• European Marine Science
• 2018-2022close
• Research data close
• Other research products close
• CA close

The tumor suppressor p53 regulates various stress responses via increasing its cellular levels. The lowest p53 levels occur in unstressed cells; however, the impact of these low levels on cell integrity remains unclear. To address the impact, we used empirical single-cell tracking of p53-expressing and silenced cells, and developed a fate-simulation algorithm. Here we show that p53-silenced cells underwent more frequent cell death and cell fusion, which further induced multipolar cell division to generate aneuploid progeny. Those results suggest that the low levels of p53 in unstressed cells indeed have a role to maintain the integrity of a cell population. Results of a cell-fate simulation that provides a flexible and dynamic virtual culture space confirmed that these aneuploid progeny could propagate. However, p53-silenced cells were unable to propagate in a virtual cell population that was mainly comprised of p53-expressing cells, supporting the notion that p53 acts as a tumor suppressor. In contrast, when DNA damage responses were repeatedly induced in 53-expressed cells, p53-silenced cells became the major cell population, as the growth of p53-expressed cells was more tightly suppressed by the response than that of p53-silenced cells. In this context, the p53-mediated damage response that is supposed to suppress tumor formation has a pro-malignant function. The cellular microenvironment could thus be a major factor to determine the fate of cancer cells and the fate-simulation algorithm can be used to reveal the fate. 

An efficient technique is presented to infer space plasma density and satellite potentials from Langmuir probe measurements, using multivariate radial basis function (RBF) regression. This inference technique goes beyond analytic approaches which have been developed over nearly a century, and which remain in use in most lab and space plasma experiments. The method is assessed by applying it to synthetic data sets constructed with three-dimensional particle in cell (PIC) simulations of fixed-bias needle Langmuir probes proposed by Jacobsen, to determine a plasma parameter, independently of the temperature. Our approach follows machine learning techniques, whereby models are constructed on training data sets consisting of the simulated collected currents as a function of voltage, corresponding to known physical parameters such as plasma density and temperature, and satellite potential. Compared to standard approaches used in RBF regression, our approach proves to be particularly efficient when working with large training sets, by implementing an evolutive selection of optimal centers. THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE

We present libami, a lightweight implementation of algorithmic Matsubara integration (AMI) written in C++. AMI is a tool for analytically resolving the sequence of nested Matsubara integrals that arise in virtually all Feynman perturbative expansions. THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE

Electric charging is one of the essential aerosol dynamic mechanisms and is harnessed for detection, capture and control of ultrafine aerosol particles in a range of devices. For simplicity, charging and transport mechanisms are commonly modelled with zero spatial dimensions (0-D) and averaged properties such as mean charge or mean particle diameter. These models often neglect localised effects of the flow distribution, diffusion, discrete charge states, and particle polydispersity, often proving inadequate to explain experimental data. This work aims to provide an open-source three-dimensional (3-D) aerosol charging and transport model including bipolar and unipolar diffusion charging, and photoelectric charging algorithms for use in detailed design and analyses of aerosol systems. The computational model consists of more than 200 particle transport equations for discrete charge states and polydisperse sizes coupled with ion conservation equations in the framework of OpenFOAM, an open-source computational fluid dynamics platform. Three test cases are introduced to verify implementation of three charging models by comparison with published literature: bipolar and unipolar diffusion charging, and photoelectric charging. Tutorial cases, which model three distinct aerosol sensors, are described and demonstrate the capabilities of the 3-D aerosol charging and transport models within the predetermined flow field. The aerosolChargingFoam code is available at https://openaerosol.sourceforge.io for widespread use and can be further modified under the GNU general public licence. THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE

Confocal image data sets and segmented meshes from various plant organs including the Arabidopsis root, flower, gynoecium, meristem, embryo and ovule. The data sets are used to demonstrate features available in MorphoGraphX software (www.MorphoGraphX.org), and how to use positional information to add spatial context to quantitative cellular data. Also included are longform video tutorials, and source code for the MorphoGraphX software. Confocal files are provided in original microscope formats, and/or as tifs exported from Fiji. Meshes extracted from the data are in .mgxm (MorphoGraphX mesh) format. Source code for MorphoGraphX is included, and has been compiled and tested on Ubuntu 20.04 with Cuda 11.4. Tutorials are in standard mp4 format. The data was collected using confocal microscopy on fixed or live imaged samples. Please see the publication for detailed methods for each dataset.

