cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9632288
title: Supplementary Material for: C-C Motif Chemokine Ligand 15 May Be a Useful Biomarker for Predicting the Prognosis of Patients with Chronic Hypersensitivity Pneumonitis

description: <b><i>Background:</i></b> Chronic hypersensitivity pneumonitis (CHP) is characterized by lymphocytic inflammation and progressive fibrosis of the lung caused by a variety of inhaled antigens. Due to the difficulty of accurately diagnosing CHP, and the poor prognosis associated with the condition, a novel clinical biomarker is urgently needed. <b><i>Objective:</i></b> To investigate the usefulness of C-C motif chemokine ligand 15 (CCL15), which had been demonstrated to highly express in the lungs of CHP patients, as a clinical biomarker for CHP. <b><i>Method:</i></b> Immunohistochemical investigations were performed on lung tissue from CHP patients, and CCL15 levels in serum and bronchoalveolar lavage fluid (BALF) were measured via the enzyme-linked immunosorbent assay. <b><i>Results:</i></b> Immunohistochemistry investigations revealed high CCL15 expression in the lungs of CHP patients. Serum CCL15 levels in CHP patients (29.1 ± 2.1 μg/mL) were significantly higher than those of idiopathic pulmonary fibrosis patients (19.7 ± 1.3 μg/mL, <i>p</i> = 0.01) and healthy subjects (19.5 ± 1.7 μg/mL, <i>p</i> = 0.003). When BALF CCL15 level was divided by BALF albumin (Alb) level (BALF CCL15/Alb), it was significantly inversely correlated with forced vital capacity (β = –0.47, <i>p</i> = 0.0006), percentage of predicted carbon monoxide diffusion capacity of the lung (β = –0.41, <i>p</i> = 0.0048), and BALF lymphocyte count (β = –0.34, <i>p</i> = 0.01) in CHP patients. Multivariate Cox proportional hazards analysis revealed that high BALF CCL15/Alb and poor prognosis were statistically significantly independently correlated in CHP patients (HR 1.1, 95% CI 1.03–1.18, <i>p</i> = 0.004). <b><i>Conclusion:</i></b> The results of the current study suggest that CCL15 may be a useful prognostic biomarker for CHP. CCL15 was highly expressed in the lung tissue of CHP patients, and BALF CCL15/Alb was significantly associated with CHP prognosis.
DOI: 10.6084/m9.figshare.9632336.v1
title: EC2_B9.nwb

description: The enclosed data is collected using a high-density 256-channel electrocorticography array implanted in a human patient during treatment for epilepsy. The subjects are reading aloud consonant-vowel syllables from a list. The data was collected by Dr. Edward Chang at the University of California, San Francisco, and curated by Ben Dichter.Data is organized by subject ID, and each file is a continuous recording session in Neurodata Without Borders: Neurophysiology (NWB:N) 2.0 format. Voltage traces are included for each of the recorded 256 channels. Microphone signal was recorded at the time but is removed for HIPAA compliance. Detailed hand-marked annotations are provided which mark what syllable was said, and the times of the start, consonant-vowel transition, and end of each syllable. A rest-period time is also included when the subject was silent, which can be used as a baseline. Hand-marked anatomical labels are included for electrodes in the relevant brain regions. All dates have been removed for HIPAA compliance and replaced with Jan 1, 1900.
DOI: 10.6084/m9.figshare.9632288.v1
title: Supplementary Material for: C-C Motif Chemokine Ligand 15 May Be a Useful Biomarker for Predicting the Prognosis of Patients with Chronic Hypersensitivity Pneumonitis

