cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5285521.v2
title: Gridded bathymetry of the Baker-Martinez fjord complex (Chile, 48°S) v1

description: We present a bathymetric map of the Baker-Martinez fjord complex (Chile, 48⁰S) constructed from multiple data sets: multibeam echosounder data of Baker channel (Harada et al., 2008) and of Steffen fjord and Baker river delta (Vandekerkhove & Bertrand, 2016), single beam echosounder data of Jorge Montt fjord (Rivera et al., 2012, Moffat, 2014 and additional data from C. Moffat) and individual bathymetry points from two SHOA nautical charts (SHOA, 2001, 2008). The heterogeneous data with distinct spatial resolution was gridded using the kriging method (3.6 arc-second resolution) in Surfer from Golden Software. We intend to update this map when new datasets become available. The deepest basin of Baker channel (73.8°W) reaches depths of 1075 m below sea level (BSL). To the west, the channel has depths ranging from 450 to 750 m BSL. Martinez channel is between 200 and 440 m deep in its eastern part and reaches depths of 535 m BSL to the west. The bullseye effect in Martinez channel is a mere artefact of the gridding procedure as there is only sparse bathymetric data available in that area. The deepest and largest basin (1405 m BSL and approx. 10 km wide) is located in Messier channel. All the channels are flanked by steep slopes (20 – 40°). Transverse ridges are present throughout the fjord complex, creating separated sub-basins (e.g. north of the deepest basin in Messier channel, in the center of Baker channel at 74.35°W). The fjord becomes shallower (200 – 300m BSL) towards its mouth in the Gulf of Penas. This bathymetric map is intended for regional oceanographic and geological research projects. <b>References:</b> Harada, N. and the shipboard scientific party, 2008. MIRAI cruise report MR06-04 Leg 3, Japan Agency for Marine Earth Science and Technology, Yokosuka, 176 pp. Moffat, C., 2014. Wind-driven modulation of warm water supply to a proglacial fjord, Jorge Montt Glacier, Patagonia. Geophysical Research Letters, <i>41</i>, 1–8. Rivera, A., Koppes, M.N., Bravo, C., Aravena, J.C., 2012. Little Ice Age advance and retreat of Glaciar Jorge Montt, Chilean Patagonia. Climate of the Past, 8, 403–414. SHOA (Servicio Hidrográfico y Oceanográfico de la Armada de Chile), 2001. "Canal Baker y Puertos Adyacentes (Canal Baker)", 6<sup>th</sup> ed., sheet 9100, 1:200 000, Mercator projection. SHOA (Servicio Hidrográfico y Oceanográfico de la Armada de Chile), 2008. “Acceso Norte a Canal Messier – Boca de Canales a Isla Van Der Meulen”, 2nd ed., sheet 9300, 1:100 000, Mercator projection. Vandekerkhove, E., Bertrand, S., 2016. Expedition report Paleo-GLOFs and HYDROPROX, 13 pp.
DOI: 10.6084/m9.figshare.5285440
title: GIWAXS for racemic and enantiopure 1-aza[6]helicene films

description: GIWAXS raw files of aged (rac)-1-aza[6]helicene and (-)-1-aza[6]helicene and of (+)-1-aza[6]helicene at three different time points: as-cast, 30 min and 20 h.
DOI: 10.6084/m9.figshare.5285440.v1
title: GIWAXS for racemic and enantiopure 1-aza[6]helicene films

description: GIWAXS raw files of aged (rac)-1-aza[6]helicene and (-)-1-aza[6]helicene and of (+)-1-aza[6]helicene at three different time points: as-cast, 30 min and 20 h.
DOI: 10.6084/m9.figshare.5285401
title: FigShare neuroimaging dataset Sarabdjitsingh 2017.xlsx

