cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5135086.v4
title: Data used in "Turbulent mixing within the Kuroshio in the Tokara Strait"

description: Data from "Turbulent mixing within the Kuroshio in the Tokara Strait" by E. Tsutsumi, T. Matsuno, R.-C. Lien, H. Nakamura, T. Senjyu, and X. Guo,, J. Geophys. Res. Oceans, 122, 7082-7094, doi:10.1002/2017JC013049.
DOI: 10.6084/m9.figshare.5135086.v3
title: Data used in "Turbulent mixing within the Kuroshio in the Tokara Strait"

description: Data from "Turbulent mixing within the Kuroshio in the Tokara Strait" by E. Tsutsumi, T. Matsuno, R.-C. Lien, H. Nakamura, T. Senjyu, and X. Guo, JGR-Oceans, doi:10.1002/2017JC013049.<br>
DOI: 10.6084/m9.figshare.5134984
title: Geometric morphometric analysis reveals that the shells of male and female siphon whelks <i>Penion chathamensis</i> are the same size and shape

description: Secondary sexual dimorphism can make the discrimination of intra and interspecific variation difficult, causing the identification of evolutionary lineages and classification of species to be challenging, particularly in palaeontology. Yet sexual dimorphism is an understudied research topic in dioecious marine snails. We use landmark-based geometric morphometric analysis to investigate whether there is sexual dimorphism in the shell morphology of the siphon whelk <i>Penion chathamensis</i>. In contrast to studies of other snails, results strongly indicate that there is no difference in the shape or size of shells between the sexes. A comparison of <i>P. chathamensis</i> and a related species demonstrates that this result is unlikely to reflect a limitation of the method. The possibility that sexual dimorphism is not exhibited by at least some species of <i>Penion</i> is advantageous from a palaeontological perspective as there is a rich fossil record for the genus across the Southern Hemisphere.
DOI: 10.6084/m9.figshare.5134990
title: NEON Data Institute 2017: Presentations

description: Presentations that accompany materials presented at the NEON Data Institute 2017: Remote Sensing with Reproducible Research.<br>Full Data Institute materials: http://neondataskills.org/workshop-event/NEON-Data-Insitute-2017<br>More information on the National Ecological Observatory Network: http://www.neonscience.org
DOI: 10.6084/m9.figshare.5134981
title: LEGO Sets Composition

description: This is the inventories of LEGO sets.
DOI: 10.6084/m9.figshare.5134984.v1
title: Geometric morphometric analysis reveals that the shells of male and female siphon whelks <i>Penion chathamensis</i> are the same size and shape

description: Secondary sexual dimorphism can make the discrimination of intra and interspecific variation difficult, causing the identification of evolutionary lineages and classification of species to be challenging, particularly in palaeontology. Yet sexual dimorphism is an understudied research topic in dioecious marine snails. We use landmark-based geometric morphometric analysis to investigate whether there is sexual dimorphism in the shell morphology of the siphon whelk <i>Penion chathamensis</i>. In contrast to studies of other snails, results strongly indicate that there is no difference in the shape or size of shells between the sexes. A comparison of <i>P. chathamensis</i> and a related species demonstrates that this result is unlikely to reflect a limitation of the method. The possibility that sexual dimorphism is not exhibited by at least some species of <i>Penion</i> is advantageous from a palaeontological perspective as there is a rich fossil record for the genus across the Southern Hemisphere.
DOI: 10.6084/m9.figshare.5134990.v1
title: NEON Data Institute 2017: Presentations

description: Presentations that accompany materials presented at the NEON Data Institute 2017: Remote Sensing with Reproducible Research.<br>Full Data Institute materials: http://neondataskills.org/workshop-event/NEON-Data-Insitute-2017<br>More information on the National Ecological Observatory Network: http://www.neonscience.org
DOI: 10.6084/m9.figshare.12581624
title: Metadata associated with analyses

description: Known cave localities throughout South Africa along with historical (Hist_occur) and current information regarding occupation by bats (Bats- any species) and Miniopterus natalensis (Mnat) : Yes - Y, No - N and unknown - U. Roost importance to Mnat is also recorded (maternity, hibernacula or unknown-U) and whether caves are tourist caves (allowed regulated visitation).Note that coordinates are only approximate localities due to the sensitive nature of cave locality data.
DOI: 10.6084/m9.figshare.5134921
title: 3D models of Quaternary-aged sedimentary successions within the Canterbury, New Zealand region

