cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8067929
title: What is the taxonomic status of East Asian otter species based on molecular evidence?: focus on the position of the Japanese otter holotype specimen from museum

description: The Japanese otter (<i>Lutra nippon</i>), once inhabited in most islands of Japan, is now considered as an extinct species. Although the Japanese otter is regarded as a distinct species from the Eurasian otter (<i>L. lutra</i>), its phylogeny and taxonomic status are based on limited information on morphological and genetic data, and thus further clarification is required. Here, we assessed the phylogenetic relationship among the genus <i>Lutra</i> and taxonomic status of <i>L. nippon</i> by using the complete sequences of cytochrome <i>b</i> gene of its holotype. The present phylogenic trees supported that the genus <i>Lutra</i> specimens largely formed monophyletic group, with <i>L. sumatrana</i> as a basal to other <i>Lutra</i> species. Within <i>Lutra</i> species, <i>L. nippon</i> was distantly related with <i>L. lutra</i>. The European otter population of <i>L. l. lutra</i> were clustered together with its subspecies, <i>L. l. chinensis</i> rather than the same subspecies, Korean otter population. The discrepancy between the genetic data and traditional taxonomy justifies the necessity of reexamination of the current subspecific classification system of Eurasian otters. Level of genetic divergence between the holotype of <i>L. nippon</i> and <i>L. lutra</i> was two to three-fold lower than those among the other sister species of the Lutrinae. Based on the level of divergence between the <i>L. nippon</i> and <i>L. lutra</i>, and insufficient evidence of morphological difference between them, it is suggested that designation of Japanese otter as a separate species from L. <i>lutra</i> will be reconsidered.
DOI: 10.6084/m9.figshare.8067929.v1
title: What is the taxonomic status of East Asian otter species based on molecular evidence?: focus on the position of the Japanese otter holotype specimen from museum

description: The Japanese otter (<i>Lutra nippon</i>), once inhabited in most islands of Japan, is now considered as an extinct species. Although the Japanese otter is regarded as a distinct species from the Eurasian otter (<i>L. lutra</i>), its phylogeny and taxonomic status are based on limited information on morphological and genetic data, and thus further clarification is required. Here, we assessed the phylogenetic relationship among the genus <i>Lutra</i> and taxonomic status of <i>L. nippon</i> by using the complete sequences of cytochrome <i>b</i> gene of its holotype. The present phylogenic trees supported that the genus <i>Lutra</i> specimens largely formed monophyletic group, with <i>L. sumatrana</i> as a basal to other <i>Lutra</i> species. Within <i>Lutra</i> species, <i>L. nippon</i> was distantly related with <i>L. lutra</i>. The European otter population of <i>L. l. lutra</i> were clustered together with its subspecies, <i>L. l. chinensis</i> rather than the same subspecies, Korean otter population. The discrepancy between the genetic data and traditional taxonomy justifies the necessity of reexamination of the current subspecific classification system of Eurasian otters. Level of genetic divergence between the holotype of <i>L. nippon</i> and <i>L. lutra</i> was two to three-fold lower than those among the other sister species of the Lutrinae. Based on the level of divergence between the <i>L. nippon</i> and <i>L. lutra</i>, and insufficient evidence of morphological difference between them, it is suggested that designation of Japanese otter as a separate species from L. <i>lutra</i> will be reconsidered.
DOI: 10.6084/m9.figshare.8067890
title: HDPE observed and attenuation corrected neutron diffraction patterns

description: Experimental investigations were performed using the Materials Probe for Internal Strain Investigations (MPISI) angle dispersive neutron strain scanner located at the SAFARI-1 nuclear research reactor. All experiments were conducted using neutrons with a wavelength of 1.659 Å which correspond to 29.7 meV in energy. Calibration procedures were followed to compensate for environmental background, determine the instrument centre of rotation (CoR), as well as gauge volume positional accuracies to within 10 µm. As the detector of MPISI covers an angular range of 13.8° in 2-theta, the detector was step-scanned in frames to produce diffraction data covering a larger 2-theta range.<br>
DOI: 10.6084/m9.figshare.8067890.v1
title: HDPE observed and attenuation corrected neutron diffraction patterns

