cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20050298.v1
title: A molecular-genetics perspective on the systematics of the parthenogenetic flowerpot blindsnake <i>Indotyphlops braminus</i> (Daudin, 1803) (Squamata: Serpentes: Typhlopidae)

description: Sri Lanka has a rich snake diversity, but the island’s scolecophidians (‘blindsnakes’) are poorly understood due to the cryptic, burrowing habits of these inconspicuous animals and lack of systematic field surveys and morphological and molecular analyses. Here we report findings from a systematic survey carried out over a decade across the island of Sri Lanka, focusing particularly on the globally widespread, parthenogenetic species <i>Indotyphlops braminus.</i> We report 780 locations across the island in which this species was recorded, at elevations of 1–1,424 m asl, and mostly &lt;1,000 m (771 out of 780 localities). We provide a molecular-systematics perspective by reporting new DNA sequence data for 15 specimens from Sri Lanka, and new analyses of asiatyphlopine molecular genetic diversity and relationships. Based on molecular results, we conclude that (i) <i>Indotyphlops</i>, as originally conceived may not be monophyletic, (ii) phenotypically the <i>I. braminus</i>-like blindsnakes widespread across most of Sri Lanka are a single, genetically homogeneous species, and (iii) some populations from peninsular India are very similar in DNA sequence to <i>I. braminus</i> from Sri Lanka, but others are genetically highly distinct and unlikely to be conspecific. Based on the estimated phylogenetic relationships, we recommend that <i>I. braminus</i> is currently best recognized as a phenotypically exceptional species of <i>Indotyphlops</i> rather than, as recently proposed, the only species of a monotypic genus (<i>Virgotyphlops</i>).
DOI: 10.6084/m9.figshare.20049722
title: Automated identification of chicken distress vocalisations using deep learning models

description: Abstract The annual global production of chickens exceeds 25 billion birds, which are often housed in very large groups, numbering thousands. Distress calling triggered by various sources of stress has been suggested as an “iceberg indicator” of chicken welfare. However, to date, the identification of distress calls largely relies on manual annotation, which is very labour-intensive and time-consuming. Thus, a novel convolutional neural network-based model, light-VGG11, was developed to automatically identify chicken distress calls using recordings (3,363 distress calls and 1,973 natural barn sounds) collected on an intensive farm. The light-VGG11 was modified from VGG11 with significantly fewer parameters (9.3 million <em>vs</em> 128 million) and 55.88% faster detection speed while displaying comparable performance, <em>i.e.</em>, precision (94.58%), recall (94.89%), F1-score (94.73%), and accuracy (95.07%), therefore more useful for model deployment in practice. To additionally improve light-VGG11’s performance, we investigated the impacts of different data augmentation techniques (<em>i.e.</em>, time masking, frequency masking, mixed spectrograms of the same class, and Gaussian noise) and found that they could improve distress calls detection by up to 1.52%. Furthermore, a distress call detection demonstration on continuous audios exhibited our research’s potential for developing technologies to monitor the output of distress calls in large, commercial chicken flocks. Methods Recordings were collected in production facilities owned by Lengfeng Poultry Ltd., in Guangxi province, People’s Republic of China, between November and December 2017 and in November 2018. Chickens (mix of Chinese “spotted” and “three-yellow” breeds) were kept in stacked cages (three cages per stack, with 13-20 individuals per cage), with approximately 2,000 to 2,500 birds per house. The microphone was positioned approximately two meters up from the floor, mounted on the top cage of a stack in the middle of the barn<strong>. </strong>This placement was chosen to ensure that the recording devices did not interfere with the farm staff cleaning and maintaining the barns. All recordings were sampled at 22.05 kHz with a 16-bit bit-depth throughout the natural lifecycle (0 – 35 days) of chickens using a portable recorder (Zoom H4n Pro, Zoom Corporation, Tokyo, Japan). These recordings were collected from two different chicken flocks at the same farm, one of which was used as the development dataset to learn the model, and the other was used as a continuous testing dataset to verify the model’s generalisation capability.
DOI: 10.5281/zenodo.6620524
title: Nearly three centuries of Lava Flow Subsidence at1 Timanfaya, Lanzarote

