cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5255017.v1
title: Amino and Carboxamido C60

description: XYZ of derivatives of C60
DOI: 10.6084/m9.figshare.5255014.v2
title: Osmundales diversity through time: stacking networks

description: This fileset includes stacked neighbour-net splits graphs (planar meta-phylogenetic networks) illustrating the taxic diversity change within the royal fern lineage (Osmundales) from the Permian to now. The networks are based on taxon subsets of the matrix compiled by <b><br>Bomfleur et al.,</b> <i>PeerJ</i> <b>5</b>: e3433, 2017, https://peerj.com/articles/3433/<br><b>Figures 1 and 2</b> show time-slice-wise networks, each network includes only species of one geological period. Permian, Triassic and Jurassic (Fig. 1); Cretaceous, Paleogene+Neogene, and modern-day (Fig. 2). Species names are abbreviated/contracted by three-letter codes. Higher taxa and according colouring of species (dot) follow Bomfleur et al. (2017). Refer to this study for basic inference methodology and information on the data.<br><b>Figures 3 to 6</b> show connected neighbour-nets, each including the species of two subsequent time-slices (older at bottom): Permian + Triassic and Triassic + Jurassic (Fig. 3); Triassic + Jurassic and Jurassic + Cretaceous (Fig. 4); Cretaceous + Paleogene and Paleogene + Neogene (Fig. 5); Paleogene + Neogene and Neogene + modern-day (Fig. 6). For the motivation to stack networks see<br> <br><b>Grimm, GW</b>. Posted 18/7/2017.Stacking neighbour-nets: ancestors and descendants. <i>The Genealogical World of Phylogenetic Networks</i> (ed. by D. Morrison). http://phylonetworks.blogspot.fr/2017/07/stacking-neighbour-nets-ancestors-and.html<br><br>The <b>XLSX-file</b> includes the basic distance matrix including the full taxon names; cells are coloured as heat-map: green = low pairwise morphological distances; red = high pairwise morphological distances.<br>All primary data files including the NEXUS-file used to generate the distance matrices for network inference can be found in the <b>ZIP-archive</b>. The *.DIST files are Split-NEXUS-formatted files and are partly colour-coded using in-built functions of SplitsTree. See Readme.txt for archive content and contact details.<br>
DOI: 10.6084/m9.figshare.5255014.v1
title: Osmundales diverstity through time: stacking networks

description: This fileset includes stacked neighbour-net splits graphs (planar meta-phylogenetic networks) illustrating the taxic diversity change within the royal fern lineage (Osmundales) from the Permian to now. The networks are based on taxon subsets of the matrix compiled by <b><br>Bomfleur et al.,</b> <i>PeerJ</i> <b>5</b>: e3433, 2017, https://peerj.com/articles/3433/<br><b>Figures 1 and 2</b> show time-slice-wise networks, each network includes only species of one geological period. Permian, Triassic and Jurassic (Fig. 1); Cretaceous, Paleogene+Neogene, and modern-day (Fig. 2). Species names are abbreviated/contracted by three-letter codes. Higher taxa and according colouring of species (dot) follow Bomfleur et al. (2017). Refer to this study for basic inference methodology and information on the data.<br><b>Figures 3 to 6</b> show connected neighbour-nets, each including the species of two subsequent time-slices (older at bottom): Permian + Triassic and Triassic + Jurassic (Fig. 3); Triassic + Jurassic and Jurassic + Cretaceous (Fig. 4); Cretaceous + Paleogene and Paleogene + Neogene (Fig. 5); Paleogene + Neogene and Neogene + modern-day (Fig. 6). For the motivation to stack networks see<br> <br><b>Grimm, GW</b>. Posted 18/7/2017.Stacking neighbour-nets: ancestors and descendants. <i>The Genealogical World of Phylogenetic Networks</i> (ed. by D. Morrison). http://phylonetworks.blogspot.fr/2017/07/stacking-neighbour-nets-ancestors-and.html<br><br>The <b>XLSX-file</b> includes the basic distance matrix including the full taxon names; cells are coloured as heat-map: green = low pairwise morphological distances; red = high pairwise morphological distances.<br>All primary data files including the NEXUS-file used to generate the distance matrices for network inference can be found in the <b>ZIP-archive</b>. The *.DIST files are Split-NEXUS-formatted files and are partly colour-coded using in-built functions of SplitsTree. See Readme.txt for archive content and contact details.<br>
DOI: 10.6084/m9.figshare.5254570
title: Free and Open Source Software (FOSS) and Technologies for the Cloud

description: There are many freely available software and technologies that can improve DevOps for the Cloud. We invite presentations on the applications and lesson-learned on these solutions. We invite presentations on container technology, orchestration and automation, container and virtual machine management, data analytic, machine learning, data management, etc.
DOI: 10.6084/m9.figshare.5254573
title: NEXUS Workshops - Big Data Analytics and Cloud Computing

description: [Introduction to Big Data Analytics using NEXUS] NEXUS is an emerging open source technology that enables horizontal processing of geospatial, array-based data for cluster and cloud environments. This workshop provides an introduction to NEXUS and hands-on exercises using Jupyter notebook to interact with NEXUS.<br>[NEXUS: Big Data Analytics and Cloud Computing] Participants should have completed the 'Introduction to NEXUS' workshop or have general understanding of NEXUS and Cloud Computing technologies. This workshop focuses deploying NEXUS on the Amazon cloud environment using AMI and ingesting data into the NEXUS platform for analysis.
DOI: 10.6084/m9.figshare.5254579.v1
title: The spawning and early life-history of a New Zealand endemic amphidromous eleotrid, bluegill bully (<i>Gobiomorphus hubbsi</i>)

description: The larval stage of fishes is critical in determining their dispersal, survival and recruitment, but little is known of the larval behaviours and tolerances of amphidromous fishes, particularly in New Zealand. We report the results of a series of observational and experimental studies on bluegill bully (<i>Gobiomorphus hubbsi</i>), including spawning sites and behaviours, larval characteristics at hatch, phototactic responses of larvae, and larval survival at different salinity levels. Spawning primarily occurred in the lower reaches of the river, and larvae from different nests exhibited marked differences in, and trade-offs between, larval characteristics at hatch, potentially affecting larval success. Larvae were positively phototactic to intense light, an unexpected result based on diel drift patterns and international research. Finally, larvae exhibited markedly higher survival rates when reared at intermediate salinities compared to freshwater or seawater, suggesting estuaries may play an important role as nursery grounds for bluegill bully and other amphidromous fish.
DOI: 10.6084/m9.figshare.5254564
title: Cloud Onboarding

description: Are you thinking of moving your existing applications to the cloud? Are you designing your next project to use the cloud? There are just too many unknowns when we consider cloud computing for our projects. This session focuses on migrating existing technologies and services to the cloud, and new projects wanting to fully leverage the cloud environment. We invite presentations on lessons learned, software and architectural approaches (e.g. 12-factor), and cost saving strategies. In addition to oral presentations, we encourage poster and demos at during the ESIP poster session.<br>
DOI: 10.6084/m9.figshare.5254573.v1
title: NEXUS Workshops - Big Data Analytics and Cloud Computing

description: [Introduction to Big Data Analytics using NEXUS] NEXUS is an emerging open source technology that enables horizontal processing of geospatial, array-based data for cluster and cloud environments. This workshop provides an introduction to NEXUS and hands-on exercises using Jupyter notebook to interact with NEXUS.<br>[NEXUS: Big Data Analytics and Cloud Computing] Participants should have completed the 'Introduction to NEXUS' workshop or have general understanding of NEXUS and Cloud Computing technologies. This workshop focuses deploying NEXUS on the Amazon cloud environment using AMI and ingesting data into the NEXUS platform for analysis.
DOI: 10.6084/m9.figshare.5254564.v1
title: Cloud Onboarding

description: Are you thinking of moving your existing applications to the cloud? Are you designing your next project to use the cloud? There are just too many unknowns when we consider cloud computing for our projects. This session focuses on migrating existing technologies and services to the cloud, and new projects wanting to fully leverage the cloud environment. We invite presentations on lessons learned, software and architectural approaches (e.g. 12-factor), and cost saving strategies. In addition to oral presentations, we encourage poster and demos at during the ESIP poster session.<br>
DOI: 10.6084/m9.figshare.5254549
title: Morphological variation in invasive mosquito <i>Culex quinquefasciatus</i> Say (Diptera: Culicidae) larvae from an urban site in Auckland, New Zealand

description: Larvae of the invasive mosquito <i>Culex quinquefasciatus</i> Say are morphologically similar to those of the native <i>Culex pervigilans</i> Bergroth, yet distinguishing these species can be hampered by morphological variations in <i>Cx. quinquefasciatus.</i> We present detail about the extent of these variations in an urban population of <i>Cx. quinquefasciatus</i> in Auckland. To aid in identification of this exotic species, we provide images of key diagnostic characters and some observed exceptions to these. Details regarding variation in diagnostic characters for 90% of larvae, although these characters were not always visible. Other characters were less reliable, for instance, the expected position of seta 1a-S in relation to the pecten teeth was observed in &lt; 10% of larvae. Further exploration of regional morphological variation in both <i>Cx. quinquefasciatus</i> and <i>Cx. pervigilans</i> is recommended, ideally with associated molecular characterisation.
DOI: 10.6084/m9.figshare.5254537
title: SAR11 SAAVs Tables and Figures

description: Figures, Supplementary Figures, and Supplementary Tables for Delmont and Kiefl et al.<br><br>
DOI: 10.6084/m9.figshare.5254501
title: Confidence Regions for Spatial Excursion Sets From Repeated Random Field Observations, With an Application to Climate

description: The goal of this article is to give confidence regions for the excursion set of a spatial function above a given threshold from repeated noisy observations on a fine grid of fixed locations. Given an asymptotically Gaussian estimator of the target function, a pair of data-dependent nested excursion sets are constructed that are sub- and super-sets of the true excursion set, respectively, with a desired confidence. Asymptotic coverage probabilities are determined via a multiplier bootstrap method, not requiring Gaussianity of the original data nor stationarity or smoothness of the limiting Gaussian field. The method is used to determine regions in North America where the mean summer and winter temperatures are expected to increase by mid-21st century by more than 2 degrees Celsius.
DOI: 10.6084/m9.figshare.5254537.v2
title: SAR11 SAAVs Tables and Figures

description: Figures, Supplementary Figures, and Supplementary Tables for Delmont and Kiefl et al.<br><br>
DOI: 10.6084/m9.figshare.5254501.v2
title: Confidence Regions for Spatial Excursion Sets From Repeated Random Field Observations, With an Application to Climate

description: The goal of this article is to give confidence regions for the excursion set of a spatial function above a given threshold from repeated noisy observations on a fine grid of fixed locations. Given an asymptotically Gaussian estimator of the target function, a pair of data-dependent nested excursion sets are constructed that are sub- and super-sets of the true excursion set, respectively, with a desired confidence. Asymptotic coverage probabilities are determined via a multiplier bootstrap method, not requiring Gaussianity of the original data nor stationarity or smoothness of the limiting Gaussian field. The method is used to determine regions in North America where the mean summer and winter temperatures are expected to increase by mid-21st century by more than 2 degrees Celsius.
DOI: 10.6084/m9.figshare.5254489
title: Comparative chemical fingerprinting of <i>Oroxylum indicum</i> and <i>Scutellaria baicalensis</i> using liquid chromatography and mass spectrometry

description: Introduction: Identification of <i>Oroxylum indicum</i> and <i>Scutellaria baicalensis</i> provides an interesting challenge in selection of biomarker compound to be used in routine analysis. Both plants have similar phytochemical profile and are rich sources of flavones and flavone glycosides. The objective of this study was to prepare the chemical fingerprinting of <i>O. indicum</i> bark and <i>S. baicalensis</i> roots using the liquid chromatography and mass spectroscopy in single chromatographic method. Materials and methods: Extracts prepared using various solvent systems (methanol, aqueous methanol, chloroform, hexane, and water) of both plants were analyzed using C18 reverse phase column with solvent system containing acetonitrile and 0.1% formic acid. Major flavonoids were identified based on mass spectra, fragmentation pattern, and UV spectra. Results: In this article, well-resolved high-performance liquid chromatographic (HPLC) separation in both plant extracts was obtained and chemical fingerprints for both plant extracts were established and flavonoids present (baicalin, oroxylin A-7-<i>O</i>-glucuronide, chrysin-7-<i>O</i>-glucuronide, baicalein, chrysin, oroxylin-A, wogonin, skullcap flavone II) were identified as possible biomarkers. Conclusion: Mass spectrometry coupled with HPLC can be a tool for fingerprinting of various natural products used in dietary supplement industry. The fingerprint developed in the article can be used for quality evaluation as well as identifying possible adulteration of extracts of both the plants.
DOI: 10.6084/m9.figshare.5254501.v1
title: Confidence regions for spatial excursion sets from repeated random field observations, with an application to climate

description: The goal of this paper is to give confidence regions for the excursion set of a spatial function above a given threshold from repeated noisy observations on a fine grid of fixed locations. Given an asymptotically Gaussian estimator of the target function, a pair of data-dependent nested excursion sets are constructed that are sub- and super-sets of the true excursion set, respectively, with a desired confidence. Asymptotic coverage probabilities are determined via a multiplier bootstrap method, not requiring Gaussianity of the original data nor stationarity or smoothness of the limiting Gaussian field. The method is used to determine regions in North America where the mean summer and winter temperatures are expected to increase by mid 21st century by more than 2 degrees Celsius.
DOI: 10.6084/m9.figshare.5254537.v1
title: SAR11 SAAVs Tables and Figures

description: Figures, Supplementary Figures, and Supplementary Tables for Delmont et al.
DOI: 10.6084/m9.figshare.5254480
title: Kaposi's sarcoma-associated herpesvirus infection promotes differentiation and polarization of monocytes into tumor-associated macrophages

description: Tumor associated macrophages (TAMs) promote angiogenesis, tumor invasion and metastasis, and suppression of anti-tumor immunity. These myeloid cells originate from monocytes, which differentiate into TAMs upon exposure to the local tumor microenvironment. We previously reported that Kaposi's sarcoma-associated herpes virus (KSHV) infection of endothelial cells induces the cytokine angiopoietin-2 (Ang-2) to promote migration of monocytes into tumors. Here we report that KSHV infection of endothelial cells induces additional cytokines including interleukin-6 (IL-6), interleukin-10 (IL-10), and interleukin-13 (IL-13) that drive monocytes to differentiate and polarize into TAMs. The KSHV-induced TAMs not only express TAM-specific markers such as CD-163 and legumain (LGMN) but also display a gene expression profile with characteristic features of viral infection. More importantly, KSHV-induced TAMs enhance tumor growth in nude mice. These results are consistent with the strong presence of TAMs in Kaposi's sarcoma (KS) tumors. Therefore, KSHV infection of endothelial cells generates a local microenvironment that not only promotes the recruitment of monocytes but also induces their differentiation and polarization into TAMs. These findings reveal a new mechanism of KSHV contribution to KS tumor development.
DOI: 10.6084/m9.figshare.5254489.v2
title: Comparative chemical fingerprinting of <i>Oroxylum indicum</i> and <i>Scutellaria baicalensis</i> using liquid chromatography and mass spectrometry

description: Introduction: Identification of <i>Oroxylum indicum</i> and <i>Scutellaria baicalensis</i> provides an interesting challenge in selection of biomarker compound to be used in routine analysis. Both plants have similar phytochemical profile and are rich sources of flavones and flavone glycosides. The objective of this study was to prepare the chemical fingerprinting of <i>O. indicum</i> bark and <i>S. baicalensis</i> roots using the liquid chromatography and mass spectroscopy in single chromatographic method. Materials and methods: Extracts prepared using various solvent systems (methanol, aqueous methanol, chloroform, hexane, and water) of both plants were analyzed using C18 reverse phase column with solvent system containing acetonitrile and 0.1% formic acid. Major flavonoids were identified based on mass spectra, fragmentation pattern, and UV spectra. Results: In this article, well-resolved high-performance liquid chromatographic (HPLC) separation in both plant extracts was obtained and chemical fingerprints for both plant extracts were established and flavonoids present (baicalin, oroxylin A-7-<i>O</i>-glucuronide, chrysin-7-<i>O</i>-glucuronide, baicalein, chrysin, oroxylin-A, wogonin, skullcap flavone II) were identified as possible biomarkers. Conclusion: Mass spectrometry coupled with HPLC can be a tool for fingerprinting of various natural products used in dietary supplement industry. The fingerprint developed in the article can be used for quality evaluation as well as identifying possible adulteration of extracts of both the plants.
DOI: 10.6084/m9.figshare.5254441
title: Online Supplement, Supp and Graham et al. study on environmental correlates of hummingbird migration

