Metagenomics Data Visualization Using R Coleman, Alex; Bose, Anupam; Mitra, Suparna
Methods in molecular biology (Clifton, N.J.),
2023, Letnik:
2649
Journal Article
Communicating key finds is a crucial part of the research process. Data visualization is the field of graphically representing data to help communicate key findings. Building on previous chapters ...around data manipulating using the R programming language this, chapter will explore how to use R to plot data and generate high-quality graphics. It will cover plotting using the base R plotting functionality and introduce the famous ggplot2 package 2 that is widely used for data visualization in R. After this general introduction to data visualization tools, the chapter will explore more specific data visualization techniques for metagenomics data and their use cases using these basic packages.
3D Printing promises to produce complex biomedical devices according to computer design using patient-specific anatomical data. Since its initial use as pre-surgical visualization models and tooling ...molds, 3D Printing has slowly evolved to create one-of-a-kind devices, implants, scaffolds for tissue engineering, diagnostic platforms, and drug delivery systems. Fueled by the recent explosion in public interest and access to affordable printers, there is renewed interest to combine stem cells with custom 3D scaffolds for personalized regenerative medicine. Before 3D Printing can be used routinely for the regeneration of complex tissues (e.g. bone, cartilage, muscles, vessels, nerves in the craniomaxillofacial complex), and complex organs with intricate 3D microarchitecture (e.g. liver, lymphoid organs), several technological limitations must be addressed. In this review, the major materials and technology advances within the last five years for each of the common 3D Printing technologies (Three Dimensional Printing, Fused Deposition Modeling, Selective Laser Sintering, Stereolithography, and 3D Plotting/Direct-Write/Bioprinting) are described. Examples are highlighted to illustrate progress of each technology in tissue engineering, and key limitations are identified to motivate future research and advance this fascinating field of advanced manufacturing.
Due to the difficulty in fabricating bioceramic scaffolds with smaller pore sizes by the current 3D printing technique, the effect of smaller pore sizes (below 400 µm) of 3D printed bioceramic ...scaffolds on the bone regeneration and biomechanical behavior is never studied. Herein beta-tricalcium phosphate (β-TCP) scaffolds with interconnected smaller pores of three different sizes (100, 250, and 400 µm) are fabricated by 3D plotting. The resultant scaffolds are then implanted into rat critical-sized calvarial defects without any seeded cells. A custom-designed device is developed to investigate the biomechanical properties of the scaffolds after surgical implantation for 4, 8, and 12 weeks. The scaffolds with the 100 µm pore size are found to present the highest maximum load and stiffness, comparable to those of the autogenous bone, after being implanted for 12 weeks. Micro-computed tomography (micro-CT) and histological analysis further indicate that the scaffolds with the 100 µm pore size achieve the highest percentage of new bone ingrowth, which correlates to their best in vivo biomechanical properties. This study demonstrates that tailoring the pore size of β-TCP scaffolds to a smaller range by 3D-plotting can be a facile and efficient approach to enhanced bone regeneration and biomechanical behaviors in bone repair.
Hydrogen-fueled internal combustion engines (H2ICEs) have been the topic of research for many decades, and contemporary reviews have surveyed the relevant literature. Because of a number of ...relatively large R&D projects that have been ongoing recently, much progress has been made that is worth reporting. Specifically, this paper reviews the advancements made in plotting the possibilities offered by direct injection of hydrogen, in-cylinder heat transfer, modeling and combustion strategies (on an engine as well as vehicle level). These efforts have resulted in impressive efficiency numbers, both at peak and part load operation, while keeping emissions far below regulatory limits and reaching satisfactory specific power outputs. New demonstration vehicles have been put on the road showing the relatively low barriers (on a vehicle level) to introduce hydrogen engined transportation and these are briefly described. The paper discusses the merits of H2ICEs but also what makes them potentially unfit as a realistic alternative. Finally, the paper concludes with the main areas of research that require further efforts.
•This paper reviews the recent work on hydrogen-fueled internal combustion engines.•The pros and cons of hydrogen engines are discussed.•Major R&D projects are enlisted, with a discussion of the most important results.•These cover direct injection, heat transfer, modeling and combustion strategies.
