GenVisR: Genomic Visualizations in R Skidmore, Zachary L; Wagner, Alex H; Lesurf, Robert ...
Bioinformatics (Oxford, England),
10/2016, Volume:
32, Issue:
19
Journal Article
Peer reviewed
Open access
Visualizing and summarizing data from genomic studies continues to be a challenge. Here, we introduce the GenVisR package to addresses this challenge by providing highly customizable, ...publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and Bioconductor.
GenVisR is an R package available via Bioconductor (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) and the Bioconductor support website.
obigriffith@wustl.edu or mgriffit@wustl.edu
Supplementary data are available at Bioinformatics online.
Fully cured epoxy resins are typically brittle materials but according to recent research, cured epoxy fibers exhibit a singular mechanical behavior, including yielding followed by large deformation, ...and very high strength, toughness, and modulus. These properties appear to intensify as the fiber diameter decreases. The microstructural origin of this unusual behavior has not been fully determined. Here we use confocal polarized Raman spectroscopy to monitor the apparent molecular reorientation induced by plastic deformation of epoxy fibers, both qualitatively and quantitatively. Based on these and previous X-ray diffraction measurements, a likely molecular explanation for the extreme mechanical behavior of micro-sized epoxy fibers is proposed.
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•Micro-sized epoxy fibers show extensive necking under tensile stress.•Polarized micro-Raman reveals molecular orientation in the necked regions.•Molecular orientation is not observed outside the necked region of the fibers.
Gilbert’s syndrome (GS) is characterized by a benign, mildly elevated bilirubin concentration in the blood. Recent reports show clear protection from cardiovascular disease in this population. ...Protection of lipids, proteins and other macromolecules from oxidation by bilirubin represents the most commonly accepted mechanism contributing to protection in this group. However, a recent meta-analysis estimated that bilirubin only accounts for ∼34% of the cardioprotective effects within analysed studies. To reveal the additional contributing variables we have explored circulating cholesterol and triacylglycerol concentrations, which appear to be decreased in hyperbilirubinemic individuals/animals, and are accompanied by lower body mass index in highly powered studies. These results suggest that bilirubin could be responsible for the development of a lean and hypolipidemic state in GS. Here we also discuss the possible contributing mechanisms that might reduce circulating cholesterol and triacylglycerol concentrations in individuals with syndromes affecting bilirubin metabolism/excretion, which we hope will stimulate future research in the area. In summary, this article is the first review of lipid status in animal and human studies of hyperbilirubinemia and explores possible mechanisms that could contribute to lowering circulating lipid parameters and further explain cardiovascular protection in Gilbert’s syndrome.
The multiscale structure of biomaterials enables their exceptional mechanical robustness, yet the impact of each constituent at their relevant length scale remains elusive. We used SAXD analysis to ...expose the intact chitin-fiber architecture within the exoskeleton on a scorpion's claw, revealing varying orientations, including Bouligand and unidirectional regions different from other arthropod species. We uncovered the contribution of individual components' constituent behavior to its mechanical properties from the micro- to the nanoscale. At the microscale, in-situ micromechanical experiments were used to determine site-specific stiffness, strength, and failure of the biocomposite due to fiber orientation, while metal-crosslinking of proteins is characterized via fluorescence maps. At the constituent level, combined with FEA simulations, we uncovered the behavior of fiber-matrix deformation with fiber diameter <53.7 nm and protein modulus in the range 1.4-11 MPa. The unveiled microstructure-mechanics relationship sheds light on the evolved structural functionalities and constituents' interactions within the scorpion cuticle. STATEMENT OF SIGNIFICANCE: The pincer exoskeleton is a fundamental part of the scorpion's body due to its multifunctionality. Precise structural and compositional analysis within the hierarchy is paramount to understand the fundamentals of the mechanical properties of the composite exoskeleton. Here, we expose the intact chitin-fiber architecture of the pincer exoskeleton using nondestructive analysis. In-situ mechanical characterization was performed at nanometer levels within the exoskeleton hierarchy, which complemented with simulations, uncovered the elastic modulus of the protein matrix. Our findings confirm the presence and distribution of metal ions and their role as reinforcements in the protein matrix via ligand coordinate bonds. In future work, these findings can be of great potential to inspire the design of composite materials.
Effective chronic illness interventions generally rely on multidisciplinary care teams. The participation of medical specialists in consultative and educational roles outside conventional referrals ...may contribute to better outcomes.
Launch-vehicle primary structures like cylindrical shells are increasingly being built as monolithic composite and sandwich composite shells. These imperfection sensitive shells are subjected to ...axial compression due to the weight of the upper structural elements and tend to buckle under axial compression. In the case of composite shells the buckling load and imperfection sensitivity depend on the laminate stacking sequence.
Within this paper multi-objective optimizations for the laminate stacking sequence of composite cylinder under axial compression are performed. The optimization is based on different geometric imperfection types and a brute force approach for three different ply angles. Decision tree-based machine learning is applied to derive general design recommendations which lead to maximum buckling load and a minimum imperfection sensitivity.