description: <b><i>Background:</i></b> Chronic hypersensitivity pneumonitis (CHP) is characterized by lymphocytic inflammation and progressive fibrosis of the lung caused by a variety of inhaled antigens. Due to the difficulty of accurately diagnosing CHP, and the poor prognosis associated with the condition, a novel clinical biomarker is urgently needed. <b><i>Objective:</i></b> To investigate the usefulness of C-C motif chemokine ligand 15 (CCL15), which had been demonstrated to highly express in the lungs of CHP patients, as a clinical biomarker for CHP. <b><i>Method:</i></b> Immunohistochemical investigations were performed on lung tissue from CHP patients, and CCL15 levels in serum and bronchoalveolar lavage fluid (BALF) were measured via the enzyme-linked immunosorbent assay. <b><i>Results:</i></b> Immunohistochemistry investigations revealed high CCL15 expression in the lungs of CHP patients. Serum CCL15 levels in CHP patients (29.1 ± 2.1 μg/mL) were significantly higher than those of idiopathic pulmonary fibrosis patients (19.7 ± 1.3 μg/mL, <i>p</i> = 0.01) and healthy subjects (19.5 ± 1.7 μg/mL, <i>p</i> = 0.003). When BALF CCL15 level was divided by BALF albumin (Alb) level (BALF CCL15/Alb), it was significantly inversely correlated with forced vital capacity (β = –0.47, <i>p</i> = 0.0006), percentage of predicted carbon monoxide diffusion capacity of the lung (β = –0.41, <i>p</i> = 0.0048), and BALF lymphocyte count (β = –0.34, <i>p</i> = 0.01) in CHP patients. Multivariate Cox proportional hazards analysis revealed that high BALF CCL15/Alb and poor prognosis were statistically significantly independently correlated in CHP patients (HR 1.1, 95% CI 1.03–1.18, <i>p</i> = 0.004). <b><i>Conclusion:</i></b> The results of the current study suggest that CCL15 may be a useful prognostic biomarker for CHP. CCL15 was highly expressed in the lung tissue of CHP patients, and BALF CCL15/Alb was significantly associated with CHP prognosis.
DOI: 10.6084/m9.figshare.9632276
title: The utility of the image analytics tool developed within the Orange Data Mining suite

description: The data in this repository comprises four different image sets to showcase the transfer learning approach and illustrate the utility of the image analytics tool developed within the Orange Data Mining suite (http://orange.biolab.si). Each of the four image sets is available in a separate zip file. List of images with additional annotations and information on the image classification is also available in the four Excel files. The images include progenitor cells in mouse bone healing, identification of developmental competence in mouse oocytes, sub-cellular protein localization in yeast, and developmental morphology of social amoebae.
DOI: 10.6084/m9.figshare.9632261
title: <i>Epichloe novae-zelandiae</i>, a new endophyte from the endemic New Zealand grass <i>Poa matthewsii</i>

description: <i>Epichloe</i> endophytes (Clavicipitaceae) infect pooid grass genera worldwide but predominantly in the Northern Hemisphere, but appear to be rare in native grasses of the Southern Hemisphere. Because of benefits that hosts may receive from the symbiosis, <i>Epichloe</i> endophytes have been extensively studied and are considered important components of sustainable agriculture. There are only a few studies available on the incidence of endophyte infection in grasses of the Southern Hemisphere and most grass species have never been examined. Here we report on a survey of native grasses of New Zealand including 25 endemic or indigenous species. We sampled up to 10 plants per species at different sites from both the North and South Island of New Zealand and examined tissues microscopically for endophyte infection. Overall, only two species were found to be infected, <i>Poa matthewsii</i> (Matthew's bluegrass) and <i>Dichelachne micrantha</i> (short-hair plume grass). Based on analyses of <i>tefA</i> and <i>tubB</i> genes, both endophytes were found to be interspecific hybrids. The endophyte of the new host <i>D. micrantha</i> was previously described as <i>Epichloe australiensis</i>, while the endophyte of <i>P. matthewsii</i> is a new species named here <i>E. novae-zelandiae</i>. The new species is a hybrid derived from <i>E. amarillans</i>, <i>E. bromicola</i> and <i>E. typhina</i> subsp. <i>poae.</i> Alkaloid analyses <i>in planta</i> suggested that <i>E. novae-zelandiae</i> can produce small amounts of peramine, early pathway indole-diterpenes and ergot alkaloids, but no lolines or lolitrems. Target specific primers suggested the presence of genes for ergot alkaloids and peramine, but genes of only early pathway steps for the other alkaloids. Furthermore, genes for both mating type idiomorphs (<i>MTA</i> and <i>MTB</i>) were present, a single copy of <i>MTA</i> and two copies of <i>MTB</i>. Endophytes of native grasses may provide a genetic resource that could be exploited for developing pasture grass cultivars with improved performance.
DOI: 10.6084/m9.figshare.9632261.v1
title: <i>Epichloe novae-zelandiae</i>, a new endophyte from the endemic New Zealand grass <i>Poa matthewsii</i>