description: The following datasets are available for each InSAR dataset - Envisat and Sentinel-1, covering the island of Lanzarote between 2004/01/17 -2010/01/30 and 2016/09/14-2020/06/25 respectively: <br> Line of Sight (LOS) velocities<br> LOS velocity standard deviations<br> LOS displacement time series<br> Vertical velocities<br> Vertical velocity standard deviations <br> East-West velocities<br> East-West velocity standard deviations The velocities and standard deviations are all geocoded (latitude/longitude in decimal degrees) geotiff files in mm/yr at 90 m resolution for Envisat and 30 m resolution for Sentinel-1. Negative values in the LOS data represent movement away from the satellite; in the vertical data represent subsidence; and in the East-West data represent westward movement. The velocities were calculated from the displacement time series as a least squares inversion and the standard deviations were calculated within LiCSBAS using a percentile bootstrap method. The Sentinel-1 time series is given as a 3D matrix (lon x lat x dates) within a .h5 file where each slice is the cumulative displacement (mm) in a lon lat grid format for each epoch date. The latitude and longitude are then given as separate vectors within the .h5 file. The Envisat time series is given as a .dat file where the first two columns are longitude and latitude. The remaining columns are the cumulative displacement (mm) for each epoch date. The epoch dates for both are given as separate text files and are given in the format YYYYMMDD.
DOI: 10.5281/zenodo.6620523
title: Nearly three centuries of Lava Flow Subsidence at1 Timanfaya, Lanzarote

description: The following datasets are available for each InSAR dataset - Envisat and Sentinel-1, covering the island of Lanzarote between 2004/01/17 -2010/01/30 and 2016/09/14-2020/06/25 respectively: <br> Line of Sight (LOS) velocities<br> LOS velocity standard deviations<br> LOS displacement time series<br> Vertical velocities<br> Vertical velocity standard deviations <br> East-West velocities<br> East-West velocity standard deviations The velocities and standard deviations are all geocoded (latitude/longitude in decimal degrees) geotiff files in mm/yr at 90 m resolution for Envisat and 30 m resolution for Sentinel-1. Negative values in the LOS data represent movement away from the satellite; in the vertical data represent subsidence; and in the East-West data represent westward movement. The velocities were calculated from the displacement time series as a least squares inversion and the standard deviations were calculated within LiCSBAS using a percentile bootstrap method. The Sentinel-1 time series is given as a 3D matrix (lon x lat x dates) within a .h5 file where each slice is the cumulative displacement (mm) in a lon lat grid format for each epoch date. The latitude and longitude are then given as separate vectors within the .h5 file. The Envisat time series is given as a .dat file where the first two columns are longitude and latitude. The remaining columns are the cumulative displacement (mm) for each epoch date. The epoch dates for both are given as separate text files and are given in the format YYYYMMDD.
DOI: 10.6084/m9.figshare.19790484
title: A new species of <i>Maomingosuchus</i> from the Eocene of the Na Duong Basin (northern Vietnam) sheds new light on the phylogenetic relationship of tomistomine crocodylians and their dispersal from Europe to Asia

description: <i>Maomingosuchus acutirostris</i> sp. nov. is a new tomistomine crocodile from the middle–upper Eocene deposits (late Bartonian–Priabonian age, 39–35 Ma) of the Na Duong Basin in northern Vietnam. <i>M. acutirostris</i> can be differentiated from the type species <i>Maomingosuchus petrolicus</i> by having an acute anterior tip of the premaxilla. Both species differ from another <i>Maomingosuchus</i> from Krabi (Thailand) by differences in the surangular–dentary suture and maxillary alveoli. According to our phylogenetic results, <i>M. acutirostris</i> seems to be the sister species to the group <i>M. petrolicus</i> + Krabi-<i>Maomingosuchus</i>. The close relationship between those three tomistomines is supported in the present phylogenetic analysis by three synapomorphies. In our phylogenetic analysis, <i>Maomingosuchus</i> was retrieved in a basal position forming the sister group to <i>Paratomistoma</i> + <i>Gavialosuchus</i> + <i>Melitosaurus</i> + <i>Tomistoma</i>, including the extant <i>Tomistoma schlegelii</i>. This phylogeny indicates three different dispersal events of Tomistominae from Europe towards eastern Asia: 1) for the stem lineage of <i>Maomingosuchus</i>, no later than the late Eocene; 2) for the stem lineage of <i>Penghusuchus pani</i> + <i>Toyotamaphimeia machikanensis</i>, no later than the early–middle Miocene; and (3) for the stem lineage of <i>T. schlegelii</i>, during the Neogene. http://zoobank.org/urn:lsid:zoobank.org:pub:19B27C1E-0A3F-4425-AA8C-F904277DF327
DOI: 10.6084/m9.figshare.19790484.v1
title: A new species of <i>Maomingosuchus</i> from the Eocene of the Na Duong Basin (northern Vietnam) sheds new light on the phylogenetic relationship of tomistomine crocodylians and their dispersal from Europe to Asia

