cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4249604
title: Insights into the structural integrity and dynamics of siRNA–PAZ complex

description: Insights into the structural integrity and dynamics of siRNA–PAZ complex
DOI: 10.6084/m9.figshare.4249604.v1
title: Insights into the structural integrity and dynamics of siRNA–PAZ complex

description: Insights into the structural integrity and dynamics of siRNA–PAZ complex
DOI: 10.6084/m9.figshare.4249592
title: Raw Data from Knowing your neighbourhood: local ecology and personal experience predict neighbourhood perceptions in Belfast, Northern Ireland

description: Evolutionary theory predicts that humans should adjust their life-history strategies in response to local ecological threats and opportunities in order to maximize their reproductive success. Cues representing threats to individuals' lives and health in modern, Western societies may come in the form of local ages at death, morbidity rate and crime rate in their local area, whereas the adult sex ratio represents a measure of the competition for reproductive partners. These characteristics are believed to have a strong influence over a wide range of behaviours, but whether they are accurately perceived has not been robustly tested. Here, we investigate whether perceptions of four neighbourhood characteristics are accurate across eight neighbourhoods in Belfast, Northern Ireland. We find that median age at death and morbidity rates are accurately perceived, whereas adult sex ratios and crime rates are not. We suggest that both neighbourhood characteristics and personal experiences contribute to the formation of perceptions. This should be considered by researchers looking for associations between area-level factors.
DOI: 10.6084/m9.figshare.4249592.v1
title: Raw Data from Knowing your neighbourhood: local ecology and personal experience predict neighbourhood perceptions in Belfast, Northern Ireland

description: Evolutionary theory predicts that humans should adjust their life-history strategies in response to local ecological threats and opportunities in order to maximize their reproductive success. Cues representing threats to individuals' lives and health in modern, Western societies may come in the form of local ages at death, morbidity rate and crime rate in their local area, whereas the adult sex ratio represents a measure of the competition for reproductive partners. These characteristics are believed to have a strong influence over a wide range of behaviours, but whether they are accurately perceived has not been robustly tested. Here, we investigate whether perceptions of four neighbourhood characteristics are accurate across eight neighbourhoods in Belfast, Northern Ireland. We find that median age at death and morbidity rates are accurately perceived, whereas adult sex ratios and crime rates are not. We suggest that both neighbourhood characteristics and personal experiences contribute to the formation of perceptions. This should be considered by researchers looking for associations between area-level factors.
DOI: 10.5517/ccdc.csd.cc25bry7
title: CCDC 2006349: Experimental Crystal Structure Determination

description: Related Article: Supriya Bhunia, Anirban Dolai, Subhas Samanta|2020|Chem.Commun.|56|10247|doi:10.1039/D0CC04098C
DOI: 10.5517/ccdc.csd.cc25fn5g
title: CCDC 2009115: Experimental Crystal Structure Determination

description: Related Article: Jing-Yun Wu, Shih-Hao Jhan, Yu-Ju Lin, Dong-Lin Cai, Zhi-Jia Hu, Hui-Ling Sung|2020|J.Solid State Chem.|291|121638|doi:10.1016/j.jssc.2020.121638
DOI: 10.5517/ccdc.csd.cc25fn6h
title: CCDC 2009116: Experimental Crystal Structure Determination

description: Related Article: Jing-Yun Wu, Shih-Hao Jhan, Yu-Ju Lin, Dong-Lin Cai, Zhi-Jia Hu, Hui-Ling Sung|2020|J.Solid State Chem.|291|121638|doi:10.1016/j.jssc.2020.121638
DOI: 10.5517/ccdc.csd.cc25sfxb
title: CCDC 2019492: Experimental Crystal Structure Determination

description: Related Article: David Marcoux, Myra Beaudoin Bertrand, Carolyn A. Weigelt, Shiuhang Yip, Michael Galella, Hyunsoo Park, Dauh-Rurng Wu, Jinhong Wang, Melissa Yarde, Mary Ellen Cvijic, Sha Li, John Hynes Jr, Joseph A. Tino, Qihong Zhao, T.G. Murali Dhar|2020|Bioorg.Med.Chem.Lett.|30|127466|doi:10.1016/j.bmcl.2020.127466
DOI: 10.5517/ccdc.csd.cc25sfyc
title: CCDC 2019493: Experimental Crystal Structure Determination