description: <i>Epichloe</i> endophytes (Clavicipitaceae) infect pooid grass genera worldwide but predominantly in the Northern Hemisphere, but appear to be rare in native grasses of the Southern Hemisphere. Because of benefits that hosts may receive from the symbiosis, <i>Epichloe</i> endophytes have been extensively studied and are considered important components of sustainable agriculture. There are only a few studies available on the incidence of endophyte infection in grasses of the Southern Hemisphere and most grass species have never been examined. Here we report on a survey of native grasses of New Zealand including 25 endemic or indigenous species. We sampled up to 10 plants per species at different sites from both the North and South Island of New Zealand and examined tissues microscopically for endophyte infection. Overall, only two species were found to be infected, <i>Poa matthewsii</i> (Matthew's bluegrass) and <i>Dichelachne micrantha</i> (short-hair plume grass). Based on analyses of <i>tefA</i> and <i>tubB</i> genes, both endophytes were found to be interspecific hybrids. The endophyte of the new host <i>D. micrantha</i> was previously described as <i>Epichloe australiensis</i>, while the endophyte of <i>P. matthewsii</i> is a new species named here <i>E. novae-zelandiae</i>. The new species is a hybrid derived from <i>E. amarillans</i>, <i>E. bromicola</i> and <i>E. typhina</i> subsp. <i>poae.</i> Alkaloid analyses <i>in planta</i> suggested that <i>E. novae-zelandiae</i> can produce small amounts of peramine, early pathway indole-diterpenes and ergot alkaloids, but no lolines or lolitrems. Target specific primers suggested the presence of genes for ergot alkaloids and peramine, but genes of only early pathway steps for the other alkaloids. Furthermore, genes for both mating type idiomorphs (<i>MTA</i> and <i>MTB</i>) were present, a single copy of <i>MTA</i> and two copies of <i>MTB</i>. Endophytes of native grasses may provide a genetic resource that could be exploited for developing pasture grass cultivars with improved performance.
DOI: 10.17028/rd.lboro.9632252
title: The development of ICP-MS methods for the study of biomedical problems particularly those involving nucleic acids. Appendices.

description: Appendices for 'The development of ICP-MS methods for the study of biomedical problems particularly those involving nucleic acids.'Contains: Appendix 1. Additional information associated with Chapter 1: An introduction to ICP-MS analysisAppendix 2. Additional information associated with Chapter 2: Method development studies for the determination of phosphorous and sulphur isotopes by ICP-QMS.Appendix 3. Additional information associated with Chapter 3: The application of methods developed for the determination of <sup>31</sup>P and <sup>32</sup>S and the study ofDNA and related material by ICP-MS.Appendix 4. Additional information associated with Chapter 4: The measurement of platinum based anti-cancer drugs and DNA by ICP-MS.Appendix 5. Additional chapter. Chapter 7: The analysis of silver isotopes in impregnated polymers by ICP-MS.<br>
DOI: 10.17028/rd.lboro.9632252.v1
title: The development of ICP-MS methods for the study of biomedical problems particularly those involving nucleic acids. Appendices.

description: Appendices for 'The development of ICP-MS methods for the study of biomedical problems particularly those involving nucleic acids.'Contains: Appendix 1. Additional information associated with Chapter 1: An introduction to ICP-MS analysisAppendix 2. Additional information associated with Chapter 2: Method development studies for the determination of phosphorous and sulphur isotopes by ICP-QMS.Appendix 3. Additional information associated with Chapter 3: The application of methods developed for the determination of <sup>31</sup>P and <sup>32</sup>S and the study ofDNA and related material by ICP-MS.Appendix 4. Additional information associated with Chapter 4: The measurement of platinum based anti-cancer drugs and DNA by ICP-MS.Appendix 5. Additional chapter. Chapter 7: The analysis of silver isotopes in impregnated polymers by ICP-MS.<br>
DOI: 10.6084/m9.figshare.9632276.v1
title: Orange-Image-Analytics

