cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4898078
title: The small-for-gestational-age fetus has an intact ability to develop lacticemia when exposed to hypoxia: a retrospective comparative register study

description: <b>Objective:</b> To investigate the ability of small-for-gestational-age (SGA) fetuses to develop lacticemia during hypoxia. <b>Methods:</b> Umbilical cord arterial and venous pH, lactate and glucose concentrations were determined in 1777 SGA (&lt;10th percentile) and 14,569 AGA newborns and related to acidemia (pH p <b>Results:</b> Glucose and lactate were linearly related and both variables correlated negatively with pH. Glucose was equal in SGA and AGA at a normal pH, but at severe acidemia it was lower in SGA. Glucose was higher in both groups during acidemia. Lactate was higher in SGA at both a normal and a low pH, and in both groups lactate increased progressively with the severity of acidemia. <b>Conclusions:</b> In both SGA and AGA fetuses, glucose was mobilized during acidemia; lactate was higher in SGA at both a normal and low pH. Considering SGA being a proxy for fetal growth restriction, and acidemia a proxy for hypoxia, it is concluded that growth-restricted fetuses have an intact ability to develop lacticemia during hypoxia.
DOI: 10.6084/m9.figshare.4898063
title: A case for realigning species limits in the southern Australian whipbirds long recognised as the Western Whipbird (<i>Psophodes nigrogularis</i>)

description: The Western Whipbird (<i>Psophodes nigrogularis</i>) has a highly disjunct west–east distribution across southern Australia. Earlier morphological analyses recognised four subspecies in one species: <i>P. n. nigrogularis</i> and <i>P. n. oberon</i> in south-west Western Australia, and <i>P. n. leucogaster</i> of the Eyre and Yorke Peninsulas and the Murray Mallee, and <i>P. n. lashmari</i>, restricted to Kangaroo Island, both in eastern Australia. Later morphological analyses elevated <i>P. n. nigrogularis</i> to monotypic species rank, and placed the remaining western and two eastern taxa as three subspecies of a second species <i>P. leucogaster</i>. Initial mtDNA analysis questioned both arrangements but could not include all taxa. We used mtDNA sequence data from all available specimens of the entire group (DNA extracted from cryo-preserved tissues, toe-pads and feathers; holotypes excepted) to derive a more stable view of species limits. The samples fell into two strongly divergent but geographically structured groups, completely reflecting the eastern and western components of the distribution. Thus we see merit in treating the two geographical groupings as two species, <i>P. nigrogularis</i> in the west and <i>P. leucogaster</i> in the east, each having two subspecies. Nuclear data could test whether the two western subspecies in particular are genetically isolated or currently exchanging genes.
DOI: 10.6084/m9.figshare.4898078.v1
title: The small-for-gestational-age fetus has an intact ability to develop lacticemia when exposed to hypoxia: a retrospective comparative register study

description: <b>Objective:</b> To investigate the ability of small-for-gestational-age (SGA) fetuses to develop lacticemia during hypoxia. <b>Methods:</b> Umbilical cord arterial and venous pH, lactate and glucose concentrations were determined in 1777 SGA (&lt;10th percentile) and 14,569 AGA newborns and related to acidemia (pH p <b>Results:</b> Glucose and lactate were linearly related and both variables correlated negatively with pH. Glucose was equal in SGA and AGA at a normal pH, but at severe acidemia it was lower in SGA. Glucose was higher in both groups during acidemia. Lactate was higher in SGA at both a normal and a low pH, and in both groups lactate increased progressively with the severity of acidemia. <b>Conclusions:</b> In both SGA and AGA fetuses, glucose was mobilized during acidemia; lactate was higher in SGA at both a normal and low pH. Considering SGA being a proxy for fetal growth restriction, and acidemia a proxy for hypoxia, it is concluded that growth-restricted fetuses have an intact ability to develop lacticemia during hypoxia.
DOI: 10.6084/m9.figshare.4898057
title: FS854 contigs and profile databases

description: anvi'o contigs database and profile database for sample FS854 from the Mid-Cayman Rise. See project description for instructions.
DOI: 10.6084/m9.figshare.4898057.v1
title: FS854 contigs and profile databases

description: anvi'o contigs database and profile database for sample FS854 from the Mid-Cayman Rise. See project description for instructions.
DOI: 10.6084/m9.figshare.4898036
title: FS848 contigs and profile databases

