cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5354293
title: Training and testing sample data used in "Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction"

description: This dataset contains the generated training and testing samples used in the paper "Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction". <br>3D Zernike descriptors are used to represent protein surface shape, while Support-Vector Machine (SVM) is the binary classification technique employed to produce a model based on the training data which predicts the class labels of the test data given only the feature vectors of the test data.<br>Data are archived in the format .tar.xz, which can be extracted by common archive utilities. Each archive file contains a number of text files in the SVM light format. Each line records 1331 colon-separated pairs of numbers (the first one being a feature index - an integer ranging from 1 to 1331, the second a floating point number). .csv file are also provided recording the precision, recall and accuracy values for test predictions.<br>The first one or two letters of the archive filename together with the "l" or "r" letters identify the protein class; the "train" keyword identifies training sets, while the "test" keyword identifies testing sets; training sets are available as either balanced or unbalanced. See the associated paper for further details.<br>Background: In the related paper we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein-Protein Docking Benchmark 5.0.<br>
DOI: 10.6084/m9.figshare.5355097.v1
title: HCV+ Subjects 29.08.17.xlsx

description: We performed a retrospective study of HCV infection in a UK teaching hospital to evaluate and compare the performance of different laboratory tests, to describe the population with active HCV infection and to determine the proportion of these individuals who access clinical review and treatment. Microbiology records for all HCV screening tests performed at Oxford University Hospitals within two defined time-intervals (Group 1 - 18 months; Jan 2013 - June 2014, Group 2 - 15 months; Jan 2015 - March 2016) were studied . For those testing positive we collected follow-up testing data. We recorded patient age, sex, and the location from which the sample was sent. We used an analytical tool to estimate ethnicity applying Onolytics software for all patients whom a full name was part of the electronic record. Ethics approval was not required, as this study was undertaken as a departmental quality improvement exercise within microbiology using anonymised patient data, and completed the audit cycle for previously approved audit projects. Data for Onolytics analysis were handled separately and were subject to a confidential disclosure agreement drawn up by University of Oxford Research Services (February 2016). <br><br><br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5354293.v1
title: Training and testing sample data used in "Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction"

description: This dataset contains the generated training and testing samples used in the paper "Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction". <br>3D Zernike descriptors are used to represent protein surface shape, while Support-Vector Machine (SVM) is the binary classification technique employed to produce a model based on the training data which predicts the class labels of the test data given only the feature vectors of the test data.<br>Data are archived in the format .tar.xz, which can be extracted by common archive utilities. Each archive file contains a number of text files in the SVM light format. Each line records 1331 colon-separated pairs of numbers (the first one being a feature index - an integer ranging from 1 to 1331, the second a floating point number). .csv file are also provided recording the precision, recall and accuracy values for test predictions.<br>The first one or two letters of the archive filename together with the "l" or "r" letters identify the protein class; the "train" keyword identifies training sets, while the "test" keyword identifies testing sets; training sets are available as either balanced or unbalanced. See the associated paper for further details.<br>Background: In the related paper we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein-Protein Docking Benchmark 5.0.<br>
DOI: 10.6084/m9.figshare.5355097.v2
title: HCV+ Subjects 29.08.17.xlsx

description: We performed a retrospective study of HCV infection in a UK teaching hospital to evaluate and compare the performance of different laboratory tests, to describe the population with active HCV infection and to determine the proportion of these individuals who access clinical review and treatment. Microbiology records for all HCV screening tests performed at Oxford University Hospitals within two defined time-intervals (Group 1 - 18 months; Jan 2013 - June 2014, Group 2 - 15 months; Jan 2015 - March 2016) were studied . For those testing positive we collected follow-up testing data. We recorded patient age, sex, and the location from which the sample was sent. We used an analytical tool to estimate ethnicity applying Onolytics software for all patients whom a full name was part of the electronic record. Ethics approval was not required, as this study was undertaken as a departmental quality improvement exercise within microbiology using anonymised patient data, and completed the audit cycle for previously approved audit projects. Data for Onolytics analysis were handled separately and were subject to a confidential disclosure agreement drawn up by University of Oxford Research Services (February 2016). <br><br><br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5355097.v3
title: HCV+ Subjects 16.10.17.xlsx