description: Related Article: David Marcoux, Myra Beaudoin Bertrand, Carolyn A. Weigelt, Shiuhang Yip, Michael Galella, Hyunsoo Park, Dauh-Rurng Wu, Jinhong Wang, Melissa Yarde, Mary Ellen Cvijic, Sha Li, John Hynes Jr, Joseph A. Tino, Qihong Zhao, T.G. Murali Dhar|2020|Bioorg.Med.Chem.Lett.|30|127466|doi:10.1016/j.bmcl.2020.127466
DOI: 10.5517/ccdc.csd.cc25sfzd
title: CCDC 2019494: Experimental Crystal Structure Determination

description: Related Article: David Marcoux, Myra Beaudoin Bertrand, Carolyn A. Weigelt, Shiuhang Yip, Michael Galella, Hyunsoo Park, Dauh-Rurng Wu, Jinhong Wang, Melissa Yarde, Mary Ellen Cvijic, Sha Li, John Hynes Jr, Joseph A. Tino, Qihong Zhao, T.G. Murali Dhar|2020|Bioorg.Med.Chem.Lett.|30|127466|doi:10.1016/j.bmcl.2020.127466
DOI: 10.5517/ccdc.csd.cc25sg0g
title: CCDC 2019495: Experimental Crystal Structure Determination

description: Related Article: David Marcoux, Myra Beaudoin Bertrand, Carolyn A. Weigelt, Shiuhang Yip, Michael Galella, Hyunsoo Park, Dauh-Rurng Wu, Jinhong Wang, Melissa Yarde, Mary Ellen Cvijic, Sha Li, John Hynes Jr, Joseph A. Tino, Qihong Zhao, T.G. Murali Dhar|2020|Bioorg.Med.Chem.Lett.|30|127466|doi:10.1016/j.bmcl.2020.127466
DOI: 10.5517/ccdc.csd.cc25sg1h
title: CCDC 2019496: Experimental Crystal Structure Determination

description: Related Article: David Marcoux, Myra Beaudoin Bertrand, Carolyn A. Weigelt, Shiuhang Yip, Michael Galella, Hyunsoo Park, Dauh-Rurng Wu, Jinhong Wang, Melissa Yarde, Mary Ellen Cvijic, Sha Li, John Hynes Jr, Joseph A. Tino, Qihong Zhao, T.G. Murali Dhar|2020|Bioorg.Med.Chem.Lett.|30|127466|doi:10.1016/j.bmcl.2020.127466
DOI: 10.6084/m9.figshare.4249406
title: Fish otoliths from the Lutetian of the Aquitaine Basin (SW France), a breakthrough in the knowledge of the European Eocene ichthyofauna

description: The fossil otolith assemblages of the Aquitaine Basin (SW France) have been extensively studied for more than 30 years and are among the best documented worldwide. However, Lutetian otoliths are less well known than those from the lower and upper Eocene. A new collection of &gt;11,000 otoliths from the Lutetian Miretrain Marl Formation from five different localities in Peyrehorade and the Donzacq Marl Formation at Saint-Geours-d'Auribat is analysed here. The oldest site at Saint-Geours-d'Auribat is dated at 47.40 Ma, and the youngest at the ‘la Téoulère’ escarpment at 44.05 Ma. At least 89 otolith-based taxa are recorded, of which 69 are identified at species level. Twenty of these are introduced here by Lin, Nolf and Girone as new species: ‘<i>Elops</i>’ <i>miiformis</i> sp. nov., ‘<i>Ophichthus</i>’ <i>mignolo</i> sp. nov., <i>Saurida trompensis</i> sp. nov., ‘<i>Scopelarchus</i>’ <i>gnocco</i> sp. nov., ‘<i>Evermannella</i>’ <i>razza</i> sp. nov., <i>Neoscopelus navicularis</i> sp. nov., ‘<i>Trachyrincus</i>’ <i>iocosus</i> sp. nov., <i>Nezumia teoulerensis</i> sp. nov., ‘<i>Neobythites</i>’ <i>auribatianus</i> sp. nov., ‘<i>Neobythites</i>’ <i>bozzolo</i> sp. nov., ‘<i>Neobythites</i>’ <i>leonardi</i> sp. nov., <i>Melamphaes acanthifer</i> sp. nov., <i>Zenion mattaccino</i> sp. nov., <i>Zenion vetustus</i> sp. nov., ‘<i>Perca</i>’ <i>lactarioides</i> sp. nov., ‘<i>Perca</i>’ <i>meiformis</i> sp. nov., ‘<i>Liopropoma</i>’ <i>sculpta</i> sp. nov., ‘<i>Branchiostegus</i>’ <i>brevis</i> sp. nov., ‘<i>Haemulon</i>’ <i>strascinate</i> sp. nov. and <i>Cepola rostislavi</i> sp. nov. The occurrence of <i>N</i>. <i>teoulerensis</i> sp. nov. is particularly important because it documents the earliest macrourid fossil record from the Northern Hemisphere. The assemblages all indicate a deep neritic environment, similar to that of several of the Ypresian and Priabonian deposits of the Aquitaine Basin. The difference in taxonomic composition between the Lutetian assemblages of Aquitaine and those of the neighbouring Anglo-Belgo-Parisian basin and Osteroden (Germany) is mainly environmentally based. The new material contains many nominal upper and/or lower Eocene species whose stratigraphical distribution is thus extended to the Lutetian, suggesting that the important faunal renewal in the Eocene of the Aquitaine Basin is more gradual than previously believed. http://zoobank.org/urn:lsid:zoobank.org:pub:C37149C7-FC3B-4267-9CD0-03E0E0059459
DOI: 10.6084/m9.figshare.4249406.v1
title: Fish otoliths from the Lutetian of the Aquitaine Basin (SW France), a breakthrough in the knowledge of the European Eocene ichthyofauna

description: The fossil otolith assemblages of the Aquitaine Basin (SW France) have been extensively studied for more than 30 years and are among the best documented worldwide. However, Lutetian otoliths are less well known than those from the lower and upper Eocene. A new collection of &gt;11,000 otoliths from the Lutetian Miretrain Marl Formation from five different localities in Peyrehorade and the Donzacq Marl Formation at Saint-Geours-d'Auribat is analysed here. The oldest site at Saint-Geours-d'Auribat is dated at 47.40 Ma, and the youngest at the ‘la Téoulère’ escarpment at 44.05 Ma. At least 89 otolith-based taxa are recorded, of which 69 are identified at species level. Twenty of these are introduced here by Lin, Nolf and Girone as new species: ‘<i>Elops</i>’ <i>miiformis</i> sp. nov., ‘<i>Ophichthus</i>’ <i>mignolo</i> sp. nov., <i>Saurida trompensis</i> sp. nov., ‘<i>Scopelarchus</i>’ <i>gnocco</i> sp. nov., ‘<i>Evermannella</i>’ <i>razza</i> sp. nov., <i>Neoscopelus navicularis</i> sp. nov., ‘<i>Trachyrincus</i>’ <i>iocosus</i> sp. nov., <i>Nezumia teoulerensis</i> sp. nov., ‘<i>Neobythites</i>’ <i>auribatianus</i> sp. nov., ‘<i>Neobythites</i>’ <i>bozzolo</i> sp. nov., ‘<i>Neobythites</i>’ <i>leonardi</i> sp. nov., <i>Melamphaes acanthifer</i> sp. nov., <i>Zenion mattaccino</i> sp. nov., <i>Zenion vetustus</i> sp. nov., ‘<i>Perca</i>’ <i>lactarioides</i> sp. nov., ‘<i>Perca</i>’ <i>meiformis</i> sp. nov., ‘<i>Liopropoma</i>’ <i>sculpta</i> sp. nov., ‘<i>Branchiostegus</i>’ <i>brevis</i> sp. nov., ‘<i>Haemulon</i>’ <i>strascinate</i> sp. nov. and <i>Cepola rostislavi</i> sp. nov. The occurrence of <i>N</i>. <i>teoulerensis</i> sp. nov. is particularly important because it documents the earliest macrourid fossil record from the Northern Hemisphere. The assemblages all indicate a deep neritic environment, similar to that of several of the Ypresian and Priabonian deposits of the Aquitaine Basin. The difference in taxonomic composition between the Lutetian assemblages of Aquitaine and those of the neighbouring Anglo-Belgo-Parisian basin and Osteroden (Germany) is mainly environmentally based. The new material contains many nominal upper and/or lower Eocene species whose stratigraphical distribution is thus extended to the Lutetian, suggesting that the important faunal renewal in the Eocene of the Aquitaine Basin is more gradual than previously believed. http://zoobank.org/urn:lsid:zoobank.org:pub:C37149C7-FC3B-4267-9CD0-03E0E0059459
DOI: 10.6084/m9.figshare.4249406.v3
title: Fish otoliths from the Lutetian of the Aquitaine Basin (SW France), a breakthrough in the knowledge of the European Eocene ichthyofauna

