br><b>Annotation protocol</b>: Using Amira to manually segment organelles in vEM for machine learning V.3 (http://dx.doi.org/10.17504/protocols.io.bp2l61rb5vqe/v3)<br><br><b>Software</b>: Amira 3D 2021.1, Classic Segmentation Workroom<br><br><b>Annotated voxel size (nm)</b>: 2 x 2 x 2 (x, y, z)<br><br><b>Annotated data dimensions (µm)</b>: 0.8 x 0.8 x 0.8 (x, y, z)<br><br><b>Annotated data offset (nm)</b>: 26823 x 3831 x 23351 (x, y, z)<br><br><b>Classes annotated</b>: nucleus<br><br><b>Dataset URL</b>: s3://janelia-cosem-datasets/jrc_sum159-1/jrc_sum159-1.zarr/recon-1/labels/groundtruth/crop97<br><br><b>Source (EM) dataset ID</b>: jrc_sum159-1<br><br><b>Source (EM) voxel size (nm)</b>: 4 x 4 x 4.56 (x, y, z)<br><br><b>Source (EM) data dimensions (µm)</b>: 64 x 11.2 x 34.8 (x, y, z)<br><br><b>Source (EM) DOI</b>: https://doi.org/10.25378/janelia.13114352<br><br><b>Visualization website</b>: https://openorganelle.janelia.org/datasets/jrc_sum159-1<br><br><b>Publication:</b> <i>CellMap Segmentation Challenge,</i> 2024.<br><br><b>The CellMap Project Team during this time consisted of:</b> David Ackerman, Davis Bennett, Marley Bryant, Hannah Nguyen, Grace Park, Alyson Petruncio, Alannah Post, Jacquelyn Price, Diana Ramirez, Jeff Rhoades, Rebecca Vorimo, Aubrey Weigel, Marwan Zouinkhi, Yurii Zubov.<br><br><b>The CellMap Project Team Steering Committee during this time consisted of:</b> Misha Ahrens, Christopher Beck, Teng-Leong Chew, Daniel Feliciano, Jan Funke, Harald Hess, Wyatt Korff, Jennifer Lippincott-Schwartz, Zhe J. Liu, Kayvon Pedram, Stephan Preibisch, Stephan Saalfeld, Ronald Vale, and Aubrey Weigel.