cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29222886.v2
title: High pathogenicity avian influenza H5N1 clade 2.3.4.4b natural infection in captive Humboldt penguins (<i>Spheniscus humboldti</i>)

description: Between 2020 and 2023, high pathogenicity avian influenza virus (HPAIV) H5Nx clade 2.3.4.4b caused devastating outbreaks across Europe and the United Kingdom among domestic poultry and wild bird populations. During winter 2022, unexpected mortality was observed in four of fourteen outdoor captive Humboldt penguins in a British zoological collection, without prior clinical signs. Swabs, one whole carcass and two heads were submitted for notifiable avian disease laboratory investigation. Clinical material was inspected by veterinary pathologists using an established <i>post mortem</i> procedure and tissues were collected for official sampling according to a standard notifiable avian disease testing algorithm. A defined selection of tissues was tested using real-time reverse transcription PCR, whole-genome sequencing, histopathology and immunohistochemistry. Following molecular testing for H5N1 infection, positive results were detected in five of the 12 birds sampled. On gross examination of the carcass, generalized congestion was present. Histopathology revealed necrosis and acute inflammation, primarily in the spleen, liver and lungs. Immunohistochemistry demonstrated viral antigen in endothelial cells and lymphoid cells particularly in lung, spleen, liver, brain and heart muscle. This finding strongly suggests that endothelial cells and lymphoid cells are the primary targets for HPAIV infection in Humboldt penguins. Molecular characterization identified the causative agent as HPAIV H5N1 clade 2.3.4.4b, genotyped as AIV223 according to the UK scheme. This was the first time that this genotype had been recorded in the UK. These findings provide novel insights into the pathobiology of this virus in naturally infected captive Humboldt penguins. Natural HPAIV H5N1 infection causes mortality and pathology in Humboldt penguins.Molecular analysis identified the aetiology as a novel H5N1 clade 2.3.4.4b genotype.Immunohistochemical analysis demonstrated infection of endothelial cells, macrophages and reticular cells in lymphoid tissue. Natural HPAIV H5N1 infection causes mortality and pathology in Humboldt penguins. Molecular analysis identified the aetiology as a novel H5N1 clade 2.3.4.4b genotype. Immunohistochemical analysis demonstrated infection of endothelial cells, macrophages and reticular cells in lymphoid tissue.
DOI: 10.6084/m9.figshare.29476743.v1
title: Immunomodulatory effects of <i>Ascardia galli</i> excretory-secretory products, including extracellular vesicles on host immune cell function

description: Gastrointestinal nematode infections, particularly <i>Ascaridia galli</i>, pose challenges to the poultry industry especially in free-range chickens. These nematodes employ sophisticated immunomodulation strategies to evade host immune defences, allowing them to establish chronic infections. Excretory-secretory (ES) products, including extracellular vesicles (EVs), play a pivotal role in host-parasite communication. Thus, this study aimed to investigate the immunomodulatory properties of nematode-derived ES/EVs, and evaluate the impact of ivermectin (IVM) on these interactions <i>in vitro</i>. Adult <i>A. galli</i> worms were collected from the jejunum of infected chickens and cultured <i>in-vitro</i> with or without IVM treatment. ES products were collected, and EVs were enriched using size-exclusion chromatography. T-cell proliferation and macrophage activation assays were performed to assess the immunomodulatory effects of ES/EVs. <i>Ascaridia galli (A. galli)</i> derived ES products suppressed T-cell activation (CD25+CD57+ cells) and reduced blast transformation in both CD4+ and CD8+ T-cells (p&lt;0.05). Furthermore, ES promoted TLR4-induced macrophage NO production, changed macrophage-activated surface phenotype, and inhibited macrophage phagocytosis in high concentration but promoted it in low concentration (p&lt;005). Additionally, <i>A. galli</i> derived EVs were detected in culture supernatants, and this EV secretion was decreased with the IVM treatment (p&lt;005). Fourier-transform infrared spectroscopy confirmed IVM treatment altered EV cargo composition. Finally, the EVs influenced cytokine profiles of activated macrophages, decreasing pro-inflammatory cytokine gene expression (IL-1β and IL-8, p&lt;005) which may mirror immune evasion <i>in vivo</i>. In summary, this study highlights immunomodulatory mechanisms of <i>A. galli</i> ES/EVs and provides fundamental information for developing diagnostic and therapeutic strategies targeting nematode ES products including EVs. Highlights
- The ES, including EVs, demonstrate immunomodulatory properties.- <i>A. galli</i> ES suppressed T-cell activation, proliferation, and macrophage phagocytosis.- <i>A.galli</i> ES including EVs may help in evading host immune system<i>.</i> The ES, including EVs, demonstrate immunomodulatory properties. <i>A. galli</i> ES suppressed T-cell activation, proliferation, and macrophage phagocytosis. <i>A.galli</i> ES including EVs may help in evading host immune system<i>.</i>
DOI: 10.25921/07qe-7796
title: NOAA/WDS Paleoclimatology - Esper - Kleiner Feldberg - PCAB - ITRDB GERM230