description: The fossil otolith assemblages of the Aquitaine Basin (SW France) have been extensively studied for more than 30 years and are among the best documented worldwide. However, Lutetian otoliths are less well known than those from the lower and upper Eocene. A new collection of &gt;11,000 otoliths from the Lutetian Miretrain Marl Formation from five different localities in Peyrehorade and the Donzacq Marl Formation at Saint-Geours-d'Auribat is analysed here. The oldest site at Saint-Geours-d'Auribat is dated at 47.40 Ma, and the youngest at the ‘la Téoulère’ escarpment at 44.05 Ma. At least 89 otolith-based taxa are recorded, of which 69 are identified at species level. Twenty of these are introduced here by Lin, Nolf and Girone as new species: ‘<i>Elops</i>’ <i>miiformis</i> sp. nov., ‘<i>Ophichthus</i>’ <i>mignolo</i> sp. nov., <i>Saurida trompensis</i> sp. nov., ‘<i>Scopelarchus</i>’ <i>gnocco</i> sp. nov., ‘<i>Evermannella</i>’ <i>razza</i> sp. nov., <i>Neoscopelus navicularis</i> sp. nov., ‘<i>Trachyrincus</i>’ <i>iocosus</i> sp. nov., <i>Nezumia teoulerensis</i> sp. nov., ‘<i>Neobythites</i>’ <i>auribatianus</i> sp. nov., ‘<i>Neobythites</i>’ <i>bozzolo</i> sp. nov., ‘<i>Neobythites</i>’ <i>leonardi</i> sp. nov., <i>Melamphaes acanthifer</i> sp. nov., <i>Zenion mattaccino</i> sp. nov., <i>Zenion vetustus</i> sp. nov., ‘<i>Perca</i>’ <i>lactarioides</i> sp. nov., ‘<i>Perca</i>’ <i>meiformis</i> sp. nov., ‘<i>Liopropoma</i>’ <i>sculpta</i> sp. nov., ‘<i>Branchiostegus</i>’ <i>brevis</i> sp. nov., ‘<i>Haemulon</i>’ <i>strascinate</i> sp. nov. and <i>Cepola rostislavi</i> sp. nov. The occurrence of <i>N</i>. <i>teoulerensis</i> sp. nov. is particularly important because it documents the earliest macrourid fossil record from the Northern Hemisphere. The assemblages all indicate a deep neritic environment, similar to that of several of the Ypresian and Priabonian deposits of the Aquitaine Basin. The difference in taxonomic composition between the Lutetian assemblages of Aquitaine and those of the neighbouring Anglo-Belgo-Parisian basin and Osteroden (Germany) is mainly environmentally based. The new material contains many nominal upper and/or lower Eocene species whose stratigraphical distribution is thus extended to the Lutetian, suggesting that the important faunal renewal in the Eocene of the Aquitaine Basin is more gradual than previously believed. http://zoobank.org/urn:lsid:zoobank.org:pub:C37149C7-FC3B-4267-9CD0-03E0E0059459
DOI: 10.6084/m9.figshare.4249406.v2
title: Fish otoliths from the Lutetian of the Aquitaine Basin (SW France), a breakthrough in the knowledge of the European Eocene ichthyofauna