description: anvi'o contigs database and profile database for sample FS848 from the Mid-Cayman Rise. See project description for instructions.
DOI: 10.6084/m9.figshare.4898036.v1
title: FS848 contigs and profile databases

description: anvi'o contigs database and profile database for sample FS848 from the Mid-Cayman Rise. See project description for instructions.
DOI: 10.6084/m9.figshare.4898033
title: FS844 contigs and profile databases

description: anvi'o contigs database and profile database for sample FS844 from the Mid-Cayman Rise. See project description for instructions.
DOI: 10.6084/m9.figshare.4897754
title: FS842 contigs and profile databases

description: anvi'o contigs database and profile database for sample FS842 from the Mid-Cayman Rise. See project description for instructions.
DOI: 10.6084/m9.figshare.4897181
title: 16S rRNA tree of Proteobacteria and Nitrospirae

description: The phylogeny of Proteobacteria and Nitrospirae based on 16S rRNA sequence. GTR+G+I was selected as the best-fit substitution model using jModelTest v2.1.2 prior to phylogeny reconstruction. The maximum-likelihood tree of 16S rRNA was constructed using RAxML v8.2.4 with 500 times of bootstrap.
DOI: 10.6084/m9.figshare.4897175
title: Gauss code-simulations of critical values for t*-test

description: An efficiency test has been constructed by employing the Fourier transformation.
DOI: 10.6084/m9.figshare.4897178
title: New Zealand collections of <i>Rhododendron</i> as a resource for ex situ conservation

description: This study uses <i>Rhododendron</i> L. collections in New Zealand to analyse the contribution of introduced species in cultivation to global ex situ conservation. Living botanical collections of Red List taxa are the fundamental resource that enable ex situ conservation, and Target 8 of the Global Strategy for Plant Conservation requires 75% of Red List taxa to be in ex situ collections by 2020. We compared <i>Rhododendron</i> taxa (species, subspecies, botanical varieties) in New Zealand with the range of taxa in international cultivation, and determined the presence of taxa from Red List categories, geographic origins and taxonomic groups. The 566 taxa in New Zealand, including 224 Red List taxa, encompass 67% of the taxa in cultivation worldwide, ranking second internationally for number of taxa in the collections investigated. New Zealand holds wild-collected material of 230 taxa, including 70 Red List taxa, and 20 taxa for which wild material is not listed in the international collections studied. China is the geographic origin of the greatest number of <i>Rhododendron</i> Red List taxa held in New Zealand. Of the 77 taxonomic subsections of <i>Rhododendron</i>, New Zealand holds 75% or more of the taxa in cultivation for 37 subsections, and 75% or more of the Red List taxa in cultivation for 24 subsections. The greatest numbers of Red List taxa in New Zealand collections are from section <i>Rhododendron</i> subsection <i>Maddenia</i> (20) and section <i>Pontica</i> subsection <i>Neriiflora</i> (17). Our analysis enables us to (1) propose conservation action for <i>Rhododendron</i> in New Zealand, (2) summarise our approach as a model for examining other introduced plant genera in New Zealand, and (3) propose our method as a component of an ex situ conservation strategy for New Zealand.
DOI: 10.6084/m9.figshare.4897178.v1
title: New Zealand collections of <i>Rhododendron</i> as a resource for ex situ conservation

description: This study uses <i>Rhododendron</i> L. collections in New Zealand to analyse the contribution of introduced species in cultivation to global ex situ conservation. Living botanical collections of Red List taxa are the fundamental resource that enable ex situ conservation, and Target 8 of the Global Strategy for Plant Conservation requires 75% of Red List taxa to be in ex situ collections by 2020. We compared <i>Rhododendron</i> taxa (species, subspecies, botanical varieties) in New Zealand with the range of taxa in international cultivation, and determined the presence of taxa from Red List categories, geographic origins and taxonomic groups. The 566 taxa in New Zealand, including 224 Red List taxa, encompass 67% of the taxa in cultivation worldwide, ranking second internationally for number of taxa in the collections investigated. New Zealand holds wild-collected material of 230 taxa, including 70 Red List taxa, and 20 taxa for which wild material is not listed in the international collections studied. China is the geographic origin of the greatest number of <i>Rhododendron</i> Red List taxa held in New Zealand. Of the 77 taxonomic subsections of <i>Rhododendron</i>, New Zealand holds 75% or more of the taxa in cultivation for 37 subsections, and 75% or more of the Red List taxa in cultivation for 24 subsections. The greatest numbers of Red List taxa in New Zealand collections are from section <i>Rhododendron</i> subsection <i>Maddenia</i> (20) and section <i>Pontica</i> subsection <i>Neriiflora</i> (17). Our analysis enables us to (1) propose conservation action for <i>Rhododendron</i> in New Zealand, (2) summarise our approach as a model for examining other introduced plant genera in New Zealand, and (3) propose our method as a component of an ex situ conservation strategy for New Zealand.
DOI: 10.6084/m9.figshare.4897181.v1
title: 16S rRNA tree of Proteobacteria and Nitrospirae