description: <br>We exposed rats to 24 hours of maternal deprivation (MD) at postnatal day 3. Using structural magnetic resonance imaging we examined: i) volumetric changes and white/grey matter properties of the whole cerebrum and of specific brain areas; and ii) whether potential alterations could be normalized by blocking glucocorticoid receptors with mifepristone during postnatal days 26 and 28. The results show that MD caused a volumetric reduction of the prefrontal cortex, particularly the ventromedial part, and the orbitofrontal cortex. Within the whole cerebrum, white (relative to grey) matter volume was decreased and region-specifically in prefrontal cortex and dorsomedial striatum following MD. A trend was found for the hippocampus. Grey matter fractions were not affected. Treatment with mifepristone did not normalize these changes.
DOI: 10.6084/m9.figshare.5285377
title: Fungal species tree

description: A set of alignment and tree files of the fungal phylogeny using publicly available fungal genomes. Files were generated using a concatenated set of 238 single copy orthologs detected using the BUSCO ancestral sequences for fungi and the genblastg tool. Alignments were built using mafft and trees constructed using FastTree2. The Astral2 program was used to create a coalescent species tree to compare to the concatenated gene tree. <br>
DOI: 10.6084/m9.figshare.5285362
title: narG

description: Folder containing gene and protein sequences of the gene encoding the membrane bound respiratory nitrate reductase <i>narG</i>.<br>
DOI: 10.6084/m9.figshare.5285365
title: napA

description: Nucleotide and protein sequences of the fungal genes encoding the periplasmic nitrate reductase napA.<br>
DOI: 10.6084/m9.figshare.5285377.v1
title: Fungal species tree

description: A set of alignment and tree files of the fungal phylogeny using publicly available fungal genomes. Files were generated using a concatenated set of 238 single copy orthologs detected using the BUSCO ancestral sequences for fungi and the genblastg tool. Alignments were built using mafft and trees constructed using FastTree2. The Astral2 program was used to create a coalescent species tree to compare to the concatenated gene tree. <br>
DOI: 10.6084/m9.figshare.5285362.v1
title: narG

description: Folder containing gene and protein sequences of the gene encoding the membrane bound respiratory nitrate reductase <i>narG</i>.<br>
DOI: 10.6084/m9.figshare.5285365.v1
title: napA

description: Nucleotide and protein sequences of the fungal genes encoding the periplasmic nitrate reductase napA.<br>
DOI: 10.6084/m9.figshare.5285326
title: GIS-based seismic hazard prediction system

description: <b>GIS</b><b> -based seismic hazard prediction system </b><b>for urban earthquake disaster prevention planning</b> <br> <br>
DOI: 10.6084/m9.figshare.5285320
title: Supplementary material for: Metabolomics-based chemotaxonomy of root endophytic fungi for natural products discovery

description: Supplementary files for Maciá-Vicente et al. (2018) Metabolomics-based chemotaxonomy of root endophytic fungi for natural products discovery. Environmental Microbiology, doi: 10.1111/1462-2920.14072
DOI: 10.6084/m9.figshare.5285326.v1
title: GIS-based seismic hazard prediction system

description: <b>GIS</b><b> -based seismic hazard prediction system </b><b>for urban earthquake disaster prevention planning</b> <br> <br>
DOI: 10.6084/m9.figshare.5285293
title: Supplementary Data from Niche construction, sources of selection and trait coevolution

description: Organisms modify and choose components of their local environments. This ‘niche construction’ can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection acting back on the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.
DOI: 10.6084/m9.figshare.5285269
title: Mycoplasma genitalium annotated assemblies

description: This is a collection of 28 Mycoplasma genitalium annotated assemblies. The de novo assemblies were created with velvet, and annotated with Prokka.
DOI: 10.6084/m9.figshare.5285293.v1
title: Supplementary Data from Niche construction, sources of selection and trait coevolution

description: Organisms modify and choose components of their local environments. This ‘niche construction’ can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection acting back on the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.
DOI: 10.6084/m9.figshare.5285242
title: Transcriptome analysis of gene expression provides new insights into the effect of mild therapeutic hypothermia on primary human cortical astrocytes cultured under hypoxia