description: A 3D high-resolution model of the Quaternary geological stratigraphic sequence in the Canterbury, New Zealand region is developed utilising datasets of over 500 high-quality water well logs from a database of 29,985, and over 370 near-surface cone penetration test (CPT) records from a database of 13,670. The model, developed using geostatistical Kriging, represents the complex interbedded regional Quaternary geology by characterising the boundaries between significant interbedded geological formations as 3D surfaces. The model is examined in the form of both geological surface contour maps and vertical cross sections, where the most evident trend identified is the easterly dip caused by the dominant alluvial deposition of terrestrial sediments. The developed 3D interbedded Quaternary stratigraphy model has several applications for hydrologic modelling, earthquake-induced ground motion simulations and seismic site characterisation. For the latter case, the role of the model in constraining surface wave analysis-based shear wave velocity profiling is illustrated.
DOI: 10.6084/m9.figshare.5134939
title: Demko Metadata 2017.csv

description: Metadata for Demko et al. 2017 Ecology
DOI: 10.6084/m9.figshare.5134939.v1
title: Demko Metadata 2017.csv

description: Metadata for Demko et al. 2017 Ecology
DOI: 10.6084/m9.figshare.5134921.v1
title: 3D models of Quaternary-aged sedimentary successions within the Canterbury, New Zealand region

description: A 3D high-resolution model of the Quaternary geological stratigraphic sequence in the Canterbury, New Zealand region is developed utilising datasets of over 500 high-quality water well logs from a database of 29,985, and over 370 near-surface cone penetration test (CPT) records from a database of 13,670. The model, developed using geostatistical Kriging, represents the complex interbedded regional Quaternary geology by characterising the boundaries between significant interbedded geological formations as 3D surfaces. The model is examined in the form of both geological surface contour maps and vertical cross sections, where the most evident trend identified is the easterly dip caused by the dominant alluvial deposition of terrestrial sediments. The developed 3D interbedded Quaternary stratigraphy model has several applications for hydrologic modelling, earthquake-induced ground motion simulations and seismic site characterisation. For the latter case, the role of the model in constraining surface wave analysis-based shear wave velocity profiling is illustrated.
DOI: 10.6084/m9.figshare.5134891
title: S1 Table.docx

description: <b>S1 Table </b>Species diversity (<i>H</i>c), species richness and species composition of single litter species and their mixtures
DOI: 10.6084/m9.figshare.5134891.v1
title: S1 Table.docx

description: <b>S1 Table </b>Species diversity (<i>H</i>c), species richness and species composition of single litter species and their mixtures
DOI: 10.6084/m9.figshare.5134870
title: NEON Data Institute 2017: Spectral Classification Data Subset

description: This data set includes data used for a Spectral Classification Tutorial written by Dr. Paul Gader (Univ. Florida) for the 2017 NEON Data Institute: Remote Sensing with Reproducible Workflows. <br>This teaching data subset is used for several tutorials on the NEON website (neonscience.org). The dataset is for educational purposes, data for research purposes can be obtained from the NEON Data Portal (data.neonscience.org).<br>
DOI: 10.6084/m9.figshare.5134870.v1
title: NEON Data Institute 2017: Spectral Classification Data Subset

description: This data set includes data used for a Spectral Classification Tutorial written by Dr. Paul Gader (Univ. Florida) for the 2017 NEON Data Institute: Remote Sensing with Reproducible Workflows. <br>This teaching data subset is used for several tutorials on the NEON website (neonscience.org). The dataset is for educational purposes, data for research purposes can be obtained from the NEON Data Portal (data.neonscience.org).<br>
DOI: 10.6084/m9.figshare.5134816
title: Dataset for: Fractional Gaussian noise: Prior specification and model comparison

description: Fractional Gaussian noise (fGn) is a self-similar stochastic process used to model anti-persistent or persistent dependency structures in observed time series. Properties of the autocovariance function of fGn are characterised by the Hurst exponent (H), which in Bayesian contexts typically has been assigned a uniform prior on the unit interval. This paper argues why a uniform prior is unreasonable and introduces the use of a penalised complexity (PC) prior for H. The PC prior is computed to penalise divergence from the special case of white noise, and is invariant to reparameterisations. An immediate advantage is that the exact same prior can be used for the autocorrelation coefficient φ a first-order autoregressive process AR(1), as this model also reflects a flexible version of white noise. Within the general setting of latent Gaussian models, this allows us to compare an fGn model component with AR(1) using Bayes factors, avoiding confounding effects of prior choices for the two hyperparameters H and φ. Among others, this is useful in climate regression models where inference for underlying linear or smooth trends depends heavily on the assumed noise model.
DOI: 10.6084/m9.figshare.5134813
title: A surprisingly derived hydrometrid (Hemiptera, Gerromorpha) from the Crato Formation, Early Cretaceous of Brazil