description: The fossil otolith assemblages of the Aquitaine Basin (SW France) have been extensively studied for more than 30 years and are among the best documented worldwide. However, Lutetian otoliths are less well known than those from the lower and upper Eocene. A new collection of &gt;11,000 otoliths from the Lutetian Miretrain Marl Formation from five different localities in Peyrehorade and the Donzacq Marl Formation at Saint-Geours-d'Auribat is analysed here. The oldest site at Saint-Geours-d'Auribat is dated at 47.40 Ma, and the youngest at the ‘la Téoulère’ escarpment at 44.05 Ma. At least 89 otolith-based taxa are recorded, of which 69 are identified at species level. Twenty of these are introduced here by Lin, Nolf and Girone as new species: ‘<i>Elops</i>’ <i>miiformis</i> sp. nov., ‘<i>Ophichthus</i>’ <i>mignolo</i> sp. nov., <i>Saurida trompensis</i> sp. nov., ‘<i>Scopelarchus</i>’ <i>gnocco</i> sp. nov., ‘<i>Evermannella</i>’ <i>razza</i> sp. nov., <i>Neoscopelus navicularis</i> sp. nov., ‘<i>Trachyrincus</i>’ <i>iocosus</i> sp. nov., <i>Nezumia teoulerensis</i> sp. nov., ‘<i>Neobythites</i>’ <i>auribatianus</i> sp. nov., ‘<i>Neobythites</i>’ <i>bozzolo</i> sp. nov., ‘<i>Neobythites</i>’ <i>leonardi</i> sp. nov., <i>Melamphaes acanthifer</i> sp. nov., <i>Zenion mattaccino</i> sp. nov., <i>Zenion vetustus</i> sp. nov., ‘<i>Perca</i>’ <i>lactarioides</i> sp. nov., ‘<i>Perca</i>’ <i>meiformis</i> sp. nov., ‘<i>Liopropoma</i>’ <i>sculpta</i> sp. nov., ‘<i>Branchiostegus</i>’ <i>brevis</i> sp. nov., ‘<i>Haemulon</i>’ <i>strascinate</i> sp. nov. and <i>Cepola rostislavi</i> sp. nov. The occurrence of <i>N</i>. <i>teoulerensis</i> sp. nov. is particularly important because it documents the earliest macrourid fossil record from the Northern Hemisphere. The assemblages all indicate a deep neritic environment, similar to that of several of the Ypresian and Priabonian deposits of the Aquitaine Basin. The difference in taxonomic composition between the Lutetian assemblages of Aquitaine and those of the neighbouring Anglo-Belgo-Parisian basin and Osteroden (Germany) is mainly environmentally based. The new material contains many nominal upper and/or lower Eocene species whose stratigraphical distribution is thus extended to the Lutetian, suggesting that the important faunal renewal in the Eocene of the Aquitaine Basin is more gradual than previously believed. http://zoobank.org/urn:lsid:zoobank.org:pub:C37149C7-FC3B-4267-9CD0-03E0E0059459
DOI: 10.6084/m9.figshare.4249400.v2
title: HCP-MMP1.0 volumetric (NIfTI) masks in native structural space

description: We in our group received with great interest the publication of the <b>HCP-MMP 1.0 parcellation</b> by Glasser et al. (Nature) created using data from the Human Connectome Project earlier this year. Often in our connectivity pipelines we use volume files for parcellation in native space, so we decided to try and convert the Connectome Workbench files to volume masks in native structural space to try out in future studies.<br>We were happy to find that someone had already gone through the trouble of generating FreeSurfer annotation files projected on fsaverage, so all we had to do was find a way to transform these <i>annot</i> files to each subject’s space and convert them to volume masks.<br>So we wrote this Linux shell script that performs a series of conversion and transformation steps using only FreeSurfer commands. It first converts the annotation files (<b>lh.HCPMMP1.annot and rh.HCPMMP1.annot</b>, downloaded from https://figshare.com/articles/HCP-MMP1_0_projected_on_fsaverage/3498446) to labels using <i>mri_annotation2label</i>, then takes each label from fsaverage to each subject’s space with <i>mri_label2label</i>, converts transformed labels back to annotation with <i>mri_label2annot</i>, and finally converts these to volume files (nii.gz) with <i>mris_label2annot</i>. Seems like too many steps, but this is how we (who are not FreeSurfer experts) got satisfactory results.<br>The default final file consists of a single volume containing the HCP-MMP1.0 regions plus the subcortical regions from the FreeSurfer segmentation, each assigned a unique voxel value. Left-hemisphere cortical HCP-MMP1.0 regions have values between 1001 and 1181, whereas right-sided regions have values between 2001 and 2181. The correspondence between each specific region and its value is given in a look-up table that is generated in each subject’s output folder. To identify the subcortical regions, one just needs to check the <i>FreeSurferColorLUT.txt</i> file provided with FreeSurfer, as they correspond to the original <i>aseg</i> parcellation.<br>Optionally, one can choose to also generate individual volume files for each parcellation region. This option requires FSL, and will only create masks for the cortical HCP-MMP1.0 parcellation, not the subcortical <i>aseg</i> regions.<br>Instructions on how to use the script can be found in the script itself, or here: <i>https://cjneurolab.org/2016/11/22/hcp-mmp1-0-volumetric-nifti-masks-in-native-structural-space/</i><br>Hope this can be of use!
DOI: 10.6084/m9.figshare.4249385.v2
title: QGIS tutorial on Linux