description: The phylogeny of Proteobacteria and Nitrospirae based on 16S rRNA sequence. GTR+G+I was selected as the best-fit substitution model using jModelTest v2.1.2 prior to phylogeny reconstruction. The maximum-likelihood tree of 16S rRNA was constructed using RAxML v8.2.4 with 500 times of bootstrap.
DOI: 10.6084/m9.figshare.4897181.v2
title: 16S rRNA tree of Proteobacteria and Nitrospirae

description: The phylogeny of Proteobacteria and Nitrospirae based on 16S rRNA sequence. GTR+G+I was selected as the best-fit substitution model using jModelTest v2.1.2 prior to phylogeny reconstruction. The maximum-likelihood tree of 16S rRNA was constructed using RAxML v8.2.4 with 500 times of bootstrap.
DOI: 10.6084/m9.figshare.4897136
title: Retweets uncertain tensor

description: The uncertain tensor produced after analyzing the retweets about Brazilian soccer teams in 2014
DOI: 10.6084/m9.figshare.4897139
title: Vélo'v uncertain tensor

description: The public bicycle network in Lyon, France.
DOI: 10.6084/m9.figshare.4897124
title: US geographic names 2017-06-01

description: A text database of named places in the United States. <br>The US Board on Geographic Names controls the database of official names of places in the US, and the US Geological Survey (USGS) maintains the database. This is a copy of the 2017-06-01 database, which I am using to create an R package for textual analyses of geographic content, to ensure this version remains. The original source was from: https://geonames.usgs.gov/domestic/download_data.htm (which is a very slow server).<br>I have chosen CC0 for the license because, as a creation of the US government, I don't think the database can be copyrighted (and CC0 is the closest match).
DOI: 10.6084/m9.figshare.4897136.v1
title: Retweets uncertain tensor

description: The uncertain tensor produced after analyzing the retweets about Brazilian soccer teams in 2014
DOI: 10.6084/m9.figshare.4897055
title: mecamylamine_acute.zip

description: Mecamylamine acute dataset<br>
DOI: 10.6084/m9.figshare.4897139.v1
title: Vélo'v uncertain tensor

description: The public bicycle network in Lyon, France.
DOI: 10.6084/m9.figshare.4897124.v1
title: US geographic names 2017-06-01

description: A text database of named places in the United States. <br>The US Board on Geographic Names controls the database of official names of places in the US, and the US Geological Survey (USGS) maintains the database. This is a copy of the 2017-06-01 database, which I am using to create an R package for textual analyses of geographic content, to ensure this version remains. The original source was from: https://geonames.usgs.gov/domestic/download_data.htm (which is a very slow server).<br>I have chosen CC0 for the license because, as a creation of the US government, I don't think the database can be copyrighted (and CC0 is the closest match).
DOI: 10.6084/m9.figshare.4896941
title: AcuteStudyFiles.zip

description: The Acute Studies are shown in the last figures of the manuscript. These are supplementary data files needed for analysis, including file lists, notes, and a C program.
DOI: 10.6084/m9.figshare.4897055.v1
title: mecamylamine_acute.zip

description: Mecamylamine acute dataset<br>
DOI: 10.6084/m9.figshare.4896911
title: behavioraldata.m

description: This matlab file contains all the d' data.
DOI: 10.6084/m9.figshare.4896914
title: scopolamine_acute.zip

description: These are the scopolamine acute study data files. You will also need the Acute Study Files to make sense of them.
DOI: 10.6084/m9.figshare.4896941.v1
title: AcuteStudyFiles.zip

description: The Acute Studies are shown in the last figures of the manuscript. These are supplementary data files needed for analysis, including file lists, notes, and a C program.
DOI: 10.6084/m9.figshare.4896911.v1
title: behavioraldata.m