description: <i>Maomingosuchus acutirostris</i> sp. nov. is a new tomistomine crocodile from the middle–upper Eocene deposits (late Bartonian–Priabonian age, 39–35 Ma) of the Na Duong Basin in northern Vietnam. <i>M. acutirostris</i> can be differentiated from the type species <i>Maomingosuchus petrolicus</i> by having an acute anterior tip of the premaxilla. Both species differ from another <i>Maomingosuchus</i> from Krabi (Thailand) by differences in the surangular–dentary suture and maxillary alveoli. According to our phylogenetic results, <i>M. acutirostris</i> seems to be the sister species to the group <i>M. petrolicus</i> + Krabi-<i>Maomingosuchus</i>. The close relationship between those three tomistomines is supported in the present phylogenetic analysis by three synapomorphies. In our phylogenetic analysis, <i>Maomingosuchus</i> was retrieved in a basal position forming the sister group to <i>Paratomistoma</i> + <i>Gavialosuchus</i> + <i>Melitosaurus</i> + <i>Tomistoma</i>, including the extant <i>Tomistoma schlegelii</i>. This phylogeny indicates three different dispersal events of Tomistominae from Europe towards eastern Asia: 1) for the stem lineage of <i>Maomingosuchus</i>, no later than the late Eocene; 2) for the stem lineage of <i>Penghusuchus pani</i> + <i>Toyotamaphimeia machikanensis</i>, no later than the early–middle Miocene; and (3) for the stem lineage of <i>T. schlegelii</i>, during the Neogene. http://zoobank.org/urn:lsid:zoobank.org:pub:19B27C1E-0A3F-4425-AA8C-F904277DF327
DOI: 10.6084/m9.figshare.20004242
title: Sample 1036 - Read2 - Library derived from 12019

description: Library PR1036. Metagenomic sequencing from a rock derived from Pescadero Basin (Sample 12019) and incubated under anaerobic conditions. Hydrothermal environment. Reads 2
DOI: 10.6084/m9.figshare.20004242.v2
title: Sample 1036 - Read2 - Library derived from 12019

description: Library PR1036. Metagenomic sequencing from a rock derived from Pescadero Basin (Sample 12019) and incubated under anaerobic conditions. Hydrothermal environment. Reads 2
DOI: 10.6084/m9.figshare.20004242.v1
title: Sample 1036 - Read2 - Library derived from 12019

description: Library PR1036. Metagenomic sequencing from a rock derived from Pescadero Basin (Sample 12019) and incubated under anaerobic conditions. Hydrothermal environment. Reads 2
DOI: 10.14278/rodare.1690
title: Dataset for Inversion of GISAXS data (3 layers)

description: The dataset consists of 50000 X-ray diffraction patterns simulated by BornAgain [1] software. For each simulation, a multilayer sample model of the following structure was used: air, tantalum oxide, tantalum, copper nitride, silicon dioxide, and substrate. Parameters of air, silicon dioxide, and substrate were kept fixed. Hence, each diffraction pattern is set to depend on the parameters of tantalum oxide, tantalum, and copper nitride layers. For each layer, those are real and complex parts of refractive index, thickness, roughness, Hurst parameter, and correlation length. Each simulation output is stored in an h5py file consisting of 1) diffraction image as a NumPy array of shape [1200, 120]; 2) parameters of a sample as a NumPy array with 18 elements. For further details regarding simulation see https://github.com/maxxxzdn/gisaxs-reconstruction/simulation/simulation. [1] Pospelov, G., Van Herck, W., Burle, J., Carmona Loaiza, J.M., Durniak, C., Fisher, J., Ganeva, M., Yurov, D., & Wuttke, J. (2020). BornAgain: software for simulating and fitting grazing-incidence small-angle scattering. <em>Journal of Applied Crystallography, 53</em>, 262 - 276.
DOI: 10.14278/rodare.1689
title: Dataset for Inversion of GISAXS data (3 layers)