The design recommendation are based on the relative membrane, bending, in-plane shear and twisting stiffnesses. Several optimal laminate stacking sequences are generated and compared with similar laminate configurations from literature. The results show that the design recommendations of this article lead to high-performance cylinders which outperform comparable composite shells considerably. The results of this article may be the basis for future lightweight design of sandwich and monolithic composite cylinders of modern launch-vehicle primary structures.
Hfq, a protein required for small RNA (sRNA)-mediated regulation in bacteria, binds RNA with low-nanomolar K(d) values and long half-lives of complexes (>100 min). This cannot be reconciled with the ...1- 2-min response time of regulation in vivo. We show that RNAs displace each other on Hfq on a short time scale by RNA concentration-driven (active) cycling. Already at submicromolar concentrations of competitor RNA, half-lives of RNA-Hfq complexes are ≈1 min. We propose that competitor RNA associates transiently with RNA-Hfq complexes, RNAs exchange binding sites, and one of the RNAs eventually dissociates. This solves the "strong binding-high turnover" paradox and permits efficient use of the Hfq pool.
Large databases of high-resolution structural MR images are being assembled to quantitatively examine the relationships between brain anatomy, disease progression, treatment regimens, and genetic ...influences upon brain structure. Quantifying brain structures in such large databases cannot be practically accomplished by expert neuroanatomists using hand-tracing. Rather, this research will depend upon automated methods that reliably and accurately segment and quantify dozens of brain regions. At present, there is little guidance available to help clinical research groups in choosing such tools. Thus, our goal was to compare the performance of two popular and fully automated tools, FSL/FIRST and FreeSurfer, to expert hand tracing in the measurement of the hippocampus and amygdala. Volumes derived from each automated measurement were compared to hand tracing for percent volume overlap, percent volume difference, across-sample correlation, and 3-D group-level shape analysis. In addition, sample size estimates for conducting between-group studies were computed for a range of effect sizes. Compared to hand tracing, hippocampal measurements with FreeSurfer exhibited greater volume overlap, smaller volume difference, and higher correlation than FIRST, and sample size estimates with FreeSurfer were closer to hand tracing. Amygdala measurement with FreeSurfer was also more highly correlated to hand tracing than FIRST, but exhibited a greater volume difference than FIRST. Both techniques had comparable volume overlap and similar sample size estimates. Compared to hand tracing, a 3-D shape analysis of the hippocampus showed FreeSurfer was more accurate than FIRST, particularly in the head and tail. However, FIRST more accurately represented the amygdala shape than FreeSurfer, which inflated its anterior and posterior surfaces.
The turtle carapace, the top dorsal part of the shell, is a remarkable multi-scale dermal armor that has evolved to withstand various types of high-stress events encountered in nature. This ...keratin-covered boney exoskeleton exhibits a number of structural motifs, including alternating rigid and flexible components, layering and functionally graded elements, designed to protect the reptile during predatory attacks, and smashing events. Here we review the multi-scale structural hierarchy of the turtle carapace and its corresponding mechanical properties. We show how the microscopic features of the carapace govern its various macroscopic mechanical responses relevant to protective functioning, including dynamic (impact and cyclic) compression and bending loading situations. In addition, the effect of hydration, a crucial factor for proper physiological-mechanical behavior of biological materials, is illustrated throughout. We also discuss carapace-inspired designs that could be advantageous over the traditional strategies adopted in impact-resistant materials, and could bring new mechanistic insights.
Summary
Spatial autocorrelation jeopardizes the validity of statistical inference, for example correlation and regression analysis. Restricted randomization methods can account for the effect of ...spatial autocorrelation in the observed data by building it into an empirical null model for hypothesis testing. This can be achieved, for example, based on conditional simulation, which fits a highly parameterized geostatistical model to the observed spatial structure, or, for data observed on a regular transect or grid, with Fourier spectral randomization methods that can flexibly model spatial structure at any scale. This study uses Moran eigenvector maps to extend spectral randomization to irregularly spaced samples.
We present different algorithms to perform restricted randomization to suit different types of research questions: individual randomization of each variable, joint randomization of a group of variables while keeping within‐group correlations fixed, and randomization with a fixed correlation between original data and randomized replicates (e.g. as input for simulation studies). The performance of the proposed Moran spectral randomization methods for regularly and irregularly spaced samples is assessed with correlation analysis of simulated data.
Moran spectral randomization closely matched the spatial structure of original simulated data sets, with identical or nearly identical Moran's I values and power spectra, depending on the algorithm. In correlation analysis of two spatially autocorrelated variables, Moran spectral randomization produced correct type I error rates for stationary spatial data, even for very small and highly irregular samples, but was sensitive to linear trend. When one or both variables lacked spatial structure, Moran spectral randomization tests were more conservative than correlation t‐tests.
The proposed Moran spectral randomization method requires a minimum of parameterization and is able to address multivariate data with spatial structure at multiple scales, with the option of controlling levels of correlation with the original data. It can provide technically unlimited numbers of randomizations even for small samples while closely maintaining the spatial characteristics of uni‐ or multivariate data at all spatial scales. The method is applicable for correlation analysis of stationary, autocorrelated spatial or temporal series. Further research should assess whether the method can be extended to multiple regression analysis.
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