description: In the present paper, we review the fossil record of the Hydrometridae (Hemiptera, Gerromorpha) and present a new species from the Early Cretaceous Crato Formation of Northeastern Brazil, <i>Christometra paradoxa</i> gen. et sp. nov. This species is based on a new specimen (a female), as well as a previously figured one (a male), providing a rare case of preservation of sexually dimorphic features in the fossil record. This is the third species coming from this deposit, which is Aptian-Albian in age and the oldest deposit to have yielded hydrometrids so far. Only five other Mesozoic species are known, being slightly younger in age (Cenomanian). So far, phylogenetic analyses have recovered Cretaceous hydrometrids as basal relative to Cenozoic genera but, <i>Christometra paradoxa</i> exhibits several advanced characteristics that unite it in a clade together with the extant genera <i>Hydrometra</i> and <i>Bacillometroides</i>, in a more derived position than any previously known fossil hydrometrid. The present publication is registered in the Official Register of Zoological Nomenclature (Zoobank), under the registration number http://zoobank.org/urn:lsid:zoobank.org:pub:3CFA88AB-3CBC-4CCC-8196-698ECC863947. The registration number for the nomenclatural act of the genus is http://zoobank.org/urn:lsid:zoobank.org:act:84744426-1259-4864-8E3F-E43E0DAB2021, and that of the species is http://zoobank.org/urn:lsid:zoobank.org:act:23700AB2-F7AD-4F50-A5E7-CB28868079B2.
DOI: 10.6084/m9.figshare.5134816.v1
title: Dataset for: Fractional Gaussian noise: Prior specification and model comparison

description: Fractional Gaussian noise (fGn) is a self-similar stochastic process used to model anti-persistent or persistent dependency structures in observed time series. Properties of the autocovariance function of fGn are characterised by the Hurst exponent (H), which in Bayesian contexts typically has been assigned a uniform prior on the unit interval. This paper argues why a uniform prior is unreasonable and introduces the use of a penalised complexity (PC) prior for H. The PC prior is computed to penalise divergence from the special case of white noise, and is invariant to reparameterisations. An immediate advantage is that the exact same prior can be used for the autocorrelation coefficient φ a first-order autoregressive process AR(1), as this model also reflects a flexible version of white noise. Within the general setting of latent Gaussian models, this allows us to compare an fGn model component with AR(1) using Bayes factors, avoiding confounding effects of prior choices for the two hyperparameters H and φ. Among others, this is useful in climate regression models where inference for underlying linear or smooth trends depends heavily on the assumed noise model.
DOI: 10.6084/m9.figshare.5134843.v1
title: KOWALSKI sandbox

description: Playground with install script for KOWALSKI.
DOI: 10.6084/m9.figshare.5134813.v1
title: A surprisingly derived hydrometrid (Hemiptera, Gerromorpha) from the Crato Formation, Early Cretaceous of Brazil

description: In the present paper, we review the fossil record of the Hydrometridae (Hemiptera, Gerromorpha) and present a new species from the Early Cretaceous Crato Formation of Northeastern Brazil, <i>Christometra paradoxa</i> gen. et sp. nov. This species is based on a new specimen (a female), as well as a previously figured one (a male), providing a rare case of preservation of sexually dimorphic features in the fossil record. This is the third species coming from this deposit, which is Aptian-Albian in age and the oldest deposit to have yielded hydrometrids so far. Only five other Mesozoic species are known, being slightly younger in age (Cenomanian). So far, phylogenetic analyses have recovered Cretaceous hydrometrids as basal relative to Cenozoic genera but, <i>Christometra paradoxa</i> exhibits several advanced characteristics that unite it in a clade together with the extant genera <i>Hydrometra</i> and <i>Bacillometroides</i>, in a more derived position than any previously known fossil hydrometrid. The present publication is registered in the Official Register of Zoological Nomenclature (Zoobank), under the registration number http://zoobank.org/urn:lsid:zoobank.org:pub:3CFA88AB-3CBC-4CCC-8196-698ECC863947. The registration number for the nomenclatural act of the genus is http://zoobank.org/urn:lsid:zoobank.org:act:84744426-1259-4864-8E3F-E43E0DAB2021, and that of the species is http://zoobank.org/urn:lsid:zoobank.org:act:23700AB2-F7AD-4F50-A5E7-CB28868079B2.
DOI: 10.6084/m9.figshare.5134843.v2
title: KOWALSKI sandbox

description: Playground with install script for KOWALSKI.
DOI: 10.6084/m9.figshare.5134792
title: Wetlands

description: Wetland inundation
DOI: 10.6084/m9.figshare.5134792.v1
title: Wetlands

description: Wetland inundation
DOI: 10.6084/m9.figshare.5134843.v4
title: KOWALSKI sandbox

description: Playground with install script for KOWALSKI.
DOI: 10.6084/m9.figshare.5134843.v5
title: KOWALSKI sandbox

description: Playground with install script for KOWALSKI.
DOI: 10.6084/m9.figshare.5134681
title: Qualitative codes for the consequences of happiness of software developers

description: Qualitative codes for the consequences of happiness of software developers
DOI: 10.6084/m9.figshare.5134843.v6
title: KOWALSKI sandbox

description: Playground with install script for KOWALSKI.
DOI: 10.6084/m9.figshare.5134843.v7
title: KOWALSKI sandbox

description: Playground with install script for KOWALSKI.
DOI: 10.6084/m9.figshare.5134600
title: Clamgulchian (Miocene–Pliocene) pollen assemblages of the Kenai Lowland, Alaska, and the persistence of the family Podocarpaceae

description: Pollen diagrams from three areas of the Kenai Lowland of Alaska demonstrate the pollen floras of the Clamgulchian Stage (∼8–2.5 Ma) of Late Miocene/Early Pliocene age. These sections, originally described based on their plant megafossils and pollen, are revisited for a more precise determination of their pollen stratigraphy. The floras from Clam Gulch on the west margin of the Kenai Lowland are compared with Clamgulchian sections of the same age on the east margin, in canyons at the head of Kachemak Bay. The results substantiate that in the Clamgulchian sections thermophile pollen types (exotic warmth-loving woody genera) represent about 2–10% of the count (and include 15 thermophile taxa), while in the earlier Homerian Stage (∼14.5–8 Ma) thermophiles are more important and more diverse (28 taxa), representing 5–15% of the count. A second difference between the Homerian and Clamgulchian is the increased diversity of herbaceous groups (such as Ranunculaceae, Urticaceae, Onagraceae, Primulaceae and others), which are few in the Homerian (∼4–5 taxa), but many in the Clamgulchian (≤15–18 taxa). These herb groups show increasing diversity near the top of the Neogene in the Alaskan flora. With a decrease in thermophiles, the Clamgulchian taxa show a transition towards a cooler climate. Pollen of the exotic gymnosperm family Podocarpaceae chiefly of the Southern Hemisphere are diverse minor elements during the entire Neogene of Alaska. These consistent elements may represent resident associates of the hardwood forests in southern Alaska as the likelihood of their pollen occurrences being the result of long-distance transport seems unlikely.
DOI: 10.6084/m9.figshare.5134600.v1
title: Clamgulchian (Miocene–Pliocene) pollen assemblages of the Kenai Lowland, Alaska, and the persistence of the family Podocarpaceae

description: Pollen diagrams from three areas of the Kenai Lowland of Alaska demonstrate the pollen floras of the Clamgulchian Stage (∼8–2.5 Ma) of Late Miocene/Early Pliocene age. These sections, originally described based on their plant megafossils and pollen, are revisited for a more precise determination of their pollen stratigraphy. The floras from Clam Gulch on the west margin of the Kenai Lowland are compared with Clamgulchian sections of the same age on the east margin, in canyons at the head of Kachemak Bay. The results substantiate that in the Clamgulchian sections thermophile pollen types (exotic warmth-loving woody genera) represent about 2–10% of the count (and include 15 thermophile taxa), while in the earlier Homerian Stage (∼14.5–8 Ma) thermophiles are more important and more diverse (28 taxa), representing 5–15% of the count. A second difference between the Homerian and Clamgulchian is the increased diversity of herbaceous groups (such as Ranunculaceae, Urticaceae, Onagraceae, Primulaceae and others), which are few in the Homerian (∼4–5 taxa), but many in the Clamgulchian (≤15–18 taxa). These herb groups show increasing diversity near the top of the Neogene in the Alaskan flora. With a decrease in thermophiles, the Clamgulchian taxa show a transition towards a cooler climate. Pollen of the exotic gymnosperm family Podocarpaceae chiefly of the Southern Hemisphere are diverse minor elements during the entire Neogene of Alaska. These consistent elements may represent resident associates of the hardwood forests in southern Alaska as the likelihood of their pollen occurrences being the result of long-distance transport seems unlikely.
DOI: 10.6084/m9.figshare.5134681.v1
title: Qualitative codes for the consequences of happiness of software developers