description: Experimental investigations were performed using the Materials Probe for Internal Strain Investigations (MPISI) angle dispersive neutron strain scanner located at the SAFARI-1 nuclear research reactor. All experiments were conducted using neutrons with a wavelength of 1.659 Å which correspond to 29.7 meV in energy. Calibration procedures were followed to compensate for environmental background, determine the instrument centre of rotation (CoR), as well as gauge volume positional accuracies to within 10 µm. As the detector of MPISI covers an angular range of 13.8° in 2-theta, the detector was step-scanned in frames to produce diffraction data covering a larger 2-theta range.<br>
DOI: 10.6084/m9.figshare.8067827
title: A6.tar.gz

description: MD simulations of the A6 TCR.<br>
DOI: 10.6084/m9.figshare.8067827.v2
title: A6.tar.gz

description: MD simulations of the A6 TCR.<br>
DOI: 10.6084/m9.figshare.8067827.v1
title: A6.tar.gz

description: MD simulations of the A6 TCR.<br>
DOI: 10.6084/m9.figshare.8067803
title: JM22.tar.gz

description: MD simulations of the JM22 TCR.<br>
DOI: 10.6084/m9.figshare.8067743
title: 1G4.tar.gz

description: MD simulations of the 1G4 TCR.<br>
DOI: 10.6084/m9.figshare.8067746
title: LC13.tar.gz

description: MD simulations of the LC13 TCR.<br>
DOI: 10.6084/m9.figshare.8067746.v1
title: LC13.tar.gz

description: MD simulations of the LC13 TCR.<br>
DOI: 10.25377/sussex.8067608
title: Dataset for research paper: Effects of Racial Bias on Composite Construction

description: <b>Data for paper published in Applied Cognitive Psychology March 2020</b><br>We presented participants with a racially-ambiguous face and biased them into thinking it was Indian or British. These participants then constructed a facial composite, using E-Fit6. The composites were rated by separate groups of participants for racial appearance (Indian or European) and degree of resemblance to the target face.Constructors and raters were European, overseas Indian or Indians living in India. <br>The datafile contains the raw data for this study: ratings of the ambiguous face's apparent race, the ratings of the composites' apparent race, and the ratings of the composites' resemblance to the target face.<br><b><br></b><b>Abstract</b>We investigated how prior bias about a face's racial characteristics can affect its encoding and resultant facial composite construction. In total, 61 participant (24 Europeans, 18 Indians living in India and 19 Indians living in Europe) saw a racially ambiguous unfamiliar face and were led to believe it was either European or Indian. They created a composite of this face, using EFIT6. Two groups of independent raters (one Indian, the other European) then assessed the apparent race of each composite. A different two groups (one Indian, one European) assessed each composite's degree of resemblance to the target face, to determine whether this was influenced by the constructors' initial categorisation of the target face as “own-race” or “otherrace.” Composites appeared significantly more “Asian” or “European” according to the bias induced in their creators, but there was no evidence of any own-race bias in the resemblance ratings for the composites. <br>
DOI: 10.25377/sussex.8067608.v1
title: Dataset for research paper: Effects of Racial Bias on Composite Construction

description: <b>Data for paper published in Applied Cognitive Psychology March 2020</b><br>We presented participants with a racially-ambiguous face and biased them into thinking it was Indian or British. These participants then constructed a facial composite, using E-Fit6. The composites were rated by separate groups of participants for racial appearance (Indian or European) and degree of resemblance to the target face.Constructors and raters were European, overseas Indian or Indians living in India. <br>The datafile contains the raw data for this study: ratings of the ambiguous face's apparent race, the ratings of the composites' apparent race, and the ratings of the composites' resemblance to the target face.<br><b><br></b><b>Abstract</b>We investigated how prior bias about a face's racial characteristics can affect its encoding and resultant facial composite construction. In total, 61 participant (24 Europeans, 18 Indians living in India and 19 Indians living in Europe) saw a racially ambiguous unfamiliar face and were led to believe it was either European or Indian. They created a composite of this face, using EFIT6. Two groups of independent raters (one Indian, the other European) then assessed the apparent race of each composite. A different two groups (one Indian, one European) assessed each composite's degree of resemblance to the target face, to determine whether this was influenced by the constructors' initial categorisation of the target face as “own-race” or “otherrace.” Composites appeared significantly more “Asian” or “European” according to the bias induced in their creators, but there was no evidence of any own-race bias in the resemblance ratings for the composites. <br>
DOI: 10.6084/m9.figshare.8067578
title: Supplementary Material for: Comparison of Frequency- and Time-Domain Autoregulation and Vasoreactivity Indices in a Piglet Model of Hypoxia-Ischemia and Hypothermia

description: <b><i>Introduction:</i></b> The optimal method to detect impairments in cerebrovascular pressure autoregulation in neonates with hypoxic-ischemic encephalopathy (HIE) is unclear. Improving autoregulation monitoring methods would significantly advance neonatal neurocritical care. <b><i>Methods:</i></b> We tested several mathematical algorithms from the frequency and time domains in a piglet model of HIE, hypothermia, and hypotension. We used laser Doppler flowmetry and induced hypotension to delineate the gold standard lower limit of autoregulation (LLA). Receiver operating characteristics curve analyses were used to determine which indices could distinguish blood pressure above the LLA from that below the LLA in each piglet. <b><i>Results:</i></b> Phase calculation in the frequency band with maximum coherence, as well as the correlation between mean arterial pressure (MAP) and near-infrared spectroscopy relative total tissue hemoglobin (HbT) or regional oxygen saturation (rSO<sub>2</sub>), accurately discriminated functional from dysfunctional autoregulation. Neither hypoxia-ischemia nor hypothermia affected the accuracy of these indices. Coherence alone and gain had low diagnostic value relative to phase and correlation. <b><i>Conclusion:</i></b> Our findings indicate that phase shift is the most accurate component of autoregulation monitoring in the developing brain, and it can be measured using correlation or by calculating phase when coherence is maximal. Phase and correlation autoregulation indices from MAP and rSO<sub>2</sub> and vasoreactivity indices from MAP and HbT are accurate metrics that are suitable for clinical HIE studies.
DOI: 10.6084/m9.figshare.8067584
title: Data From : Role of sociality in the response of killer whales to an additive mortality event

description: The fileset contains supporting data for the paper: <br>Role of sociality in the response of killer whales to an additive mortality event <br><br>The fileset contains data used to analyse the social structure and survival of the killer whales Crozet populations.
DOI: 10.6084/m9.figshare.8067572
title: Supplementary Material for: Prediction Model of Cardiac Risk for Dental Extraction in Elderly Patients with Cardiovascular Diseases

description: <b><i>Background:</i></b> With the rapidly increasing population of elderly people, dental extraction in elderly individuals with cardiovascular diseases (CVDs) has become quite common. The issue of how to assure the safety of elderly patients with CVDs undergoing dental extraction has perplexed dentists and internists for many years. And it is important to derive an appropriate risk prediction tool for this population. <b><i>Objectives:</i></b> The aim of this retrospective, observational study was to establish and validate a prediction model based on the random forest (RF) algorithm for the risk of cardiac complications of dental extraction in elderly patients with CVDs. <b><i>Methods:</i></b> Between August 2017 and May 2018, a total of 603 patients who fulfilled the inclusion criteria were used to create a training set. An independent test set contained 230 patients between June 2018 and July 2018. Data regarding clinical parameters, laboratory tests, clinical examinations before dental extraction, and 1-week follow-up were retrieved. Predictors were identified by using logistic regression (LR) with penalized LASSO (least absolute shrinkage and selection operator) variable selection. Then, a prediction model was constructed based on the RF algorithm by using a 5-fold cross-validation method. <b><i>Results:</i></b> The training set, based on 603 participants, including 282 men and 321 women, had an average participant age of 72.38 ± 8.31 years. Using feature selection methods, 11 predictors for risk of cardiac complications were screened out. When the RF model was constructed, its overall classification accuracy was 0.82 at the optimal cutoff value of 18.5%. In comparison to the LR model, the RF model showed a superior predictive performance. The AUROC (area under the receiver operating characteristic curve) scores of the RF and LR models were 0.83 and 0.80, respectively, in the independent test set. The AUPRC (area under the precision-recall curve) scores of the RF and LR models were 0.56 and 0.35, respectively, in the independent test set. <b><i>Conclusion:</i></b> The RF-based prediction model is expected to be applicable for preoperative clinical assessment for preventing cardiac complications in elderly patients with CVDs undergoing dental extraction. The findings may aid physicians and dentists in making more informed recommendations to prevent cardiac complications in this patient population.
DOI: 10.6084/m9.figshare.8067569
title: A simple root-soil coupling system