description: We performed a retrospective study of HCV infection in a UK teaching hospital to evaluate and compare the performance of different laboratory tests, to describe the population with active HCV infection and to determine the proportion of these individuals who access clinical review and treatment. Microbiology records for all HCV screening tests performed at Oxford University Hospitals within two defined time-intervals (Group 1 - 18 months; Jan 2013 - June 2014, Group 2 - 15 months; Jan 2015 - March 2016) were studied . For those testing positive we collected follow-up testing data. We recorded patient age, sex, and the location from which the sample was sent. We used an analytical tool to estimate ethnicity applying Onolytics software for all patients whom a full name was part of the electronic record. Ethics approval was not required, as this study was undertaken as a departmental quality improvement exercise within microbiology using anonymised patient data, and completed the audit cycle for previously approved audit projects. Data for Onolytics analysis were handled separately and were subject to a confidential disclosure agreement drawn up by University of Oxford Research Services (February 2016). <br><br><br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5354131
title: Wintering ecology and nomadic movement patterns of Short-eared Owls <i>Asio flammeus</i> on a subtropical island

description: <b>Capsule:</b> Short-eared Owls <i>Asio flammeus</i> showed a female-biased sex ratio in their southernmost wintering grounds in Oriental Asia. This is the first description of a nomadic movement pattern in this area. <b>Aims:</b> To investigate the sex ratio, movement patterns, home range size and habitat preference of non-breeding Short-eared Owls in subtropical Taiwan. <b>Methods:</b> Eleven Short-eared Owls were radio tracked following trapping and transportation away from an airport as part of the management of bird-strike risk for aeroplanes. <b>Results:</b> Our results indicated a female-skewed (75%) sex ratio for Short-eared Owls wintering in Taiwan. The owls demonstrated a nomadic behaviour by showing a repetitive pattern of high roosting site fidelity in the short term, followed by a long-distance movement to a different discrete area. Grasslands were commonly used as day-roosting sites but agricultural habitats were favoured at night. <b>Conclusion:</b> Compared to on the breeding ground, the wintering owls exhibited a much larger home range size and exploit more dispersed patches of suitable habitats. These results revealed a notable conservation issue for the wintering owls, especially in the degraded and partially developed landscapes in subtropical countries.
DOI: 10.6084/m9.figshare.5355097.v4
title: HCV+ Subjects 16.10.17.xlsx

description: We performed a retrospective study of HCV infection in a UK teaching hospital to evaluate and compare the performance of different laboratory tests, to describe the population with active HCV infection and to determine the proportion of these individuals who access clinical review and treatment. Microbiology records for all HCV screening tests performed at Oxford University Hospitals within two defined time-intervals (Group 1 - 18 months; Jan 2013 - June 2014, Group 2 - 15 months; Jan 2015 - March 2016) were studied . For those testing positive we collected follow-up testing data. We recorded patient age, sex, and the location from which the sample was sent. We used an analytical tool to estimate ethnicity applying Onolytics software for all patients whom a full name was part of the electronic record. Ethics approval was not required, as this study was undertaken as a departmental quality improvement exercise within microbiology using anonymised patient data, and completed the audit cycle for previously approved audit projects. Data for Onolytics analysis were handled separately and were subject to a confidential disclosure agreement drawn up by University of Oxford Research Services (February 2016). <br><br><br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5354125
title: Future breeding and foraging sites of a southern edge population of the locally endangered Black Guillemot <i>Cepphus grylle</i>

description: <b>Capsule:</b> One of the southernmost populations of the Black Guillemot <i>Cepphus grylle</i> is currently endangered, and the risk may be exacerbated by climate change. <b>Aims:</b> We evaluated the future vulnerability of the Black Guillemot by predicting the impact of climate change on the geographic distribution of its breeding and foraging range in the Baltic Sea. <b>Methods:</b> We used MaxEnt, a species distribution modelling technique, to predict the current and future breeding grounds and foraging sites. <b>Results:</b> We found that although the foraging range is expected to increase in the southern Baltic Sea in future, these areas will no longer be suitable as breeding grounds due to a changing climate, creating a spatial mismatch. <b>Conclusion:</b> Our predictions indicate where threats to the species may be most severe and can be used to guide conservation planning. We advocate conservation measures which integrate potential future threats and focus on breeding sites across the current and future potential geographic range of the Black Guillemot.
DOI: 10.6084/m9.figshare.5354125.v1
title: Future breeding and foraging sites of a southern edge population of the locally endangered Black Guillemot <i>Cepphus grylle</i>

description: <b>Capsule:</b> One of the southernmost populations of the Black Guillemot <i>Cepphus grylle</i> is currently endangered, and the risk may be exacerbated by climate change. <b>Aims:</b> We evaluated the future vulnerability of the Black Guillemot by predicting the impact of climate change on the geographic distribution of its breeding and foraging range in the Baltic Sea. <b>Methods:</b> We used MaxEnt, a species distribution modelling technique, to predict the current and future breeding grounds and foraging sites. <b>Results:</b> We found that although the foraging range is expected to increase in the southern Baltic Sea in future, these areas will no longer be suitable as breeding grounds due to a changing climate, creating a spatial mismatch. <b>Conclusion:</b> Our predictions indicate where threats to the species may be most severe and can be used to guide conservation planning. We advocate conservation measures which integrate potential future threats and focus on breeding sites across the current and future potential geographic range of the Black Guillemot.
DOI: 10.6084/m9.figshare.5355097.v6
title: HCV+ Subjects 14.08.18.xlsx