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: Missing rings were inserted with the value 1. NOAA Template Raw Measurements file added 2020-09-03.
DOI: 10.5517/cc95bc4
title: CCDC 273245: Experimental Crystal Structure Determination

description: Related Article: F.Antolini, B.Gehrhus, P.B.Hitchcock, M.F.Lappert|2005|Chem.Commun.||5112|doi:10.1039/b509310d
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/cc95bd5
title: CCDC 273246: Experimental Crystal Structure Determination

description: Related Article: F.Antolini, B.Gehrhus, P.B.Hitchcock, M.F.Lappert|2005|Chem.Commun.||5112|doi:10.1039/b509310d
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: 10.6084/m9.figshare.29222886.v1
title: High pathogenicity avian influenza H5N1 clade 2.3.4.4b natural infection in captive Humboldt penguins <i>(Spheniscus humboldti)</i>

description: Between 2020 and 2023, high pathogenicity avian influenza virus (HPAIV) H5Nx clade 2.3.4.4b caused devastating outbreaks across Europe and the United Kingdom among domestic poultry and wild bird populations. During winter 2022, unexpected mortality was observed in four of fourteen outdoor captive Humboldt penguins in a British zoological collection, without prior clinical signs. Swabs, one whole carcass and two heads were submitted for notifiable avian disease laboratory investigation. Clinical material was inspected by veterinary pathologists using an established post-mortem procedure and tissues were collected for official sampling according to a standard notifiable avian disease testing algorithm. A defined selection of tissues was tested using real-time reverse transcription PCR, whole-genome sequencing, histopathology and immunohistochemistry. Following molecular testing for H5N1 infection, positive results were detected in 5 of the 12 animals sampled. On gross examination of the carcass, generalised congestion was present. Histopathology revealed necrosis and acute inflammation, primarily in the spleen, liver and lungs. Immunohistochemistry demonstrated viral antigen in endothelial cells and lymphoid cells particularly in lung, spleen, liver, brain and heart muscle. This finding strongly suggests that endothelial cells and lymphoid cells are the primary targets for HPAIV infection in Humboldt penguins. Molecular characterisation identified the causative agent as HPAIV H5N1 clade 2.3.4.4b, genotyped as AIV223 according to the UK scheme. This was the first time that this genotype had been recorded in the UK. These findings provide novel insights into the pathobiology of this virus in naturally infected captive Humboldt penguins. Research Highlights
Natural HPAIV H5N1 infection causes mortality and pathology in Humboldt Penguins.Molecular analysis identified the aetiology as a novel H5N1 clade 2.3.4.4b genotype.Immunohistochemical analysis demonstrated infection of endothelial cells and macrophages and reticular cells in lymphoid tissue. Natural HPAIV H5N1 infection causes mortality and pathology in Humboldt Penguins. Molecular analysis identified the aetiology as a novel H5N1 clade 2.3.4.4b genotype. Immunohistochemical analysis demonstrated infection of endothelial cells and macrophages and reticular cells in lymphoid tissue.
DOI: 10.25574/26923
title: Chandra X-ray Observatory ObsId 26923

description: Completing Observations of the Highest-Redshift Planck SZ Clusters
DOI: 10.25921/0znj-3e47
title: NOAA/WDS Paleoclimatology - Indian Ocean Sea Surface Temperature Reconstruction and Mg/Ca Data during the Last Deglaciation

description: Sea surface temperature and oxygen isotopic records from two well-dated Indian Ocean cores covering the last deglaciation show the occurrence of two periods of increased salinity along the route of warm surface water transport from the Indian to the Atlantic Ocean, one between 18 and 14.5 ka and the other during the Younger Dryas. Our results imply that during these periods, salt accumulated in the tropical Atlantic, creating favorable conditions for an abrupt resumption of the thermohaline circulation and abrupt northern hemisphere warming. Furthermore, we suggest that the observed pattern of millennial climate variability during the last glacial and deglaciation resulted from the interaction between the relatively slow rhythm of expansion and decay of the northern hemisphere ice sheets, and El Niño–Southern Oscillation variability, through changes in the position of the Intertropical Convergence Zone. This interaction generated an oscillator with millennial time response that operated at times of sufficient northern hemisphere ice sheets extent.
description: This dataset was contributed as part of the Temperature-12k project (https://doi.org/10.25921/4RY2-G808). Data were contributed to the project from the original data generators, who are listed in the Investigator field of this template file. Additional notes regarding the use of these data in the Temperature-12k project can be found in the LiPD file listed as an Online_Resource of this template file.
DOI: 10.5517/cc8zpb7
title: CCDC 267819: Experimental Crystal Structure Determination