description: The data in this repository comprises four different image sets to showcase the transfer learning approach and illustrate the utility of the image analytics tool developed within the Orange Data Mining suite (http://orange.biolab.si). Each of the four image sets is available in a separate zip file. List of images with additional annotations and information on the image classification is also available in the four Excel files. The images include progenitor cells in mouse bone healing, identification of developmental competence in mouse oocytes, sub-cellular protein localization in yeast, and developmental morphology of social amoebae.
DOI: 10.6084/m9.figshare.9632258.v1
title: From Vagrant to Resident: occurrence, residency and births of leopard seals (<i>Hydrurga leptonyx</i>) in New Zealand waters

description: In contrast to previous reports that leopard seals (<i>Hydrurga leptonyx</i>) are rare vagrants to New Zealand, we show that this species is a regular member of the marine fauna of this region. We present a first analysis from the New Zealand Leopard Seal Database – an extensive collation of 2,711 records of leopard seals within New Zealand between 1200 and 2018. Of these records, 51.2% (<i>n</i> = 1,408) were photographic. Leopard seal sightings have increased over time and been reported in all seasons and regions of New Zealand. Sightings are predominantly of adult individuals of good or excellent body condition, which differs to previous hypotheses suggesting that leopard seals visiting New Zealand shores are primarily juvenile animals in poor health condition. A total of 176 unique individuals have been identified in the New Zealand Leopard Seal Catalogue between 2014 and 2018 and preliminary results indicate that numbers per annum have continued to increase over time. Three leopard seal births and a number of juvenile animals (34% of the NZ records) have been documented. Considering the information presented here and the current definitions in the New Zealand Threat Classification System, the threat status of leopard seals within New Zealand waters should be reclassified from Vagrant to Resident.
DOI: 10.25392/leicester.data.9632213
title: Datasets to accompany Resilience, where to begin? A lay theories approach. (Currently under submission)

description: Samples relating to 12 analyses of lay-theories of resilience among participants from USA, New Zealand, India, Iran, Russia (Moscow; Kazan). Central variables relate to participant endorsements of resilience descriptors. Demographic data includes (though not for all samples), Sex/Gender, Age, Ethnicity, Work, and Educational Status.<br> <br>Analysis 1. USA Exploratory Factor Analysis data<br>Analysis 2. New Zealand Exploratory Factor Analysis data<br>Analysis 3. India Exploratory Factor Analysis data<br>Analysis 4. Iran Exploratory Factor Analysis data<br>Analysis 5. Russian (Moscow) Exploratory Factor Analysis data<br>Analysis 6. Russian (Kazan) Exploratory Factor Analysis data<br>Analysis 7. USA Confirmatory Factor Analysis data<br>Analysis 8. New Zealand Confirmatory Factor Analysis data<br>Analysis 9. India Confirmatory Factor Analysis data<br>Analysis 10. Iran Confirmatory Factor Analysis data<br>Analysis 11. Russian (Moscow) Confirmatory Factor Analysis data<br>Analysis 12. Russian (Kazan) Confirmatory Factor Analysis data
DOI: 10.6084/m9.figshare.9632198
title: Energetic strategies modulate the distribution and abundance of butterflies Data sets

description: In our study, we hypothesized that species can allocate more energy towards dispersal and reproduction if they compensate their energetic costs by reducing mobility costs or increasing energy uptake or both. Furthermore, according to the central assumption of trait-based approaches, we predict that the effects of morphological traits on species’ distribution and abundance are not direct but mediated by components of the energy budget. <br>As proxies for the energetic strategies of butterfly species associated with the two main components of their energy budget, we first assessed wingbeat frequencies of 102 butterfly species based on high-speed camera footage and their nectar-foraging propensities by estimating the relative time species spent collecting nectar. We combined these data with information on the occupancy of species across Europe and Switzerland, population densities from Switzerland (i.e. regional distribution, local distribution and local abundance) and estimates of the average body size, colour darkness and wing size of species from standardised images. <br>To test whether species compensate an investment into body size and melanisation by reducing their mobility costs or increasing energy uptake as adults, we investigated the effects of interactions between morphological traits and components of the energy budget on the distribution and abundance of species using generalised least-squares models that included a Brownian correlation structure to account for the phylogenetic relatedness of species. <br>We tested our second hypothesis that the effects of morphological traits on the distribution and abundance of species are mediated by components of the energy budget and integrated the complex interdependencies of the considered morphological traits by fitting two different piecewise structural equation models. In the first model, we assumed that morphological traits directly affect the distribution and abundance of species, whereas in the second model we assumed indirect effects via mobility costs and energy uptake. All components of the structural equation models were controlled for species’ phylogenetic relatedness. In addition, we considered habitat availability (i.e. occupancy of larval host plants) as a potential constraint on the distribution of species.
DOI: 10.17028/rd.lboro.9632207
title: Video partitioning for wireless applications. Additional material.