description: We performed a retrospective study of HCV infection in a UK teaching hospital to evaluate and compare the performance of different laboratory tests, to describe the population with active HCV infection and to determine the proportion of these individuals who access clinical review and treatment. Microbiology records for all HCV screening tests performed at Oxford University Hospitals within two defined time-intervals (Group 1 - 18 months; Jan 2013 - June 2014, Group 2 - 15 months; Jan 2015 - March 2016) were studied . For those testing positive we collected follow-up testing data. We recorded patient age, sex, and the location from which the sample was sent. We used an analytical tool to estimate ethnicity applying Onolytics software for all patients whom a full name was part of the electronic record. Ethics approval was not required, as this study was undertaken as a departmental quality improvement exercise within microbiology using anonymised patient data, and completed the audit cycle for previously approved audit projects. Data for Onolytics analysis were handled separately and were subject to a confidential disclosure agreement drawn up by University of Oxford Research Services (February 2016). <br><br><br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5354122
title: So similar and yet so different: taxonomic status of Pallid Swift <i>Apus pallidus</i> and Common Swift <i>Apus apus</i>

description: <b>Capsule:</b> Common Swift <i>Apus apus</i> and Pallid Swift <i>Apus Pallidus</i> are morphologically very similar but are genetically distinct and diverged 1.9–2.1 million years ago (mya). <b>Aims:</b> To examine genetic differentiation and to estimate separation time between Common and Pallid Swifts. <b>Methods:</b> Estimation of differences in three different mitochondrial DNA markers (<i>COI</i>, <i>ND2</i> and control region), and a fourth marker, the <i>cytb</i>, that did not differ between taxa. Fossils were used to calibrate the estimate of separation date between the two taxa. <b>Results:</b> The genetic between-species distances were 0.010, 0.006 and 0.033 for the three markers, respectively. These values were from three to ten times higher than within-species distances. Results show that the separation dates back to 1.9–2.1 mya, at the Plio-Pleistocene transition, when global climate underwent a period of significant cooling and Northern latitudes were probably more favourable to the Common than to the Pallid Swift. <b>Conclusion:</b> Differences in breeding biology, migration, moult and vocalizations between the two species are mirrored by a clear genetic separation.
DOI: 10.6084/m9.figshare.5354131.v1
title: Wintering ecology and nomadic movement patterns of Short-eared Owls <i>Asio flammeus</i> on a subtropical island

description: <b>Capsule:</b> Short-eared Owls <i>Asio flammeus</i> showed a female-biased sex ratio in their southernmost wintering grounds in Oriental Asia. This is the first description of a nomadic movement pattern in this area. <b>Aims:</b> To investigate the sex ratio, movement patterns, home range size and habitat preference of non-breeding Short-eared Owls in subtropical Taiwan. <b>Methods:</b> Eleven Short-eared Owls were radio tracked following trapping and transportation away from an airport as part of the management of bird-strike risk for aeroplanes. <b>Results:</b> Our results indicated a female-skewed (75%) sex ratio for Short-eared Owls wintering in Taiwan. The owls demonstrated a nomadic behaviour by showing a repetitive pattern of high roosting site fidelity in the short term, followed by a long-distance movement to a different discrete area. Grasslands were commonly used as day-roosting sites but agricultural habitats were favoured at night. <b>Conclusion:</b> Compared to on the breeding ground, the wintering owls exhibited a much larger home range size and exploit more dispersed patches of suitable habitats. These results revealed a notable conservation issue for the wintering owls, especially in the degraded and partially developed landscapes in subtropical countries.
DOI: 10.6084/m9.figshare.5354107
title: Structure and Behavior of Gasless Combustion Waves in Powders

description: The method of simulation of the structure of powder mixture, which allows calculating the samples with a relative density from 15% up to practically close packing, is described. The 3D model of discrete combustion wave in powder mixture, which uses the actual structure of the sample, is considered. The parametric investigations of combustion of powder mixture in the wide range of relative density and particle ignition temperature are carried out. The model predicts the steady-state combustion, oscillating combustion, and extinction depending on the parameters of powder mixture. The results of the simulation are compared with experimental data.
DOI: 10.6084/m9.figshare.5354107.v1
title: Structure and Behavior of Gasless Combustion Waves in Powders