description: This matlab file contains all the d' data.
DOI: 10.6084/m9.figshare.4896836
title: RNA-binding protein RBM14 regulates dissociation and association of non-homologous end joining proteins

description: Defects in the DNA damage response (DDR) are associated with multiple diseases, including cancers and neurodegenerative disorders. Emerging evidence indicates involvement of RNA-binding proteins (RBPs) in DDR. However, functions of RBPs in the DDR pathway remain elusive. We have shown previously that the RNA-binding protein RBM14 is required for non-homologous end joining (NHEJ). Here we show that RBM14 is required for efficient recruitment of XRCC4 and XLF to chromatin and the release of KU proteins from chromatin upon DNA damage. Failure of this process leads to accumulation of double-strand breaks (DSBs) in cells. Thus RBM14 plays crucial role in regulation of NHEJ upon DNA damage.
DOI: 10.6084/m9.figshare.4896842
title: Temperature-dependent regulation of rDNA condensation in <i>Saccharomyces cerevisiae</i>

description: Chromatin condensation during mitosis produces detangled and discrete DNA entities required for high fidelity sister chromatid segregation during mitosis and positions DNA away from the cleavage furrow during cytokinesis. Regional condensation during G1 also establishes a nuclear architecture through which gene transcription is regulated but remains plastic so that cells can respond to changes in nutrient levels, temperature and signaling molecules. To date, however, the potential impact of this plasticity on mitotic chromosome condensation remains unknown. Here, we report results obtained from a new condensation assay that wildtype budding yeast cells exhibit dramatic changes in rDNA conformation in response to temperature. rDNA hypercondenses in wildtype cells maintained at 37°C, compared with cells maintained at 23°C. This hypercondensation machinery can be activated during preanaphase but readily inactivated upon exposure to lower temperatures. Extended mitotic arrest at 23°C does not result in hypercondensation, negating a kinetic-based argument in which condensation that typically proceeds slowly is accelerated when cells are placed at 37°C. Neither elevated recombination nor reduced transcription appear to promote this hypercondensation. This heretofore undetected temperature-dependent hypercondensation pathway impacts current views of chromatin structure based on conditional mutant gene analyses and significantly extends our understanding of physiologic changes in chromatin architecture in response to hypothermia.
DOI: 10.6084/m9.figshare.4896842.v1
title: Temperature-dependent regulation of rDNA condensation in <i>Saccharomyces cerevisiae</i>

description: Chromatin condensation during mitosis produces detangled and discrete DNA entities required for high fidelity sister chromatid segregation during mitosis and positions DNA away from the cleavage furrow during cytokinesis. Regional condensation during G1 also establishes a nuclear architecture through which gene transcription is regulated but remains plastic so that cells can respond to changes in nutrient levels, temperature and signaling molecules. To date, however, the potential impact of this plasticity on mitotic chromosome condensation remains unknown. Here, we report results obtained from a new condensation assay that wildtype budding yeast cells exhibit dramatic changes in rDNA conformation in response to temperature. rDNA hypercondenses in wildtype cells maintained at 37°C, compared with cells maintained at 23°C. This hypercondensation machinery can be activated during preanaphase but readily inactivated upon exposure to lower temperatures. Extended mitotic arrest at 23°C does not result in hypercondensation, negating a kinetic-based argument in which condensation that typically proceeds slowly is accelerated when cells are placed at 37°C. Neither elevated recombination nor reduced transcription appear to promote this hypercondensation. This heretofore undetected temperature-dependent hypercondensation pathway impacts current views of chromatin structure based on conditional mutant gene analyses and significantly extends our understanding of physiologic changes in chromatin architecture in response to hypothermia.
DOI: 10.6084/m9.figshare.4896839
title: Integrative epigenetic and genetic pan-cancer somatic alteration portraits