description: Using a simple novel dual porosity system, we try to understand redistribution of water and changes in the evaporation patterns in the presence of a root-mimic (consisting of smaller particles) surrounded by a soil-mimic consisting of larger particles.<br>
DOI: 10.6084/m9.figshare.8067578.v1
title: Supplementary Material for: Comparison of Frequency- and Time-Domain Autoregulation and Vasoreactivity Indices in a Piglet Model of Hypoxia-Ischemia and Hypothermia

description: <b><i>Introduction:</i></b> The optimal method to detect impairments in cerebrovascular pressure autoregulation in neonates with hypoxic-ischemic encephalopathy (HIE) is unclear. Improving autoregulation monitoring methods would significantly advance neonatal neurocritical care. <b><i>Methods:</i></b> We tested several mathematical algorithms from the frequency and time domains in a piglet model of HIE, hypothermia, and hypotension. We used laser Doppler flowmetry and induced hypotension to delineate the gold standard lower limit of autoregulation (LLA). Receiver operating characteristics curve analyses were used to determine which indices could distinguish blood pressure above the LLA from that below the LLA in each piglet. <b><i>Results:</i></b> Phase calculation in the frequency band with maximum coherence, as well as the correlation between mean arterial pressure (MAP) and near-infrared spectroscopy relative total tissue hemoglobin (HbT) or regional oxygen saturation (rSO<sub>2</sub>), accurately discriminated functional from dysfunctional autoregulation. Neither hypoxia-ischemia nor hypothermia affected the accuracy of these indices. Coherence alone and gain had low diagnostic value relative to phase and correlation. <b><i>Conclusion:</i></b> Our findings indicate that phase shift is the most accurate component of autoregulation monitoring in the developing brain, and it can be measured using correlation or by calculating phase when coherence is maximal. Phase and correlation autoregulation indices from MAP and rSO<sub>2</sub> and vasoreactivity indices from MAP and HbT are accurate metrics that are suitable for clinical HIE studies.
DOI: 10.6084/m9.figshare.8067557
title: Supplementary Material for: Seizures Are Associated with Blood-Brain Barrier Disruption in a Piglet Model of Neonatal Hypoxic-Ischaemic Encephalopathy

description: Seizures in the neonatal period are most often symptomatic of central nervous system (CNS) dysfunction and the most common cause is hypoxic-ischaemic encephalopathy (HIE). Seizures are associated with poor long-term outcomes and increased neuropathology. Blood-brain barrier (BBB) disruption and inflammation may contribute to seizures and increased neuropathology but are incompletely understood in neonatal HIE. The aim of this study was to investigate the impact of seizures on BBB integrity in a preclinical model of neonatal hypoxic-ischaemic (HI) injury. Piglets (age: &lt;24 h) were subjected to a 30-min HI insult followed by recovery to 72 h post-insult. Amplitude-integrated electroencephalography (aEEG) was performed and seizure burden and background aEEG pattern were analysed. BBB disruption was evaluated in the parietal cortex and hippocampus by means of immunohistochemistry and Western blot. mRNA and protein expression of tight-junction proteins (zonula-occludens 1 [ZO1], occludin [OCLN], and claudin-5 [CLDN5]) was assessed using quantitative polymerase chain reaction (qPCR) and Western blot. In addition, mRNA from genes associated with BBB disruption vascular endothelial growth factor (VEGF) and matrix metalloproteinase 2 (MMP2) as well as inflammatory cytokines and chemokines was assessed with qPCR. Piglets that developed seizures following HI (HI-Sz) had significantly greater injury, as demonstrated by poorer aEEG background pattern scores, lower neurobehavioural scores, and greater histopathology. HI-Sz animals had severe IgG extravasation into brain tissue and uptake into neurons as well as significantly greater levels of IgG in both brain regions as assessed by Western blot. IgG protein in both brain regions was significantly associated with seizure burden, aEEG pattern scores, and neurobehavioural scores. There was no difference in mRNA expression of the tight junctions, however a significant loss of ZO1 and OCLN protein was observed in the parietal cortex. The inflammatory genes TGFβ, IL1β, IL8, IL6, and TNFα were significantly upregulated in HI-Sz animals. MMP2 was significantly increased in animals with seizures compared with animals without seizures. Increasing our understanding of neuropathology associated with seizure is vital because of the association between seizure and poor outcomes. Investigating the BBB is a major untapped area of research and a potential avenue for novel treatments.
DOI: 10.6084/m9.figshare.8067557.v1
title: Supplementary Material for: Seizures Are Associated with Blood-Brain Barrier Disruption in a Piglet Model of Neonatal Hypoxic-Ischaemic Encephalopathy