description: The method of simulation of the structure of powder mixture, which allows calculating the samples with a relative density from 15% up to practically close packing, is described. The 3D model of discrete combustion wave in powder mixture, which uses the actual structure of the sample, is considered. The parametric investigations of combustion of powder mixture in the wide range of relative density and particle ignition temperature are carried out. The model predicts the steady-state combustion, oscillating combustion, and extinction depending on the parameters of powder mixture. The results of the simulation are compared with experimental data.
DOI: 10.6084/m9.figshare.5355097.v5
title: HCV+ Subjects 16.10.17.xlsx

description: We performed a retrospective study of HCV infection in a UK teaching hospital to evaluate and compare the performance of different laboratory tests, to describe the population with active HCV infection and to determine the proportion of these individuals who access clinical review and treatment. Microbiology records for all HCV screening tests performed at Oxford University Hospitals within two defined time-intervals (Group 1 - 18 months; Jan 2013 - June 2014, Group 2 - 15 months; Jan 2015 - March 2016) were studied . For those testing positive we collected follow-up testing data. We recorded patient age, sex, and the location from which the sample was sent. We used an analytical tool to estimate ethnicity applying Onolytics software for all patients whom a full name was part of the electronic record. Ethics approval was not required, as this study was undertaken as a departmental quality improvement exercise within microbiology using anonymised patient data, and completed the audit cycle for previously approved audit projects. Data for Onolytics analysis were handled separately and were subject to a confidential disclosure agreement drawn up by University of Oxford Research Services (February 2016). <br><br><br><br><br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.5354122.v2
title: So similar and yet so different: taxonomic status of Pallid Swift <i>Apus pallidus</i> and Common Swift <i>Apus apus</i>

description: <b>Capsule:</b> Common Swift <i>Apus apus</i> and Pallid Swift <i>Apus Pallidus</i> are morphologically very similar but are genetically distinct and diverged 1.9–2.1 million years ago (mya). <b>Aims:</b> To examine genetic differentiation and to estimate separation time between Common and Pallid Swifts. <b>Methods:</b> Estimation of differences in three different mitochondrial DNA markers (<i>COI</i>, <i>ND2</i> and control region), and a fourth marker, the <i>cytb</i>, that did not differ between taxa. Fossils were used to calibrate the estimate of separation date between the two taxa. <b>Results:</b> The genetic between-species distances were 0.010, 0.006 and 0.033 for the three markers, respectively. These values were from three to ten times higher than within-species distances. Results show that the separation dates back to 1.9–2.1 mya, at the Plio-Pleistocene transition, when global climate underwent a period of significant cooling and Northern latitudes were probably more favourable to the Common than to the Pallid Swift. <b>Conclusion:</b> Differences in breeding biology, migration, moult and vocalizations between the two species are mirrored by a clear genetic separation.
DOI: 10.6084/m9.figshare.5354035
title: Palaeoarchaean materials in the Tibetan Plateau indicated by zircon

description: The early tectonic evolution of the Lhasa Terrane remains poorly understood, although evidence for a substantial prehistory has been reported recently. We have carried out <i>in situ</i> zircon U–Pb dating and Hf–O isotopes of late Early Cretaceous monzogranites and get a surprising package of inherited zircons, not only because of their age profile, but also because the oldest Palaeoarchaean zircons are euhedral. The discovery of Palaeoarchaean euhedral zircons in the region suggests the presence of extremely old rocks in Tibet. Zircons from the Nagqu monzogranite yield five age peaks at ~3.45 Ga, ~2.56 Ga, ~1.76 Ga, ~900 Ma, and ~111 Ma. They have large variations in <i>ε</i><sub>Hf</sub>(<i>t</i>) values (−45.1–9.2) and old Hf model ages (924–3935 Ma), with variable <i>δ</i><sup>18</sup>O values of −5.80–9.64. Palaeoarchaean zircons (~3.20–3.45 Ga) are euhedral with magmatic zircon characteristics. One of the grains has negative <i>ε</i><sub>Hf</sub>(<i>t</i>) value (−4.8), old Hf model age (3935 Ma), and high positive <i>δ</i><sup>18</sup>O value (7.27), which suggests an ancient crustal origin. The source of Palaeoarchaean euhedral zircons should be proximal to prevent long-distance transport and abrasion, whereas the late Early Cretaceous monzogranites are I-type. Thus, Palaeoarchaean euhedral zircons are most likely captured from the country rocks by assimilation at depth or may be relics of previous magmatic zircons. Notwithstanding their exact history, Palaeoarchaean euhedral zircons indicate Palaeoarchaean materials near Nagqu in the Tibetan Plateau. The inherited zircons also experienced a Late Palaeoproterozoic event (~1.76 Ga) likely related to the evolution of the India block. The peak at ~900 Ma suggests affinity to the Qiangtang and Himalaya blocks.