description: Genetic and epigenetic alterations are required for carcinogenesis and the mutation burden across tumor types has been investigated. Here, we investigate epigenetic alterations with a novel measure of global DNA methylation dysregulation, the methylation dysregulation index (MDI), across 14 cancer types in The Cancer Genome Atlas (TCGA) database. DNA methylation data—obtained using Illumina HumanMethylation450 BeadChip—was accessed from TCGA. We calculated the MDI in 14 tumor types (n = 5,592 tumors), using adjacent normal tissues (n = 701) from each tumor site. Copy number alteration, and mutation burden were retrieved from cBioportal (n = 5,152). We tested the relation of subject MDI across tumors and with age, gender, tumor stage, estimated tumor purity, and copy number alterations for both overall MDI and genomic-context-specific MDI. We also investigated the top most dysregulated loci shared across tumor types. There was a broad range of extent in methylation dysregulation across tumor types (<i>P</i> &lt; 2.2E-16). However, a consistent pattern of methylation dysregulation stratified by genomic context was observed across tumor types where the highest dysregulation occurred at non-CpG island regions. Considering other summary measures of somatic alteration, MDI was correlated with copy number alterations but not with mutation burden. Using the top dysregulated CpG sites in common across tumors, 4 classes of cancer types were observed, and the functional consequences of these alterations to gene expression were confirmed. This work identified the global DNA methylation dysregulation patterns across 14 cancer types showing a higher impact for the non-CpG island areas. The most dysregulated loci across cancer types identified common clusters across cancer types that may have implications for future treatment and prevention measures.
DOI: 10.6084/m9.figshare.4896848.v2
title: Modeling the firm's response to research & development tax credit policies

description: In this article, we develop a microeconomic model of normative firm behavior under the incentive of a research and development (R&D) tax credit. The model is based on the well-known concept of a two-factor learning model in which R&D expenditures and manufacturing capacity expansion are the principle determinants of cost reduction in a new technology product. We distinguish between the behavior of start-up firms and ongoing firms and study the potential impacts of progressively larger R&D tax credits. We find highly significant differences in the potential impact of the credit on start-up firms versus ongoing firms. We also find that the credit can significantly impact optimal product pricing of the technology when introduced into the marketplace. We examine the implications of this latter fact on the overall social cost of the R&D tax credit.
DOI: 10.6084/m9.figshare.4896839.v1
title: Integrative epigenetic and genetic pan-cancer somatic alteration portraits

description: Genetic and epigenetic alterations are required for carcinogenesis and the mutation burden across tumor types has been investigated. Here, we investigate epigenetic alterations with a novel measure of global DNA methylation dysregulation, the methylation dysregulation index (MDI), across 14 cancer types in The Cancer Genome Atlas (TCGA) database. DNA methylation data—obtained using Illumina HumanMethylation450 BeadChip—was accessed from TCGA. We calculated the MDI in 14 tumor types (n = 5,592 tumors), using adjacent normal tissues (n = 701) from each tumor site. Copy number alteration, and mutation burden were retrieved from cBioportal (n = 5,152). We tested the relation of subject MDI across tumors and with age, gender, tumor stage, estimated tumor purity, and copy number alterations for both overall MDI and genomic-context-specific MDI. We also investigated the top most dysregulated loci shared across tumor types. There was a broad range of extent in methylation dysregulation across tumor types (<i>P</i> &lt; 2.2E-16). However, a consistent pattern of methylation dysregulation stratified by genomic context was observed across tumor types where the highest dysregulation occurred at non-CpG island regions. Considering other summary measures of somatic alteration, MDI was correlated with copy number alterations but not with mutation burden. Using the top dysregulated CpG sites in common across tumors, 4 classes of cancer types were observed, and the functional consequences of these alterations to gene expression were confirmed. This work identified the global DNA methylation dysregulation patterns across 14 cancer types showing a higher impact for the non-CpG island areas. The most dysregulated loci across cancer types identified common clusters across cancer types that may have implications for future treatment and prevention measures.
DOI: 10.6084/m9.figshare.4896848.v1
title: Modeling the firm's response to research & Development tax credit policies

description: In this paper we develop a microeconomic model of normative firm behavior under the incentive of a research and development (R&D) tax credit. The model is based on the well-known concept of a two factor learning model in which R&D expenditures and manufacturing capacity expansion are the principle determinants of cost reduction in a new technology product. We distinguish between the behavior of start-up firms and on-going firms and study the potential impacts of progressively larger R&D tax credits. We find highly significant differences in the potential impact of the credit on start-up firms versus on-going firms. We also find that the credit can significantly impact optimal product pricing of the technology when introduced into the marketplace. We examine the implications of this latter fact on the overall social cost of the R&D tax credit.
DOI: 10.6084/m9.figshare.4896803
title: RDP V3-V4 ver. 11.5 database

description: RDP database dereplicated, only the V3-V4 region. For use with mg_classifier; metagenomic sequence classifier (https://github.com/GenomicaMicrob/mg_classifier).