description: Online Supplement to Supp and Graham et al. study, "Alternate migration scenarios provide novel insights into environmental associations for migrating hummingbird populations in North America". Data and code.<br>The code and data in this supplement allow for the analyses and figures to be fully replicated using eBird citizen science datasets for hummingbird observation and remotely sensed datasets from movebank for environment. Details on the code and files can be found in the Supplement_text file in the zipped folder.
DOI: 10.6084/m9.figshare.5254480.v2
title: Kaposi's sarcoma-associated herpesvirus infection promotes differentiation and polarization of monocytes into tumor-associated macrophages

description: Tumor associated macrophages (TAMs) promote angiogenesis, tumor invasion and metastasis, and suppression of anti-tumor immunity. These myeloid cells originate from monocytes, which differentiate into TAMs upon exposure to the local tumor microenvironment. We previously reported that Kaposi's sarcoma-associated herpes virus (KSHV) infection of endothelial cells induces the cytokine angiopoietin-2 (Ang-2) to promote migration of monocytes into tumors. Here we report that KSHV infection of endothelial cells induces additional cytokines including interleukin-6 (IL-6), interleukin-10 (IL-10), and interleukin-13 (IL-13) that drive monocytes to differentiate and polarize into TAMs. The KSHV-induced TAMs not only express TAM-specific markers such as CD-163 and legumain (LGMN) but also display a gene expression profile with characteristic features of viral infection. More importantly, KSHV-induced TAMs enhance tumor growth in nude mice. These results are consistent with the strong presence of TAMs in Kaposi's sarcoma (KS) tumors. Therefore, KSHV infection of endothelial cells generates a local microenvironment that not only promotes the recruitment of monocytes but also induces their differentiation and polarization into TAMs. These findings reveal a new mechanism of KSHV contribution to KS tumor development.
DOI: 10.6084/m9.figshare.5254426
title: Raw Data.rar

description: This dataset includes ECG waveform data from 110 patients during during under anesthesia. And the corresponding five doctor's evaluation of anesthetic depth curve are uploaded together. These raw data is for PeerJ journal manuscirpt"<i>HRV derived data similarity and distribution index to measure anesthetic depth based on ensemble neural network</i>".
DOI: 10.6084/m9.figshare.5254489.v1
title: Comparative Chemical Fingerprinting of <i>Oroxylum Indicum</i> and <i>Scutellaria Baicalensis</i> Using Liquid Chromatography & Mass Spectrometry

description: <b>Introduction</b>: Identification of <i>Oroxylum indicum</i> and <i>Scutellaria baicalensis</i> provide an interesting challenge in selection of biomarker compound to be used in routine analysis. Both plants have similar phytochemical profile and are rich source flavones and flavon- glycosides. <b>Objective</b>: To prepare the chemical fingerprinting of <i>Oroxylum indicum</i> bark and <i>Scutellaria baicalensis</i> roots using the Liquid chromatography and Mass Spectroscopy using single chromatographic method. <b>Methods and Material</b>- Extracts prepared using various solvent system (methanol, Aq methanol, chloroform, hexane and water) of both plants were analyzed using C18 reverse phase column with solvent system containing acetonitrile and 0.1% formic acid. Major Flavonoids were identified based on mass spectra, fragmentation pattern and UV spectra. <b>Results</b>: In this article well resolved HPLC separation in both plant extracts was obtained and chemical fingerprints for both plant extracts were established and flavonoids present(Baicalin, Oroxylin A -7-O-glucuronide,Chrysin-7-O-glucuronide, Baicalein, Chrysin, Oroxylin-A, Wogonin, Skullcap Flavone II) were identified as possible biomarkers. <b>Conclusion</b>: Mass spectrometry coupled with high performance liquid chromatography can be a tool for fingerprinting of various natural products used in dietary supplement industry. The fingerprint developed in the article can be used for quality evaluation as well as identifying possible adulteration of extracts of both the plants.