description: The dataset consists of 50000 X-ray diffraction patterns simulated by BornAgain [1] software. For each simulation, a multilayer sample model of the following structure was used: air, tantalum oxide, tantalum, copper nitride, silicon dioxide, and substrate. Parameters of air, silicon dioxide, and substrate were kept fixed. Hence, each diffraction pattern is set to depend on the parameters of tantalum oxide, tantalum, and copper nitride layers. For each layer, those are real and complex parts of refractive index, thickness, roughness, Hurst parameter, and correlation length. Each simulation output is stored in an h5py file consisting of 1) diffraction image as a NumPy array of shape [1200, 120]; 2) parameters of a sample as a NumPy array with 18 elements. For further details regarding simulation see https://github.com/maxxxzdn/gisaxs-reconstruction/simulation/simulation. [1] Pospelov, G., Van Herck, W., Burle, J., Carmona Loaiza, J.M., Durniak, C., Fisher, J., Ganeva, M., Yurov, D., & Wuttke, J. (2020). BornAgain: software for simulating and fitting grazing-incidence small-angle scattering. <em>Journal of Applied Crystallography, 53</em>, 262 - 276.
DOI: 10.14278/rodare.1687
title: Dataset for Inversion of GISAXS data (1 layer)

description: The dataset consists of 50000 X-ray diffraction patterns simulated by BornAgain [1] software. For each simulation, a multilayer sample model of the following structure was used: air, tantalum oxide, silicon dioxide, and substrate. Parameters of each layer but tantalum oxide were kept fixed. Hence, each diffraction pattern depends on the parameters of the tantalum oxide layer: real and complex part of refractive index, thickness, roughness, Hurst parameter, and correlation length. Each simulation output is stored in an h5py file consisting of 1) diffraction image as a NumPy array of shape [1024, 512]; 2) sample parameters as a NumPy array with 6 elements. For further details regarding simulation, see https://github.com/maxxxzdn/gisaxs-reconstruction/simulation/simulation. [1] Pospelov, G., Van Herck, W., Burle, J., Carmona Loaiza, J.M., Durniak, C., Fisher, J., Ganeva, M., Yurov, D., & Wuttke, J. (2020). BornAgain: software for simulating and fitting grazing-incidence small-angle scattering. <em>Journal of Applied Crystallography, 53</em>, 262 - 276.
DOI: 10.14278/rodare.1686
title: Dataset for Inversion of GISAXS data (1 layer)

description: The dataset consists of 50000 X-ray diffraction patterns simulated by BornAgain [1] software. For each simulation, a multilayer sample model of the following structure was used: air, tantalum oxide, silicon dioxide, and substrate. Parameters of each layer but tantalum oxide were kept fixed. Hence, each diffraction pattern depends on the parameters of the tantalum oxide layer: real and complex part of refractive index, thickness, roughness, Hurst parameter, and correlation length. Each simulation output is stored in an h5py file consisting of 1) diffraction image as a NumPy array of shape [1024, 512]; 2) sample parameters as a NumPy array with 6 elements. For further details regarding simulation, see https://github.com/maxxxzdn/gisaxs-reconstruction/simulation/simulation. [1] Pospelov, G., Van Herck, W., Burle, J., Carmona Loaiza, J.M., Durniak, C., Fisher, J., Ganeva, M., Yurov, D., & Wuttke, J. (2020). BornAgain: software for simulating and fitting grazing-incidence small-angle scattering. <em>Journal of Applied Crystallography, 53</em>, 262 - 276.
DOI: 10.5281/zenodo.6631311
title: Spanish melon landraces: revealing useful diversity by ge-nomic, morphologic, and metabolomic analysis. Supplementary data.