description: Seizures in the neonatal period are most often symptomatic of central nervous system (CNS) dysfunction and the most common cause is hypoxic-ischaemic encephalopathy (HIE). Seizures are associated with poor long-term outcomes and increased neuropathology. Blood-brain barrier (BBB) disruption and inflammation may contribute to seizures and increased neuropathology but are incompletely understood in neonatal HIE. The aim of this study was to investigate the impact of seizures on BBB integrity in a preclinical model of neonatal hypoxic-ischaemic (HI) injury. Piglets (age: &lt;24 h) were subjected to a 30-min HI insult followed by recovery to 72 h post-insult. Amplitude-integrated electroencephalography (aEEG) was performed and seizure burden and background aEEG pattern were analysed. BBB disruption was evaluated in the parietal cortex and hippocampus by means of immunohistochemistry and Western blot. mRNA and protein expression of tight-junction proteins (zonula-occludens 1 [ZO1], occludin [OCLN], and claudin-5 [CLDN5]) was assessed using quantitative polymerase chain reaction (qPCR) and Western blot. In addition, mRNA from genes associated with BBB disruption vascular endothelial growth factor (VEGF) and matrix metalloproteinase 2 (MMP2) as well as inflammatory cytokines and chemokines was assessed with qPCR. Piglets that developed seizures following HI (HI-Sz) had significantly greater injury, as demonstrated by poorer aEEG background pattern scores, lower neurobehavioural scores, and greater histopathology. HI-Sz animals had severe IgG extravasation into brain tissue and uptake into neurons as well as significantly greater levels of IgG in both brain regions as assessed by Western blot. IgG protein in both brain regions was significantly associated with seizure burden, aEEG pattern scores, and neurobehavioural scores. There was no difference in mRNA expression of the tight junctions, however a significant loss of ZO1 and OCLN protein was observed in the parietal cortex. The inflammatory genes TGFβ, IL1β, IL8, IL6, and TNFα were significantly upregulated in HI-Sz animals. MMP2 was significantly increased in animals with seizures compared with animals without seizures. Increasing our understanding of neuropathology associated with seizure is vital because of the association between seizure and poor outcomes. Investigating the BBB is a major untapped area of research and a potential avenue for novel treatments.
DOI: 10.6084/m9.figshare.8067515
title: Stay awhile in my burrow! Interspecific associations of vertebrates to Indian crested porcupine burrows

description: The Indian crested porcupine, <i>Hystrix indica</i>, is a significant ecosystem engineer that builds extensive burrows in the semi-arid regions of north-west India. Many different animals use these burrows as temporary retreats or permanent shelters. Camera-traps were used to record 22 species using porcupine burrows, including 10 mammals, 8 birds, 3 reptiles, and 1 amphibian. In addition to birds foraging inside and around the entrance, the most common and persistent visitors were mongooses, rats, squirrels, hares, jungle cats, and small Indian civets. A bat species, <i>Hipposideros</i> sp. was found to be permanent occupants of porcupine burrows, while Indian rock pythons and jackals exhibited seasonal use. During winter, pythons basked outside the burrows and constricted their activities to the daytime. Conversely, porcupines are nocturnal and use deeper parts of their burrows than the pythons. Temporal usage patterns and spatial segregation allows for mutualistic behaviour between pythons and porcupines. Jackals were also found to use porcupine burrows during their summer breeding season, employing aggression to evict both porcupines and pythons. The study demonstrates a functional role for porcupines, which are capable of constructing “landmark” structures in the semi-arid regions of north-west India that support a range of micro-communities.
DOI: 10.6084/m9.figshare.8067569.v2
title: A simple root-soil coupling system

description: Using a simple novel dual porosity system, we try to understand redistribution of water and changes in the evaporation patterns in the presence of a root-mimic (consisting of smaller particles) surrounded by a soil-mimic consisting of larger particles.<br>
DOI: 10.6084/m9.figshare.8067584.v1
title: Data-Busson et al. PNAS.xlsx

description: Dataset of the paper Busson et al., 2019 published in PNAS