cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21312270
title: Computational prediction of RNA–RNA interactions between small RNA tracks from <em>Betacoronavirus</em> nonstructural protein 3 and neurotrophin genes during infection of an epithelial lung cancer cell line: Potential role of novel small regulatory RNA

description: Whether RNA–RNA interactions of cytoplasmic RNA viruses, such as <i>Betacoronavirus</i>, might end in the biogenesis of putative virus-derived small RNAs as miRNA-like molecules has been controversial. Even more, whether RNA–RNA interactions of wild animal viruses may act as virus-derived small RNAs is unknown. Here, we address these issues in four ways. First, we use conserved RNA structures undergoing negative selection in the genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 circulating in different bat species, intermediate animals, and human hosts. Second, a systematic literature review was conducted to identify <i>Betacoronavirus</i>-targeting hsa-miRNAs involved in lung cell infection. Third, we employed sophisticated long-range RNA–RNA interactions to refine the seed sequence homology of hsa-miRNAs with conserved RNA structures. Fourth, we used high-throughput RNA sequencing of a <i>Betacoronavirus</i>-infected epithelial lung cancer cell line (Calu-3) to validate the results. We proposed nine potential virus-derived small RNAs: two vsRNAs in SARS-CoV (Bats: SB-vsRNA-ORF1a-3p; SB-vsRNA-S-5p), one vsRNA in MERS-CoV (Bats: MB-vsRNA-ORF1b-3p), and six vsRNAs in SARS-CoV-2 (Bats: S2B-vsRNA-ORF1a-5p; intermediate animals: S2I-vsRNA-ORF1a-5p; and humans: S2H-vsRNA-ORF1a-5p, S2H-vsRNA-ORF1a-3p, S2H-vsRNA-ORF1b-3p, S2H-vsRNA-ORF3a-3p), mainly encoded by nonstructural protein 3. Notably, <i>Betacoronavirus</i>-derived small RNAs targeted 74 differentially expressed genes in infected human cells, of which 55 upregulate the molecular mechanisms underlying acute respiratory distress syndrome (ARDS), and the 19 downregulated genes might be implicated in neurotrophin signaling impairment. These results reveal a novel small RNA-based regulatory mechanism involved in neuropathogenesis that must be further studied to validate its therapeutic use.
DOI: 10.35077/add-rot
title: Male_2_6to7_days_ventral: Image stack of a wild type Canton S fly head (ventral)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_2_6to7_days_ventral: Image stack of a wild type Canton S fly head (ventral)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_2_6to7_days_ventral', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'6 to 7', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_2_6to7_days_ventral', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.35077/add-row
title: Male_3_5to6_days_anterior: Image stack of a wild type Canton S fly head (anterior)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_5to6_days_anterior: Image stack of a wild type Canton S fly head (anterior)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_5to6_days_anterior', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'5 to 6', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_5to6_days_anterior', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.12751/g-node.46h2gl
title: Reference induces biases in late visual processing

description: The dataset and codes for the manuscript Reference induces biases in late visual processing.
description: IsSupplementTo: Su Y, Wachtler T, Shi Z: Reference induces biases in late visual processing. Submitted.
DOI: 10.35077/add-rub
title: Male_3_5to6_days_dorsal: Image stack of a wild type Canton S fly head (dorsal)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_5to6_days_dorsal: Image stack of a wild type Canton S fly head (dorsal)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_5to6_days_dorsal', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'5 to 6', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_5to6_days_dorsal', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.6084/m9.figshare.23627790.v1
title: Supplementary Material for: Women in interventional pulmonology – results from a worldwide survey

description: Background and Objectives: Gender inequality in medicine remains an issue. Despite the increasing proportion of female physicians, women still appear underrepresented in interventional pulmonology careers. To date, no data is available on the gender distribution in interventional pulmonology. Method: An online survey was sent to pulmonary physicians internationally between July and December 2022. The survey included questions on gender diversity in the pulmonology departments, such as the proportion of male, female and gender diverse physicians performing bronchoscopy, career progression and social life. Results: Responses from 92 physicians (mean age 45±10 years) from 47 hospitals across 17 countries were analyzed, of whom 52% were women. Overall, 79% of the respondents were pulmonologists and 83% perform bronchoscopy. Although men continue to dominate bronchoscopy (65% vs. 43%) and are more likely to be involved in research (89% vs. 77%), the observed difference is statistically not significant (p=0.135 and p=0.281). Leading positions are held by 60% of male respondents vs. 23% of female respondents (p=0.002). Men are also more often reported to have academic awards. Discrimination based on gender was reported by 5.3% of all men and 26.8% of all women (p=0.023). Conclusions: Men and women are almost equally involved in interventional pulmonology, especially in female-led bronchoscopy units. However, leading positions and academic awards are still predominantly held by men.
DOI: 10.6084/m9.figshare.23627790
title: Supplementary Material for: Women in interventional pulmonology – results from a worldwide survey