description: Original data linked to the publication Spanish melon landraces: revealing useful diversity by genomic, morphologic, and metabolomic analysis. It includes, Supp. Table 1: Genomic data; Supp. Table 2: Characterization data; Supp. Table 3: Metabolomic data; Supp. Table 4: Germplasm details
DOI: 10.6084/m9.figshare.19400904.v1
title: Site occupation spans at Middle Ceramic Antelope Creek phase sites in the Southern Plains of Texas

description: Twenty-one AMS radiocarbon and optical stimulated luminescence assays from Early Ceramic (Plains Woodland) and Middle Ceramic (Antelope Creek) periods are reported from sites on the Cross Bar Ranch in Potter County, Texas including the first direct date on <i>Phaseolus</i> sp. remains in the Southern Plains. Calibrated radiocarbon dates and a single luminescence assay are used to evaluate site occupation spans during the Middle Ceramic Antelope Creek phase (ca. AD 1150–1450). A method for determining occupation sequences between sites using combined probabilities is presented for Antelope Creek occupations on the Cross Bar Ranch and the entire period of occupation at the Cross Bar Ranch is compared to other direct dates on cultigens from the greater Antelope Creek phase in the Southern Plains of Texas.
DOI: 10.6084/m9.figshare.19400904
title: Site occupation spans at Middle Ceramic Antelope Creek phase sites in the Southern Plains of Texas

description: Twenty-one AMS radiocarbon and optical stimulated luminescence assays from Early Ceramic (Plains Woodland) and Middle Ceramic (Antelope Creek) periods are reported from sites on the Cross Bar Ranch in Potter County, Texas including the first direct date on <i>Phaseolus</i> sp. remains in the Southern Plains. Calibrated radiocarbon dates and a single luminescence assay are used to evaluate site occupation spans during the Middle Ceramic Antelope Creek phase (ca. AD 1150–1450). A method for determining occupation sequences between sites using combined probabilities is presented for Antelope Creek occupations on the Cross Bar Ranch and the entire period of occupation at the Cross Bar Ranch is compared to other direct dates on cultigens from the greater Antelope Creek phase in the Southern Plains of Texas.
DOI: 10.5517/ccdc.csd.cc1ptxkz
title: CCDC 1574042: Experimental Crystal Structure Determination

description: Related Article: Dhivya Sivaraj, Ray J. Butcher, Jerry P. Jasinski, Saikumar Sathyanarayanan, Revathi Ponnusamy, Sreeja Puthanpura Sasidharan, Kasipandi Muniyandi, Parimelazhagan Thangaraj, Karuppusamy Arunachalam|2022|Evidence-Based Complementary and Alternative Medicine|2022|20|doi:10.1155/2022/4797884
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.cc1ptxl0
title: CCDC 1574043: Experimental Crystal Structure Determination

description: Related Article: Dhivya Sivaraj, Ray J. Butcher, Jerry P. Jasinski, Saikumar Sathyanarayanan, Revathi Ponnusamy, Sreeja Puthanpura Sasidharan, Kasipandi Muniyandi, Parimelazhagan Thangaraj, Karuppusamy Arunachalam|2022|Evidence-Based Complementary and Alternative Medicine|2022|20|doi:10.1155/2022/4797884
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.cc256rsy
title: CCDC 2002500: Experimental Crystal Structure Determination

description: Related Article: Lei Gao, Xianrui Zhang|2021|J.Chem.|2021|3834368|doi:10.1155/2021/3834368
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.cc289cts
title: CCDC 2094385: Experimental Crystal Structure Determination

description: Related Article: Xiaochuan Jia, Liqiang Jiang, Shubei Cui, Haidong Jia|2022|Int. J. Polym. Sci.|2022|4609960|doi:10.1155/2022/4609960
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.cc273gpj
title: CCDC 2058917: Experimental Crystal Structure Determination

description: Related Article: Greta Colombo Dugoni, Matteo Mori, Valentina Dichiarante, Alessandro Sacchetti, Fiorella Meneghetti|2022|J.Mol.Struct.|1265|133398|doi:10.1016/j.molstruc.2022.133398
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.cc28btfw
title: CCDC 2095768: Experimental Crystal Structure Determination

description: Related Article: Zhanfang Chen, Hongbin Fang, Xuewen Hua, Wenrui Liu, Yi Liu, Chenmeng Xue, Bingxiang Wang, Dzmitry Bazhanau, Xiaohe Zhu, Man Yuan, Jing Ru, Pengfei Chu|2021|J.Chem.|2021|10|doi:10.1155/2021/1036199
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.cc28gmt6
title: CCDC 2099438: Experimental Crystal Structure Determination

description: Related Article: Lei Gao, Xianrui Zhang|2021|J.Chem.|2021|3834368|doi:10.1155/2021/3834368
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.