description: Contains: Images and spreadsheets embedded within thesis, ordered by relevant chapter.Video sequences and frames. <br>See read me file for overview of folder contents.
DOI: 10.17028/rd.lboro.9632207.v1
title: Video partitioning for wireless applications. Additional material.

description: Contains: Images and spreadsheets embedded within thesis, ordered by relevant chapter.Video sequences and frames. <br>See read me file for overview of folder contents.
DOI: 10.6084/m9.figshare.9632198.v2
title: Energetic strategies modulate the distribution and abundance of butterflies Data sets

description: In our study, we hypothesized that species can allocate more energy towards dispersal and reproduction if they compensate their energetic costs by reducing mobility costs or increasing energy uptake or both. Furthermore, according to the central assumption of trait-based approaches, we predict that the effects of morphological traits on species’ distribution and abundance are not direct but mediated by components of the energy budget. <br>As proxies for the energetic strategies of butterfly species associated with the two main components of their energy budget, we first assessed wingbeat frequencies of 102 butterfly species based on high-speed camera footage and their nectar-foraging propensities by estimating the relative time species spent collecting nectar. We combined these data with information on the occupancy of species across Europe and Switzerland, population densities from Switzerland (i.e. regional distribution, local distribution and local abundance) and estimates of the average body size, colour darkness and wing size of species from standardised images. <br>To test whether species compensate an investment into body size and melanisation by reducing their mobility costs or increasing energy uptake as adults, we investigated the effects of interactions between morphological traits and components of the energy budget on the distribution and abundance of species using generalised least-squares models that included a Brownian correlation structure to account for the phylogenetic relatedness of species. <br>We tested our second hypothesis that the effects of morphological traits on the distribution and abundance of species are mediated by components of the energy budget and integrated the complex interdependencies of the considered morphological traits by fitting two different piecewise structural equation models. In the first model, we assumed that morphological traits directly affect the distribution and abundance of species, whereas in the second model we assumed indirect effects via mobility costs and energy uptake. All components of the structural equation models were controlled for species’ phylogenetic relatedness. In addition, we considered habitat availability (i.e. occupancy of larval host plants) as a potential constraint on the distribution of species.
DOI: 10.6084/m9.figshare.9632198.v1
title: Energetic strategies modulate the distribution and abundance of butterflies Data sets

description: In our study, we hypothesized that species can allocate more energy towards dispersal and reproduction if they compensate their energetic costs by reducing mobility costs or increasing energy uptake or both. Furthermore, according to the central assumption of trait-based approaches, we predict that the effects of morphological traits on species’ distribution and abundance are not direct but mediated by components of the energy budget. <br>As proxies for the energetic strategies of butterfly species associated with the two main components of their energy budget, we first assessed wingbeat frequencies of 102 butterfly species based on high-speed camera footage and their nectar-foraging propensities by estimating the relative time species spent collecting nectar. We combined these data with information on the occupancy of species across Europe and Switzerland, population densities from Switzerland (i.e. regional distribution, local distribution and local abundance) and estimates of the average body size, colour darkness and wing size of species from standardised images. <br>To test whether species compensate an investment into body size and melanisation by reducing their mobility costs or increasing energy uptake as adults, we investigated the effects of interactions between morphological traits and components of the energy budget on the distribution and abundance of species using generalised least-squares models that included a Brownian correlation structure to account for the phylogenetic relatedness of species. <br>We tested our second hypothesis that the effects of morphological traits on the distribution and abundance of species are mediated by components of the energy budget and integrated the complex interdependencies of the considered morphological traits by fitting two different piecewise structural equation models. In the first model, we assumed that morphological traits directly affect the distribution and abundance of species, whereas in the second model we assumed indirect effects via mobility costs and energy uptake. All components of the structural equation models were controlled for species’ phylogenetic relatedness. In addition, we considered habitat availability (i.e. occupancy of larval host plants) as a potential constraint on the distribution of species.