description: Related Article: M.Scheer, Junfeng Bai, B.P.Johnson, R.Merkle, A.V.Virovets, C.E.Anson|2005|Eur.J.Inorg.Chem.|2005|4023|doi:10.1002/ejic.200500616
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/cc9ccjj
title: CCDC 279047: Experimental Crystal Structure Determination

description: Related Article: H.Koshikawa, M.Okazaki, S.Matsumoto, K.Ueno, H.Tobita, H.Ogino|2005|Chem.Lett.|34|1412|doi:10.1246/cl.2005.1412
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: 10.6084/m9.figshare.29327023
title: Fowl adenoviruses (FAdVs) in Iran between 2020 and 2022: the first comprehensive phylogenetic study

description: Inclusion body hepatitis (IBH) outbreaks have been reported globally over the past two decades, predominantly affecting broiler flocks and resulting in significant economic losses due to increased mortality and diminished production performance. In Iran, fowl adenovirus (FAdV) infections have been circulating for several years, with recurrent reports of clinical cases suggesting IBH and hepatitis-hydropericardium syndrome (HHS) in commercial poultry operations. In response to these concerns, the present study was conducted to comprehensively characterize circulating FAdV strains in Iranian poultry farms over a 3-year period. A total of 200 pooled liver samples were collected from 200 broiler flocks that exhibited clinical signs consistent with IBH/HHS. Partial amplification and sequencing of the hexon gene were performed to detect and genotype the FAdV strains. The phylogenetic analysis assigned 66.32% of the detected strains to FAdV-D, 16.32% to FAdV-C, 11.22% to FAdV-E, and 6.12% to FAdV-B. Notably, this investigation provided the first genomic evidence of FAdV serotype 5 in Iran. Within the FAdV-C group, both serotypes 4 and 10 were identified. Additionally, serotype 6, closely related (98% nucleotide identity) to a Chinese reference strain, was reported for the first time in Iran. Given the high diversity of FAdV serotypes, continued vaccination of broiler breeders, using vaccines that cover the strains circulating in the country, is recommended. Monitoring broilers and broiler breeders remain essential for effective disease control and prevention.
DOI: 10.6084/m9.figshare.29327023.v2
title: Fowl adenoviruses (FAdVs) in Iran between 2020 and 2022: the first comprehensive phylogenetic study

description: Inclusion body hepatitis (IBH) outbreaks have been reported globally over the past two decades, predominantly affecting broiler flocks and resulting in significant economic losses due to increased mortality and diminished production performance. In Iran, fowl adenovirus (FAdV) infections have been circulating for several years, with recurrent reports of clinical cases suggesting IBH and hepatitis-hydropericardium syndrome (HHS) in commercial poultry operations. In response to these concerns, the present study was conducted to comprehensively characterize circulating FAdV strains in Iranian poultry farms over a 3-year period. A total of 200 pooled liver samples were collected from 200 broiler flocks that exhibited clinical signs consistent with IBH/HHS. Partial amplification and sequencing of the hexon gene were performed to detect and genotype the FAdV strains. The phylogenetic analysis assigned 66.32% of the detected strains to FAdV-D, 16.32% to FAdV-C, 11.22% to FAdV-E, and 6.12% to FAdV-B. Notably, this investigation provided the first genomic evidence of FAdV serotype 5 in Iran. Within the FAdV-C group, both serotypes 4 and 10 were identified. Additionally, serotype 6, closely related (98% nucleotide identity) to a Chinese reference strain, was reported for the first time in Iran. Given the high diversity of FAdV serotypes, continued vaccination of broiler breeders, using vaccines that cover the strains circulating in the country, is recommended. Monitoring broilers and broiler breeders remain essential for effective disease control and prevention.
DOI: 10.25921/0hgj-p478
title: NOAA/WDS Paleoclimatology - Esper - Kuusipää Dry - PISY - ITRDB FINL087

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: NOAA Template Raw Measurements file added 2021-10-19.
DOI: 10.5517/cc9cp0b
title: CCDC 279341: Experimental Crystal Structure Determination

description: Related Article: M.Yoshizawa, N.Sato, M.Fujita|2005|Chem.Lett.|34|1392|doi:10.1246/cl.2005.1392
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/cc9fx2p
title: CCDC 281482: Experimental Crystal Structure Determination

description: Related Article: R.Kitashima, S.Imatomi, M.Yamada, N.Matsumoto, Y.Maeda|2005|Chem.Lett.|34|1388|doi:10.1246/cl.2005.1388
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: 10.6084/m9.figshare.29222862
title: The role of YbdO in regulating acid resistance and biofilm formation in avian pathogenic <i>Escherichia coli</i>