description: Qualitative codes for the consequences of unhappiness of software developers
DOI: 10.6084/m9.figshare.5133193
title: Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia

description: <i>Purpose</i>: Exosomes derived from human mesenchymal stem cells (hMSCs) cultured under hypoxic conditions contain proteins and growth factors that promote angiogenesis. This study investigated the effect of intravitreal administration of these exosomes on retinal ischemia using a murine model. <i>Methods</i>: Oxygen-induced retinopathy (OIR) was induced by exposing one-week-old male C57BL/6J mice to 5 days of 75% hyperoxic conditioning, and returning to room air. After hyperoxic conditioning, the right eye of each mouse was injected intravitreally with 1 µl saline or exosomes derived from hMSCs and compared to control mice of the same age raised in room air without OIR injected intravitreally with saline. Two weeks post-injection, fluorescein angiography (FA) and phase-variance optical coherence tomography angiography (pvOCTA) were used to assess retinal perfusion. Retinal thickness was determined by OCT. The extent of retinal neovascularization was quantitated histologically by counting vascular nuclei on the retinal surface. <i>Results</i>: Among eyes with OIR, intravitreal exosome treatment partially preserved retinal vascular flow <i>in vivo</i> and reduced associated retinal thinning; retinal thickness on OCT was 111.1 ± 7.4µm with saline versus 132.1 ± 11.6µm with exosome, p &lt; 0.001. Retinal neovascularization among OIR eyes was reduced with exosome treatment when compared to saline-treated eyes (7.75 ± 3.68 versus 2.68 ± 1.35 neovascular nuclei per section, p &lt; 0.0001). No immunogenicity or ocular/systemic adverse effect was associated with intravitreal exosome treatment. <i>Conclusions</i>: Intravitreal administration of exosomes derived from hMSCs was well tolerated without immunosuppression and decreased the severity of retinal ischemia in this murine model. This appealing novel non-cellular therapeutic approach warrants further exploration.
DOI: 10.6084/m9.figshare.5133001
title: Data and code to reproduce analyses from "Experimental evidence of a pathogen invasion threshold"

description: This repository contains code (in the form of an R markdown document--`Dallas2017.Rmd`) and data (`expData.csv`) from <br>&gt; Dallas, Krkosek, and Drake 2017 "Experimental evidence of a pathogen invasion threshold"<br><br>
DOI: 10.6084/m9.figshare.5133193.v1
title: Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia

description: <i>Purpose</i>: Exosomes derived from human mesenchymal stem cells (hMSCs) cultured under hypoxic conditions contain proteins and growth factors that promote angiogenesis. This study investigated the effect of intravitreal administration of these exosomes on retinal ischemia using a murine model. <i>Methods</i>: Oxygen-induced retinopathy (OIR) was induced by exposing one-week-old male C57BL/6J mice to 5 days of 75% hyperoxic conditioning, and returning to room air. After hyperoxic conditioning, the right eye of each mouse was injected intravitreally with 1 µl saline or exosomes derived from hMSCs and compared to control mice of the same age raised in room air without OIR injected intravitreally with saline. Two weeks post-injection, fluorescein angiography (FA) and phase-variance optical coherence tomography angiography (pvOCTA) were used to assess retinal perfusion. Retinal thickness was determined by OCT. The extent of retinal neovascularization was quantitated histologically by counting vascular nuclei on the retinal surface. <i>Results</i>: Among eyes with OIR, intravitreal exosome treatment partially preserved retinal vascular flow <i>in vivo</i> and reduced associated retinal thinning; retinal thickness on OCT was 111.1 ± 7.4µm with saline versus 132.1 ± 11.6µm with exosome, p &lt; 0.001. Retinal neovascularization among OIR eyes was reduced with exosome treatment when compared to saline-treated eyes (7.75 ± 3.68 versus 2.68 ± 1.35 neovascular nuclei per section, p &lt; 0.0001). No immunogenicity or ocular/systemic adverse effect was associated with intravitreal exosome treatment. <i>Conclusions</i>: Intravitreal administration of exosomes derived from hMSCs was well tolerated without immunosuppression and decreased the severity of retinal ischemia in this murine model. This appealing novel non-cellular therapeutic approach warrants further exploration.