description: Background and Objectives: Gender inequality in medicine remains an issue. Despite the increasing proportion of female physicians, women still appear underrepresented in interventional pulmonology careers. To date, no data is available on the gender distribution in interventional pulmonology. Method: An online survey was sent to pulmonary physicians internationally between July and December 2022. The survey included questions on gender diversity in the pulmonology departments, such as the proportion of male, female and gender diverse physicians performing bronchoscopy, career progression and social life. Results: Responses from 92 physicians (mean age 45±10 years) from 47 hospitals across 17 countries were analyzed, of whom 52% were women. Overall, 79% of the respondents were pulmonologists and 83% perform bronchoscopy. Although men continue to dominate bronchoscopy (65% vs. 43%) and are more likely to be involved in research (89% vs. 77%), the observed difference is statistically not significant (p=0.135 and p=0.281). Leading positions are held by 60% of male respondents vs. 23% of female respondents (p=0.002). Men are also more often reported to have academic awards. Discrimination based on gender was reported by 5.3% of all men and 26.8% of all women (p=0.023). Conclusions: Men and women are almost equally involved in interventional pulmonology, especially in female-led bronchoscopy units. However, leading positions and academic awards are still predominantly held by men.
DOI: 10.35077/add-rug
title: Male_3_5to6_days_posterior: Image stack of a wild type Canton S fly head (posterior)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_5to6_days_posterior: Image stack of a wild type Canton S fly head (posterior)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_5to6_days_posterior', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'5 to 6', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_5to6_days_posterior', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.13140/rg.2.2.34988.23685
title: Interpretations of Hongisto et. al. floor data, -Spectra, improvements and comparisons Box frame wood, CLT, both with and without resilient ceilings and a concrete floor.
DOI: 10.13140/rg.2.2.13177.85608
title: Interpretations of Hongisto et. al. floor data, -Spectra, improvements and comparisons Box frame wood, CLT, both with and without resilient ceilings and a concrete floor.
DOI: 10.35077/add-run
title: Male_3_5to6_days_ventral: Image stack of a wild type Canton S fly head (ventral)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_5to6_days_ventral: Image stack of a wild type Canton S fly head (ventral)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_5to6_days_ventral', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'5 to 6', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_5to6_days_ventral', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.13140/rg.2.2.16533.29926
title: Primer design steps using NCBI
DOI: 10.13140/rg.2.2.29955.07207
title: Primer design steps using NCBI
DOI: 10.35077/add-rut
title: Male_3_6to7_days_anterior: Image stack of a wild type Canton S fly head (anterior)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_6to7_days_anterior: Image stack of a wild type Canton S fly head (anterior)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_6to7_days_anterior', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'6 to 7', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_6to7_days_anterior', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.35077/add-rye
title: Male_3_6to7_days_dorsal: Image stack of a wild type Canton S fly head (dorsal)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_6to7_days_dorsal: Image stack of a wild type Canton S fly head (dorsal)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_6to7_days_dorsal', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'6 to 7', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_6to7_days_dorsal', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.35077/add-sad
title: Male_3_6to7_days_posterior: Image stack of a wild type Canton S fly head (posterior)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_6to7_days_posterior: Image stack of a wild type Canton S fly head (posterior)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_6to7_days_posterior', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'6 to 7', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_6to7_days_posterior', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.35077/add-sag
title: Male_3_6to7_days_ventral: Image stack of a wild type Canton S fly head (ventral)

description: Image stacks of wild type Canton S fly heads using white light illumination. These images were used to classify and quantify the head bristles (mechanosensory structures). The processed images are published in Figure 1 and Figure 1 – figure supplements 1-2 of the manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”. The stacks used to produce these images are organized based on gender, individual (e.g. Fly_1 and Fly_2), and head orientation (e.g. anterior and posterior).
description: A full protocol describing this work is available in the associated manuscript at manuscript “Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila (https://doi.org/10.1101/2023.02.11.528119)”.
description: DATASET METADATA: title:'Male_3_6to7_days_ventral: Image stack of a wild type Canton S fly head (ventral)', GeneralModality:'other', Technique:'other', Other:'bright field' SPECIMEN METADATA: LocalID:'Male_3_6to7_days_ventral', Species:'Fruit fly', NCBITaxonomy:'NCBI:txid7227', Age:'6 to 7', Ageunit:'Days', Sex:'Male', Genotype:'Canton S (wild type)', OrganName:'Peripheral', SampleLocalID:'Male_3_6to7_days_ventral', Locations:'Peripheral' INSTRUMENT METADATA: MicroscopeType:'Confocal', MicroscopeManufacturerAndModel:'Zeiss Axio Examiner D1', ObjectiveName:'Zeiss 10x objective (Achroplan 10x/0.25) ', ObjectiveNA:'0.25', ObjectiveMagnification:'10x' IMAGE METADATA: xAxis:'left-to-right', yAxis:'left-to-right', zAxis:'left-to-right', Number:'white', displayColor:'white', stepSizeX:'0.432129', stepSizeY:'0.432129'
DOI: 10.5517/ccdc.csd.cc2ffzd8
title: CCDC 2247760: Experimental Crystal Structure Determination

description: Related Article: D. Christopher Braddock, Ben C. Rowley, Paul D. Lickiss, Steven J. Fussell, Rabia Qamar, David Pugh, Henry S. Rzepa, Andrew J. P. White|2023|J.Org.Chem.|88|9853|doi:10.1021/acs.joc.3c00585
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ffzf9
title: CCDC 2247761: Experimental Crystal Structure Determination

description: Related Article: D. Christopher Braddock, Ben C. Rowley, Paul D. Lickiss, Steven J. Fussell, Rabia Qamar, David Pugh, Henry S. Rzepa, Andrew J. P. White|2023|J.Org.Chem.|88|9853|doi:10.1021/acs.joc.3c00585
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.