description: Avian pathogenic <i>Escherichia coli</i> (APEC) causes severe systemic infectious diseases known as colibacillosis in avian species, resulting in significant economic losses to the poultry industry worldwide, and threatening food security and human health. Previous studies showed that acid resistance is an indispensable mechanism that allows <i>E. coli</i> to survive in the gastrointestinal tract. Biofilm formation results in persistent and recurrent infections in the host, and is the main reason why treatment of colibacillosis with antimicrobial agents is difficult. In this study, we confirmed YbdO as a transcriptional regulator that increases biofilm formation by upregulating the transcription of the biofilm-associated genes <i>bcsE</i>, <i>csgD</i>, <i>pgaA</i>, <i>wcaD</i>, <i>fimH</i>, and <i>flhD</i> and acid resistance by activating the expression of acid stress chaperone HdeA and acid stress response protein YqgB in APEC CE1. Additionally, electrophoretic mobility shift assay (EMSA) indicated that YbdO directly activated the expression of CsgD, HdeA and YqgB by directly binding to the promoters of <i>csgD</i>, <i>hdeA</i> and <i>yqgB</i>, respectively. These findings demonstrate the regulatory mechanism of YbdO on acid resistance and biofilm formation and enhance our understanding of how APEC improves its adaptability to environmental stresses, thereby increasing the pathogenicity of APEC. Therefore, this study might provide a paradigm for the regulation of biofilm formation and acid resistance that can be used to study other bacterial pathogens. YbdO increases biofilm formation and acid resistance.YbdO upregulates the transcription levels of the biofilm-associated genes <i>bcsE</i>, <i>csgD</i>, <i>pgaA</i>, <i>wcaD</i>, <i>fimH</i>, and <i>flhD.</i>YbdO activates the expression of acid stress-associated genes <i>hdeA</i> and <i>yqgB.</i>YbdO contributes to improving the adaptability of APEC to environmental stresses. YbdO increases biofilm formation and acid resistance. YbdO upregulates the transcription levels of the biofilm-associated genes <i>bcsE</i>, <i>csgD</i>, <i>pgaA</i>, <i>wcaD</i>, <i>fimH</i>, and <i>flhD.</i> YbdO activates the expression of acid stress-associated genes <i>hdeA</i> and <i>yqgB.</i> YbdO contributes to improving the adaptability of APEC to environmental stresses.
DOI: 10.6084/m9.figshare.29222862.v1
title: The role of YbdO in regulating acid resistance and biofilm formation in avian pathogenic <i>Escherichia coli</i>

description: Avian pathogenic <i>Escherichia coli</i> (APEC) causes severe systemic infectious diseases known as colibacillosis in avian species, resulting in significant economic losses to the poultry industry worldwide, and threatening food security and human health. Previous studies showed that acid resistance is an indispensable mechanism that allows <i>E. coli</i> to survive in the gastrointestinal tract. Biofilm formation results in persistent and recurrent infections in the host, and is the main reason why treatment of colibacillosis with antimicrobial agents is difficult. In this study, we confirmed YbdO as a transcriptional regulator that increases biofilm formation by upregulating the transcription of the biofilm-associated genes <i>bcsE</i>, <i>csgD</i>, <i>pgaA</i>, <i>wcaD</i>, <i>fimH</i>, and <i>flhD</i> and acid resistance by activating the expression of acid stress chaperone HdeA and acid stress response protein YqgB in APEC CE1. Additionally, electrophoretic mobility shift assay (EMSA) indicated that YbdO directly activated the expression of CsgD, HdeA and YqgB by directly binding to the promoters of <i>csgD</i>, <i>hdeA</i> and <i>yqgB</i>, respectively. These findings demonstrate the regulatory mechanism of YbdO on acid resistance and biofilm formation and enhance our understanding of how APEC improves its adaptability to environmental stresses, thereby increasing the pathogenicity of APEC. Therefore, this study might provide a paradigm for the regulation of biofilm formation and acid resistance that can be used to study other bacterial pathogens. YbdO increases biofilm formation and acid resistance.YbdO upregulates the transcription levels of the biofilm-associated genes <i>bcsE</i>, <i>csgD</i>, <i>pgaA</i>, <i>wcaD</i>, <i>fimH</i>, and <i>flhD.</i>YbdO activates the expression of acid stress-associated genes <i>hdeA</i> and <i>yqgB.</i>YbdO contributes to improving the adaptability of APEC to environmental stresses. YbdO increases biofilm formation and acid resistance. YbdO upregulates the transcription levels of the biofilm-associated genes <i>bcsE</i>, <i>csgD</i>, <i>pgaA</i>, <i>wcaD</i>, <i>fimH</i>, and <i>flhD.</i> YbdO activates the expression of acid stress-associated genes <i>hdeA</i> and <i>yqgB.</i> YbdO contributes to improving the adaptability of APEC to environmental stresses.