description: The following book draft written in Indonesia language showcases several basic aspects of QGIS. More materials will be added slowly based on the project that we are working on. <br>We'd like to hear your comments as we will revise it until it is ready to be printed and published by ITB Press. <br>Best wishes,<br>Aditya Erwin (@dasaptaerwin)
DOI: 10.6084/m9.figshare.4249166
title: Phylogeography of the pelagic fish <i>Seriola lalandi</i> at different scales: confirmation of inter-ocean population structure and evaluation of southern African genetic diversity

description: The study investigated the global and regional phylogeography of the yellowtail kingfish <i>Seriola lalandi</i> by examining genetic diversity and population genetic structure of this species at inter-and intra-ocean level and on a regional scale. DNA fragments of two mitochondrial genes, cytochrome <i>b</i> (Cytb) and cytochrome <i>c</i> oxidase subunit I (COI) and one nuclear gene, recombination activating gene 1 (RAG1), were sequenced to investigate the global-scale phylogeography of this species. The population genetic structure within the South Pacific, as well as along the South African coastline, was examined further using six microsatellite markers. Three distinct clades were identified for <i>S. lalandi</i>, which correspond with previously described subspecies of the North-East Pacific, North-West Pacific and the Southern Hemisphere. Within the latter, additional divergence was observed between the South Pacific and the South-East Atlantic regions. Divergence estimates were indicative of a Pacific origin for <i>S. lalandi</i> populations, because of Pleistocene vicariant events. Microsatellite analyses revealed overall significant genetic differentiation between South African and South Pacific samples. This corroborates recent findings on the global phylogeography of the species. No population differentiation was observed within South Africa, indicating high levels of gene flow.
DOI: 10.6084/m9.figshare.4249166.v2
title: Phylogeography of the pelagic fish <i>Seriola lalandi</i> at different scales: confirmation of inter-ocean population structure and evaluation of southern African genetic diversity

description: The study investigated the global and regional phylogeography of the yellowtail kingfish <i>Seriola lalandi</i> by examining genetic diversity and population genetic structure of this species at inter-and intra-ocean level and on a regional scale. DNA fragments of two mitochondrial genes, cytochrome <i>b</i> (Cytb) and cytochrome <i>c</i> oxidase subunit I (COI) and one nuclear gene, recombination activating gene 1 (RAG1), were sequenced to investigate the global-scale phylogeography of this species. The population genetic structure within the South Pacific, as well as along the South African coastline, was examined further using six microsatellite markers. Three distinct clades were identified for <i>S. lalandi</i>, which correspond with previously described subspecies of the North-East Pacific, North-West Pacific and the Southern Hemisphere. Within the latter, additional divergence was observed between the South Pacific and the South-East Atlantic regions. Divergence estimates were indicative of a Pacific origin for <i>S. lalandi</i> populations, because of Pleistocene vicariant events. Microsatellite analyses revealed overall significant genetic differentiation between South African and South Pacific samples. This corroborates recent findings on the global phylogeography of the species. No population differentiation was observed within South Africa, indicating high levels of gene flow.