description: <br>Hypothermia is increasingly used as a therapeutic measure against brain injury. However, the cellular mechanisms underpinning its actions are complex and not fully elucidated. Astrocytes are the most abundant cell type of the brain and as such are likely to play a critical role in the hypothermia effects. In this study, the transcriptional changes and protein expression profile were investigated in human primary cortical astrocytes cultured under hypoxic conditions for 6h, with and without a mild hypothermic intervention 2h post-insult hypoxia/hypothermia to mimic the <i>in vivo</i> treatment situation following traumatic brain injury (TBI) and/or stroke.<br>Hypothermia is a complex intervention, this study provides the first detailed longitudinal comparison at the transcript and protein expression levels investigating the molecular effects of therapeutic hypothermic intervention following hypoxia on human primary cortical astrocytes.
DOI: 10.6084/m9.figshare.5285245
title: Suicidal thoughts among university students in Ethiopia

description: This data that we have used to determine the suicidal thoughts and associated factors among University students in Ethiopia. The analyses were carried out using SPSS version 20 software.
DOI: 10.6084/m9.figshare.5285242.v2
title: Transcriptome analysis of gene expression provides new insights into the effect of mild therapeutic hypothermia on primary human cortical astrocytes cultured under hypoxia

description: <br>Hypothermia is increasingly used as a therapeutic measure against brain injury. However, the cellular mechanisms underpinning its actions are complex and not fully elucidated. Astrocytes are the most abundant cell type of the brain and as such are likely to play a critical role in the hypothermia effects. In this study, the transcriptional changes and protein expression profile were investigated in human primary cortical astrocytes cultured under hypoxic conditions for 6h, with and without a mild hypothermic intervention 2h post-insult hypoxia/hypothermia to mimic the <i>in vivo</i> treatment situation following traumatic brain injury (TBI) and/or stroke.<br>Hypothermia is a complex intervention, this study provides the first detailed longitudinal comparison at the transcript and protein expression levels investigating the molecular effects of therapeutic hypothermic intervention following hypoxia on human primary cortical astrocytes.
DOI: 10.6084/m9.figshare.5285245.v1
title: Suicidal thoughts among university students in Ethiopia

description: This data that we have used to determine the suicidal thoughts and associated factors among University students in Ethiopia. The analyses were carried out using SPSS version 20 software.
DOI: 10.6084/m9.figshare.5285242.v1
title: Transcriptome analysis of gene expression provides new insights into the effect of mild therapeutic hypothermia on primary human cortical astrocytes cultured under hypoxia

description: <br>Hypothermia is increasingly used as a therapeutic measure against brain injury. However, the cellular mechanisms underpinning its actions are complex and not fully elucidated. Astrocytes are the most abundant cell type of the brain and as such are likely to play a critical role in the hypothermia effects. In this study, the transcriptional changes and protein expression profile were investigated in human primary cortical astrocytes cultured under hypoxic conditions for 6h, with and without a mild hypothermic intervention 2h post-insult hypoxia/hypothermia to mimic the <i>in vivo</i> treatment situation following traumatic brain injury (TBI) and/or stroke.<br>Hypothermia is a complex intervention, this study provides the first detailed longitudinal comparison at the transcript and protein expression levels investigating the molecular effects of therapeutic hypothermic intervention following hypoxia on human primary cortical astrocytes.
DOI: 10.6084/m9.figshare.5285128
title: Metabolic diversity and in vitro pancreatic lipase inhibition activity of some varieties of <i>Mangifera indica</i> L. fruits

description: Mango fruits from different varieties vary in aroma and taste. In this study, methanol extracts of fruit pulps obtained from seven Indian varieties of <i>Mangifera indica</i> (Amrapali, Fazli, Golapkhas, Gopalbhog, Himsagar, Langra, and Mohanbhog) were profiled using a metabolomics approach. Chemometric methods were used to understand the contribution of metabolites to varietal differences. The extracts were also assayed for pancreatic lipase inhibitory activities in vitro. All the pulp extracts were analyzed by GC-MS and HPLC to detect their metabolites. In sum, 63 metabolites were identified. The varieties were distinctly different chemically in terms of the identified metabolites, as revealed by principal component analysis (PCA) and partial least squares – discriminant analysis (PLS-DA). From the biplot and VIP scores, it was observed that in addition to some organic acids, amino acids, sugars, and phenolic constituents (e.g., benzene-1,2,4-triol, mangiferin, and pyrogallol) contributed to this variation. All the varieties also inhibited pancreatic lipase in a dose-dependent manner. Gallic acid (IC<sub>50</sub> value 0.47 nM) and 4-hydroxy benzoic acid (IC<sub>50</sub> value 1.15 nM) showed high anti-lipase activity. Three amino acids (L-proline (IC<sub>50</sub> value 0.01 µM), L-alanine (IC<sub>50</sub> value 0.14 µM) and aspartic acid (IC<sub>50</sub> value 0.02 µM)), and the inorganic acid phosphoric acid (0.02 µM) also showed activity against pancreatic lipase.
DOI: 10.6084/m9.figshare.5285128.v1
title: Metabolic diversity and in vitro pancreatic lipase inhibition activity of some varieties of <i>Mangifera indica</i> L. fruits

description: Mango fruits from different varieties vary in aroma and taste. In this study, methanol extracts of fruit pulps obtained from seven Indian varieties of <i>Mangifera indica</i> (Amrapali, Fazli, Golapkhas, Gopalbhog, Himsagar, Langra, and Mohanbhog) were profiled using a metabolomics approach. Chemometric methods were used to understand the contribution of metabolites to varietal differences. The extracts were also assayed for pancreatic lipase inhibitory activities in vitro. All the pulp extracts were analyzed by GC-MS and HPLC to detect their metabolites. In sum, 63 metabolites were identified. The varieties were distinctly different chemically in terms of the identified metabolites, as revealed by principal component analysis (PCA) and partial least squares – discriminant analysis (PLS-DA). From the biplot and VIP scores, it was observed that in addition to some organic acids, amino acids, sugars, and phenolic constituents (e.g., benzene-1,2,4-triol, mangiferin, and pyrogallol) contributed to this variation. All the varieties also inhibited pancreatic lipase in a dose-dependent manner. Gallic acid (IC<sub>50</sub> value 0.47 nM) and 4-hydroxy benzoic acid (IC<sub>50</sub> value 1.15 nM) showed high anti-lipase activity. Three amino acids (L-proline (IC<sub>50</sub> value 0.01 µM), L-alanine (IC<sub>50</sub> value 0.14 µM) and aspartic acid (IC<sub>50</sub> value 0.02 µM)), and the inorganic acid phosphoric acid (0.02 µM) also showed activity against pancreatic lipase.
DOI: 10.17608/k6.auckland.5285044
title: Supplementary spreadsheet 3: Effects of spatial obesity and type 2 diabetes eQTLs in subcutaneous adipose, visceral adipose, skeletal muscle, liver and pancreas

description: Regulatory Links Between Obesity and Type 2 Diabetes Revealed using Hi-C Data and Expression Quantitative Traits Loci
DOI: 10.17608/k6.auckland.5285041
title: Supplementary spreadsheet 2: Type 2 diabetes spatial eQTL-gene interactions

description: Regulatory Links Between Obesity and Type 2 Diabetes Revealed using Hi-C Data and Expression Quantitative Traits Loci.
DOI: 10.17608/k6.auckland.5285038
title: Supplementary spreadsheet 1: Obesity spatial eQTL-gene interactions

description: Regulatory Links Between Obesity and Type 2 Diabetes Revealed using Hi-C Data and Expression Quantitative Traits Loci.
DOI: 10.17608/k6.auckland.5285044.v1
title: Supplementary spreadsheet 3: Effects of spatial obesity and type 2 diabetes eQTLs in subcutaneous adipose, visceral adipose, skeletal muscle, liver and pancreas

description: Regulatory Links Between Obesity and Type 2 Diabetes Revealed using Hi-C Data and Expression Quantitative Traits Loci
DOI: 10.17608/k6.auckland.5285038.v1
title: Supplementary spreadsheet 1: Obesity spatial eQTL-gene interactions

description: Regulatory Links Between Obesity and Type 2 Diabetes Revealed using Hi-C Data and Expression Quantitative Traits Loci.
DOI: 10.26208/139c-8x65
title: Exploring the landscape of model representations

description: The success of any physical model critically depends upon adopting an appropriate representation for the phenomenon of interest. Unfortunately, it remains generally challenging to identify the essential degrees of freedom or, equivalently, the proper order parameters for describing complex phenomena. Here we develop a statistical physics framework for exploring and quantitatively characterizing the space of order parameters for representing physical systems. Specifically, we examine the space of low-resolution representations that correspond to particle based coarse-grained (CG) models for a simple microscopic model of protein fluctuations. We employ Monte Carlo (MC) methods to sample this space and determine the density of states for CG representations as a function of their ability to preserve the configurational information, I, and large-scale fluctuations, Q, of the microscopic model. These two metrics are uncorrelated in high-resolution representations but become anticorrelated at lower resolutions. Moreover, our MC simulations suggest an emergent length scale for coarse-graining proteins, as well as a qualitative distinction between good and bad representations of proteins. Finally, we relate our work to recent approaches for clustering graphs and detecting communities in networks.
DOI: 10.6084/m9.figshare.5284486
title: p450nor

description: Folder containing alignments and tree of <i>p450nor </i>gene sequences detected in fungal and algal genomes. Bacterial homologs of each gene (when applicable) were collected from an analysis of the gene against the bacterial RefSeq protein database are included as well.<br>
DOI: 10.6084/m9.figshare.5284492
title: nirK

description: This folder contains alignments (nucleotide and protein) and tree files for <i>nirK</i> genes detected in fungal genomes. <br>
DOI: 10.6084/m9.figshare.5284483
title: Python vs C

description: Data related to the paper "A controlled experiment on Python vs C for an Introductory Programming course: students' outcomes" by Jacques Wainer and Eduardo Xavier, to be published in ACM Transactions on Computer Education.
DOI: 10.6084/m9.figshare.5284423
title: Dataset for: Spatio-temporal multivariate mixture models for Bayesian model selection in disease mapping

description: It is often the case that researchers wish to simultaneously explore the behavior of multiple diseases while accounting for potential spatial and/or temporal correlation. In this paper, we propose a flexible class of multivariate spatio-temporal mixture models to fill this role. Further, these models offer flexibility with the potential for model selection as well as the ability to accommodate lifestyle, socio-economic, and physical environmental variables with spatial, temporal, or both structures. Here, we explore the capability of this approach via a large scale simulation study and examine a real data example. The results which are focused on four model variants suggest that all models possess the ability to recover simulation ground truth and display improved model fit over two baseline Knorr-Held spatio-temporal interaction model variants in a real data application.
DOI: 10.6084/m9.figshare.5284417
title: Dataset for: Influence Diagnostics in Spatial Models with Censored Response

description: Environmental data are often spatially correlated and sometimes include observations below or above detection limits (i.e., censored values reported as less or more than a level of detection). Existing research mainly concentrate on parameter estimation using Gibbs sampling, and most researches conducted from a frequentist perspective in spatial censored models are elusive. In this paper, we propose an exact estimation procedure to obtain the maximum likelihood estimates of the fixed effects and variance components, using a stochastic approximation of the EM (SAEM) algorithm (Delyon et al., 1999). This approach permits estimation of the parameters of spatial linear models when censoring is present in an easy and fast way. As a byproduct, predictions of unobservable values of the response variable are possible. Motivated by this algorithm, we develop local and global influence measures on the basis of the conditional expectation of the complete-data log-likelihood function which eliminates the complexity associated with the approach of Cook (1977, 1986) for spatial censored models. Some useful perturbation schemes are discussed. The newly developed method is illustrated using data from a dioxin contaminated site in Missouri that contain left-censored data as well as a dataset related to depths of a geological horizon that contains both left- and right-censored observations. In addition, a simulation study is presented that, explores the accuracy of the proposed measures in detecting influential observations under different perturbation schemes. The methodology addressed in this paper is implemented in the R package CensSpatial.