phenotypic dataDescription: Phenotypic measurement and covariates used for animal model and for estimation of the genetic covariance of trait with fitness. The population of bighorn sheep (Ovis canadensis) is located at Ram Moutnain, Alberta, Canada(52°8’N, 115°8’W, elevation 1082 to 2173 m). Measurements where taken between 1973 and 2013. Animals aged 13 and older where grouped for analysis due to small sample size. Animals translocated from the Cadomin population where excluded. NA is used for missing values Columns: ID: unique identifier for each animal. yr: year of measurement. age: age at measurement. sex: sex of animal(1=male, 0=female). cohort: year of birth. hlM: horn length of males aged 2 to 5 in cm adjusted to 15 September. hlF: horn length of females aged 2 to 5 in cm adjusted to 15 September. Avhb114M: horn base of males aged 2 to 5 in cm adjusted to 15 September. Avhb114F: horn base of females in cm adjusted to 15 September. relLongM: relative longevity of males. Longevity divided by the mean longevity of males of the same cohort. relLongF: relative longevity of females. Longevity divided by the mean longevity of females of the same cohort.data.csvpedigreeDescription: Pedigree of the population of bighorn sheep (Ovis canadensis), located at Ram Moutnain, Alberta, Canada(52°8’N, 115°8’W, elevation 1082 to 2173 m). NA is used for missing values Columns: Id: id of the animal dam: id of the dam sire: id of the sire The potential for selective harvests to induce rapid evolutionary change is an important question for conservation and evolutionary biology, with numerous biological, social and economic implications. We analyze 39 years of phenotypic data on horn size in bighorn sheep (Ovis canadensis) subject to intense trophy hunting for 23 years, after which harvests nearly ceased. Our analyses revealed a significant decline in genetic value for horn length of rams, consistent with an evolutionary response to artificial selection on this trait. The probability that the observed change in male horn length was due solely to drift is 9.9%. Female horn length and male horn base, traits genetically correlated to the trait under selection, showed weak declining trends. There was no temporal trend in genetic value for female horn base circumference, a trait not directly targeted by selective hunting and not genetically correlated with male horn length. The decline in genetic value for male horn length stopped, but was not reversed, when hunting pressure was drastically reduced. Our analysis provides support for the contention that selective hunting led to a reduction in horn length through evolutionary change. It also confirms that after artificial selection stops, recovery through natural selection is slow.

Among polar bears (Ursus maritimus), fitness is dependent on body size through males' abilities to win mates, females' abilities to provide for their young, and all bears' abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449-individual pedigree and an array of 5433 single-nucleotide polymorphisms (SNPs) to provide the first quantitative genetics study of polar bears. We used animal models to estimate heritability (h2) among polar bears handled between 1966 and 2011, obtaining h2 estimates of 0.34-0.48 for strictly skeletal traits and 0.18 for axillary girth (which is also dependent on fatness). We genotyped 859 individuals with the SNP array to test for marker-trait association and combined p-values over genetic pathways using gene-set analysis. Variation in all traits appeared to be polygenic, but we detected one region of moderately large effect size in body length near a putative noncoding RNA in an unannotated region of the genome. Gene-set analysis suggested that variation in body length was associated with genes in the regulatory cascade of cyclin expression, which has previously been associated with body size in mice. A greater understanding of the genetic architecture of body size variation will be valuable in understanding the potential for adaptation in polar bear populations challenged by climate change. Western Hudson Bay pedigree (TXT)Tab-delimited text file formatted for use in R (i.e., unknown parents are indicated with NA.) For use in ASReml, the data should be reformatted as columns id, sire, dam with "0" used to indicate unknown parents. For details of the pedigree, see doi: 10.1007/s00300-015-1871-0pedigree.txtSNP genotypes (ZIP)Raw SNP genotypes in PLINK format (i.e., .ped & .map file) before quality-control filtering.genotypes.zipLOCO RepeatABEL R scriptImplements a leave-one-chromosome-out GWAS using RepeatABELrepeatabel_loco.rRepeatABEL GWAS R scriptConducts a vanilla GWAS using RepeatABELrepeatabel.rField DataPhenotypes for adult polar bears used for heritability calculations and GWASphenotypes.csv

We have developed Procrustes, a free, open-source, cross-platform, and user-friendly Python library implementing a wide-range of algorithmic solutions to Procrustes problems. The goal of Procrustes analysis is to find an optimal transformation that makes two matrices as close as possible to each other, where the matrices are often (but need not always be) a list of multidimensional points specifying the systems of interest. We demonstrate the functionality of the package through various examples, mostly from cheminformatics. However, Procrustes analysis has broad applicability including image recognition, signal processing, data science, machine learning, computational biology, chemistry, and physics. Our library includes methods for one-sided Procrustes problems using orthogonal, rotational, symmetric, and permutation transformation matrices, as well as two-sided Procrustes problems using orthogonal and permutation transformation matrices. For the two-sided permutation Procrustes problem, we include heuristic algorithms along with a rigorous (but slow) method based on softassign. In addition, we include a general formulation of the Procrustes problem. The Procrustes source code and documentation is hosted on GitHub (https://github.com/theochem/procrustes). THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE