Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Repositories
  • ArrayExpress (63)
  • BioProject (96)
  • ClinicalTrials.gov (2)
  • Dataverse (4)
  • Dryad (15)
  • Figshare (44)
  • GEMMA (2)
  • ICPSR (28)
  • OmicsDI (42)
  • PDB (21)
  • UniProt:Swiss-Prot (2)

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.

Displaying 15 of 15 results for "SCARA3"
i
Switch View:
Sorted By:
Title Date Issued Date Released Description
Data from: Diagnostic gene expression biomarkers of coral thermal stress
01-10-2014 06-16-2014
Gene expression biomarkers can enable rapid assessment of physiological conditions in situ, providing a valuable tool for reef managers interested in linking organism physiology with large-scale climatic conditions. Here, we assessed the ability of quantitative PCR (qPCR) based gene expression biomarkers to evaluate (1) the immediate cellular stress response (CSR) of Porites astreoides to incremental thermal stress and (2) the magnitude of CSR and cellular homeostasis response (CHR) during a natural bleaching event. Expression levels largely scaled with treatment temperature, with the strongest responses occurring in heat shock proteins. This is the first demonstration of a “tiered” CSR in a coral, where the magnitude of expression change is proportional to stress intensity. Analysis of a natural bleaching event revealed no signature of an acute CSR in normal or bleached corals, indicating that the bleaching stressor(s) had abated by the day of sampling. Another long-term stress CHR-based indicator assay was significantly elevated in bleached corals; though assay values overall were low, suggesting good prospects for recovery. This study represents the first step in linking variation in gene expression biomarkers to stress tolerance and bleaching thresholds in situ by quantifying the severity of ongoing thermal stress and its accumulated long-term impacts.
Data from: On the relative importance of CSR ecological strategies and integrative traits to explain species dominance at local scales
05-03-2017 05-10-2017
PLEASE NOTE, PART OF THESE DATA ARE ALSO REFERRED TO ANOTHER ARTICLE. PLEASE SEE http://dx.doi.org/10.1111/j.1654-1103.2009.01119.x FOR MORE INFORMATION. 1. Identifying ecological strategies based on functional traits has been one of the main focuses of studies on plant community assembly. Recently, an important and timely tool, “StrateFy”, has been proposed for detecting plant strategies across the globe according to the CSR scheme. The CSR scheme is undeniably efficient across scales, and distinct CSR strategies among species have been proposed to explain differing degrees of dominance among species. However, in a previous study we showed that dominance ranking of woody species in a resource-poor habitat (coastal sandy plain) was not explained by morphological traits commonly measured in functional approaches (such as those used to estimate CSR strategies), but by integrative traits (i.e. traits that are the result of different combinations of functional traits) more related to plant performance. 2. Here, we used CSR analysis and StrateFy on a dataset collected on a coastal sandy plain to test the hypothesis that the dominance ranking would be compatible with the CSR strategies; i.e., that dominant species would show a greater proportion of the stress-tolerance (S%) strategy than subordinate species. 3. Contrary to our hypothesis, all species exhibited an S/CS strategy, and the most-dominant species had neither similar values nor the highest S%. The inability of CSR analysis (as applied using StrateFy) to predict dominance ranking suggests that it can explain relative dominance when different strategies co-occur, but not in cases where dominant and subordinate plants share the same strategy. 4. We argue that the relative importance of CSR and integrative traits for describing dominance ranking may depend on how CSR strategies are filtered in each environment. In environments where only a narrow range of strategy classes are viable, integrative traits may be more important for explaining variation in degrees of dominance. Thus, the ability of a given species to achieve dominance may depend on integrative traits resulting from multiple trait arrays, not necessarily captured by the SLA, LDMC and LA measurements that are used to calculate the relative proportions of strategies in StrateFy.
Data from: Heritable variation in heat shock gene expression: a potential mechanism for adaptation to thermal stress in embryos of sea turtles
01-13-2016 01-14-2016
The capacity of species to respond adaptively to warming temperatures will be key to their survival in the Anthropocene. The embryos of egg-laying species such as sea turtles have limited behavioural means for avoiding high nest temperatures, and responses at the physiological level may be critical to coping with predicted global temperature increases. Using the loggerhead sea turtle (Caretta caretta) as a model, we used quantitative PCR to characterise variation in the expression response of heat shock genes (hsp60, hsp70, and hsp90; molecular chaperones involved in cellular stress response) to an acute non-lethal heat shock. We show significant variation in gene expression at the clutch and population levels for some, but not all hsp genes. Using pedigree information, we estimated heritabilities of the expression response of hsp genes to heat shock and demonstrated both maternal and additive genetic effects. This is the first evidence that the heat shock response is heritable in sea turtles and operates at the embryonic stage in any reptile. The presence of heritable variation in the expression of key thermotolerance genes is necessary for sea turtles to adapt at a molecular level to warming incubation environments.
Penny et al Data Set
05-04-2009 10-29-2015
n/a
rubus_photos2
07-10-2012 04-22-2013
Photographs of plants at sites CMB, CSR, CSP, and CFX. Sample IDs are shown within the images. Images are in .jpg format.
Rosado and de Mattos dataset
05-10-2017 05-10-2017
Functional traits (morphological, physiological and phenological) measured in ten woody species occuring in a coastal sandy plain (restinga) in Brazil
RIAT Restoring Study 329 data files
09-16-2015 09-16-2015
Zip file containing: Original SKB CSR (both Appendix D & Appendix G); ii) RIAT Excel spreadsheet for Harms/Adverse Event data; RIAT Excel spreadsheet for Withdrawals/dropouts from the study. R code used to analyse Efficacy data; Original SKB Study 329 Trial protocol which was followed in Restoring Study 329 (RIAT).
Data from: Spatial analysis of gene regulation reveals new insights into the molecular basis of upper thermal limits
11-17-2014 12-30-2014
The cellular stress response has long been the primary model for studying the molecular basis of thermal adaptation, yet the link between gene expression, RNA metabolism and physiological responses to thermal stress remains largely unexplored. We address this by comparing the transcriptional and physiological responses of three geographically distinct populations of D. melanogaster from eastern Australia in response to, and recovery from, a severe heat stress with and without a pre-stress hardening treatment. We focus on Starvin (stv), recently identified as an important thermally responsive gene. Intriguingly, stv encodes seven transcripts from alternative transcription sites and alternative splicing, yet appears to be rapidly heat-inducible. First, we show genetic differences in upper thermal limits of the populations tested. We then demonstrate that the stv locus does not ubiquitously respond to thermal stress but is expressed as three distinct thermal and temporal RNA phenotypes (isoforms). The shorter transcript isoforms are rapidly up-regulated under stress in all populations and show similar molecular signatures to Heat shock proteins. Multiple stress exposures seem to generate a reserve of pre-mRNAs, effectively ‘priming’ the cells for subsequent stress. Remarkably, we demonstrate a bypass in the splicing blockade in these isoforms, suggesting an essential role for these transcripts under heat stress. Temporal profiles for the weakly heat responsive stv isoform subset show opposing patterns in the two most divergent populations. Innate and induced transcriptome responses to hyperthermia are complex, and warrant moving beyond gene-level analyses.
Timmermannetal2014JAEdata
11-20-2014 11-20-2014
Vegetation data on species cover collected in the field through the Danish National Monitoring and Assessment Programme for the Aquatic and Terrestrial Environments (NOVANA). Columns include a site number (SiteNo), the habitat type (NatureType) according to the definitions of the EU-habitat directive, Year, cover of species, and species.
Data from: Substrate adaptations of sessile benthic metazoans during the Cambrian radiation
02-23-2015 04-29-2015
Many marine benthic metazoans must stabilize themselves upon the seafloor for survival, and as a result their morphologies are controlled in part by local substrate conditions. The Agronomic Revolution (AR), spurred by increasing vertical bioturbation during the Ediacaran–Cambrian transition, permanently altered the nature of shallow marine substrate conditions and led to a major shift in adaptive strategies among benthic metazoans. These ecological and evolutionary changes, known as the Cambrian Substrate Revolution (CSR), are generally understood from observations of benthic metazoan fossils across the Ediacaran/Cambrian boundary, but the timing and geographic extent of this transition are less well known. This analysis attempts to constrain the temporal and spatial pattern of the AR and CSR by performing a global-scale paleoecological analysis of the adaptive strategies of benthic fauna living during the Cambrian. This analysis focused on Burgess Shale-type (BST) faunas because of their exceptional preservation, and was conducted through direct observation of fossil specimens, analysis of data compiled from the Paleobiology Database, and literature review. From these analyses, faunal groups are assigned a metric, the Substrate Adaptability Index (SAI), that relates the overall affinity the fauna demonstrates toward either Proterozoic-style (SAI=0) or Phanerozoic-style (SAI=1) substrate conditions. The results of this analysis demonstrate that most early and middle Cambrian faunas were mixtures of Phanerozoic- and Proterozoic-style adaptive strategists, suggesting that Proterozoic-style substrates were still influential in controlling adaptive strategies in marine environments until at least that time. This is further supported by ichnofabric analysis of many of these localities, where overall bioturbation levels are exceedingly low, indicating a lack of mixed-layer development and the prevalence of firm Proterozoic-style substrates well into the Cambrian.
Data from: Clinical study reports of randomised controlled trials: an exploratory review of previously confidential industry reports
02-26-2013 03-11-2013
Objective: To explore the structure and content of a non-random sample of clinical study reports (CSRs) to guide clinicians and systematic reviewers. Search strategy: We searched public sources and lodged Freedom of Information requests for previously confidential CSRs primarily written by industry for regulators. Selection criteria: CSR reporting sufficient information for extraction (“adequate”). Primary outcome measures: Presence and length of essential elements of trial design and reporting and compression factor (ratio of page length for CSR compared to its published counterpart in a scientific journal). Data extraction: data were extracted on standard forms and cross-checked for accuracy. Results: We assembled a population of 78 CSRs (covering 90 RCTs; 144,610 pages total) dated 1991-2011 of 14 pharmaceuticals. Report synopses had a median length of 5 pages, efficacy evaluation 13.5 pages, safety evaluation 17 pages, attached tables 337 pages, trial protocol 62 pages, statistical analysis plan 15 pages, and individual efficacy and safety listings had a median length of 447 and 109.5 pages, respectively. While 16 (21%) of CSRs contained completed case report forms, these were accessible to us in only one case (765 pages representing 16 individuals). Compression factors ranged between 1 and 8805. Conclusions: Clinical study reports represent a hitherto mostly hidden and untapped source of detailed and exhaustive data on each trial. They should be consulted by independent parties interested in a detailed record of a clinical trial, and should form the basic unit for evidence synthesis as their use is likely to minimize the problem of reporting bias. We cannot say whether our sample is representative and whether our conclusions are generalizable to an undefined and undefineable population of CSRs.
Description of the columns headers
01-22-2015 03-18-2015
oviposition.data (first tab in the Excel file) has 12 columns : - mosquito number - the experimental cage the mosquito comes from (where he bloodfed) - whether the bird he fed on was infected or not : infection - the identity of that bird (ring color and number) - the parasitaemia of that bird (when he is infected) at the acute phase of the infection (10 days after the infection onset) : J10 - the color of the mosquito (to identify which strains it belongs to) - mosquito strain - the egg-laying date (to which 6 days should be removed to get the graphs in the article) : lay - the number of eggs laid by the females : eggs - eggs hatching date : hatch - the number of larvae hatched from those eggs - if and when mosquito died in the water before egg laying : drown oocyst.data (second tab) has 5 columns : - the experimental infected cage the mosquito comes from (where he bloodfed) - mosquito strain (bas4 = SA4B4, aslab = SLAB, csr = SR) - the number of oocysts counted after dissection - the number of eggs laid by the females : eggs - the number of larvae hatched from those eggs
Data from: Characterization of regional left ventricular function in nonhuman primates using magnetic resonance imaging biomarkers: a test-retest repeatability and inter-subject variability study
05-26-2015 06-09-2015
Pre-clinical animal models are important to study the fundamental biological and functional mechanisms involved in the longitudinal evolution of heart failure (HF). Particularly, large animal models, like nonhuman primates (NHPs), that possess greater physiological, biochemical, and phylogenetic similarity to humans are gaining interest. To assess the translatability of these models into human diseases, imaging biomarkers play a significant role in non-invasive phenotyping, prediction of downstream remodeling, and evaluation of novel experimental therapeutics. This paper sheds insight into NHP cardiac function through the quantification of magnetic resonance (MR) imaging biomarkers that comprehensively characterize the spatiotemporal dynamics of left ventricular (LV) systolic pumping and LV diastolic relaxation. MR tagging and phase contrast (PC) imaging were used to quantify NHP cardiac strain and flow. Temporal inter-relationships between rotational mechanics, myocardial strain and LV chamber flow are presented, and functional biomarkers are evaluated through test-retest repeatability and inter subject variability analyses. The temporal trends observed in strain and flow was similar to published data in humans. Our results indicate a dominant dimension based pumping during early systole, followed by a torsion dominant pumping action during late systole. Early diastole is characterized by close to 65% of untwist, the remainder of which likely contributes to efficient filling during atrial kick. Our data reveal that moderate to good intra-subject repeatability was observed for peak strain, strain-rates, E/circumferential strain-rate (CSR) ratio, E/longitudinal strain-rate (LSR) ratio, and deceleration time. The inter-subject variability was high for strain dyssynchrony, diastolic strain-rates, peak torsion and peak untwist rate. We have successfully characterized cardiac function in NHPs using MR imaging. Peak strain, average systolic strain-rate, diastolic E/CSR and E/LSR ratios, and deceleration time were identified as robust biomarkers that could potentially be applied to future pre-clinical drug studies.
Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition
01-01-1999 05-31-2017
We explore the tree of mammalian mtDNA sequences, using particularly the LogDet transform on amino acid sequences, the distance Hadamard transform, and the Closest Tree selection criterion. The amino acid composition of different species show significant differences, even within mammals. After compensating for these differences, nearest-neighbor bootstrap results suggest that the tree is locally stable, though a few groups show slightly greater rearrangements when a large proportion of the constant sites are removed. Many parts of the trees we obtain agree with those on published protein ML trees. Interesting results include a preference for rodent monophyly. The detection of a few alternative signals to those on the optimal tree were obtained using the distance Hadamard transform (with results expressed as a Lento plot). One rearrangement suggested was the interchange of the position of primates and rodents on the optimal tree. The basic stability of the tree, combined with two calibration points (whale/cow and horse/rhinoceros), together with a distant secondary calibration from the mammal/bird divergence, allows inferences of the times of divergence of putative clades. Allowing for sampling variances due to finite sequence length, most major divergences amongst lineages leading to modern orders, appear to occur well before the Cretaceous/Tertiary (K/T) boundary. Implications arising from these early divergences are discussed, particularly the possibility of competition between the small dinosaurs and the new mammal clades.
Data from: Pervasive early 21st-century vegetation changes across Danish semi-natural ecosystems – more losers than winners and a shift towards competitive, tall-growing species
11-12-2014 02-05-2015
1. Semi-natural open habitats in northwestern Europe are highly prioritized for conservation and optimization of management planning is essential for continued protection of their diversity. We evaluate whether current management practices, which consist mainly of summer grazing by livestock, are sufficient to maintain plant species composition in a stable state across semi-natural areas in Denmark, or if shifts in functional composition are taking place. Further, we investigate important drivers of any on-going changes through trait differences between winner and loser species. 2. Using a dataset of 6513 annually inventoried (2004–2010) vegetation plots from 202 semi-natural NATURA 2000 protected areas, we assessed changes in cover of all plant species and, using boosted regression trees, whether winners and losers differ in regard to autecological characteristics and traits. 3. There were consistent changes in cover for 123 out of 603 species across the six-year study period, with more species losing than winning (78 versus 45). Winner and loser species were strongly differentiated by competition-related traits, but traits related to soil nutrients and soil moisture also had some importance. Generally, our results indicate a trend towards a species composition consisting of taller and more competitive species. 4. Synthesis and applications. Despite conservation actions in order to maintain so-called favourable conservation status, vegetation in NATURA 2000 protected areas is still undergoing compositional changes. Overall, autecological characteristics and trait differences between winners and losers match expectations given the contemporary anthropogenic pressures, especially with reduced livestock grazing. Atmospheric nitrogen deposition and increased soil moisture due to reduced drainage might also be involved in observed changes. Current management (i.e. summer grazing by livestock) is insufficient to preserve the diversity of less-competitive, low-statured and stress-tolerant herbaceous species, potentially leading to species losses. Such patterns can thus be expected across semi-natural ecosystems in northwestern Europe and other places where traditional land use (i.e. previous widespread extensive livestock grazing) have been replaced with various degrees of conservation management. A greater focus on returning large grazing herbivores to conservation areas is recommended for the protection of plant species diversity and to counteract on-going changes.