To combat the emergence of drug-resistant bacteria, a locally isolated bacteriophage (HZJ) targeting H5α Escherichia coli was used as an antibacterial agent to make wound dressing samples in this ...study. The phages were physically embedded within an alginate hydrogel sample so that they could later be released with their tails being free during the infection process, which preserves their lytic activity. The HZJ phage isolated in the study have a 20 min latent period and are stable between pH 6 and pH 9 and at temperatures below 45 °C. The addition of phage to an E. coli culture suppressed over 99% of bacterial growth in 2-h (p < 0.001). Phage-embedded hydrogel fibers were used to create porous wound dressing material using three-dimensional (3D) printing. The majority of phage lytic activity (85%–90%) was preserved after encapsulation. After they were embedded in samples, HZJ lysed 57% to 67% of bacteria (p < 0.001) within 2 h and the antibacterial effects lasted at least 24 h. The small amount of phage released in 2 h was able to quickly replicate and effectively lysed the majority of the bacterial hosts. Phage-embedded alginate samples released 10% of its incorporated phage particles in 24 h. The SEM micrographs show that, compared to phage-free samples, fewer E.coli cells were observed on phage-embedded samples 2 h after bacteria were exposed to the samples. The phage-embedded sample was not cytotoxic to L929 cells. The presence of HZJ in alginate hydrogel promoted cell growth (p < 0.01) and adhesion to the samples. Further, the existence of phage did not alter the tensile strength and modulus of samples (p > 0.05). An antibacterial dressing capable of slowly releasing lytic phages and effectively suppressing bacterial growth for up to 24 h was produced in this study. This model represents an attractive means to reduce use of antibiotics and other additives in conventional dressings.
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•Bacteriophage-embedded hydrogel wound dressing successfully created by 3D plotting.•Purified phages lysed 99% bacteria in 2 h and stable under physiological conditions.•0.03% bacteriophages released from dressing reduced 57% of bacteria in 2 h.•Lytic phages released from dressing exhibited antibacterial activity for up to 24 h.•Phage-embedded dressings are compatible with fibroblast cells.
The inclusion of dynamical and static electron correlation (SEC) is mandatory for accurate quantum chemistry (QC). SEC is particularly difficult to calculate and hence a qualitative understanding is ...important to judge the applicability of approximate QC methods. Existing scalar SEC diagnostics, however, lack the important information where the SEC effects occur in a molecule. We introduce an analysis tool based on a fractional occupation number weighted electron density (ρFOD) that is plotted in 3D for a pre‐defined contour surface value. The scalar field is obtained by finite‐temperature DFT calculations with pre‐defined electronic temperature (e.g. TPSS at 5000 K). FOD plots only show the contribution of the “hot” (strongly correlated) electrons. We discuss illustrative plots for a broad range of chemical systems from small molecules to large conjugated molecules with polyradicaloid character. Spatial integration yields a single number which can be used to globally quantify SEC.
Hot FOD: The inclusion of static electron correlation (SEC) is mandatory for accurate quantum chemistry yet is particularly difficult to calculate. An analysis tool is developed based on a fractional occupation number weighted electron density (ρFOD) that is plotted as an isosurface and shows the “hot” (strongly correlated) electrons. Spatial integration of ρFOD yields a single number which can be used to globally quantify SEC.
Abstract Objectives Comparison of estimation of the two-parameter Weibull distribution by two least squares (LS) methods with interchanged axes. Investigation of the influence of plotting positions ...and sample size. Derivation of 95% confidence intervals (95%CI) for Weibull parameters applicable in the context of LS estimation. Preparation of a free available Excel template for computation of point estimates and 95%CI for Weibull modulus ( m ) and characteristic strength ( s ). Methods Monte Carlo simulation covering a wide range of Weibull parameters and sample sizes. Mathematical derivation of formulae for computation of 95%CI according to a Menon-type approach for both m and s . Empirical proof that the practically observed coverage agrees with the nominal one of 95%. Results Relative and absolute performance of LS estimators depended on sample size, plotting positions and parameter to be estimated. For most situations they outperformed the corresponding Maximum Likelihood (ML) estimator in terms of bias, while precision was almost the same. Naïve Wald-type 95%CI based on standard errors of LS regression coefficients did not reach targeted coverage. An easy-to-apply alternative based on asymptotic standard errors (Menon 95%CI) resulted in excellent coverage. Conclusion Accuracy of the LS methods for Weibull modulus and characteristic strength essentially depend on plotting position and sample size. Large sample sizes ( n ≥ 30) support a credible Weibull parameters estimation. An important complement of the point estimates of Weibull parameters is provided by the Menon 95%CI. A free available Excel template considerably facilitating computation of point and interval estimates of Weibull parameters is provided.
In the present paper we analyze the diffusion coefficients, D, of the component elements, measured recently in CoCrFeMnNi high-entropy alloy. Our analysis, based on the use of the correct form of the ...well-known semi-empirical rules (law of corresponding states) i.e. plotting the logarithm of the normalized (dimensionless) value of D vs. the reduced temperature, confirms the sluggish character of the diffusion as compared to the pure reference metals, but this behavior can mostly be attributed to a more or less temperature independent factor in the diffusion coefficients i.e. to correlation effects rather than the higher activation energies.
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•Diffusion data analysis using the correct form of the law of corresponding states.•Reduced activation energies of high-entropy alloys and fcc metals are almost equal.•Correlation effects rather than high activation energies explain sluggish diffusion.
Abstract
A concrete justification unavailability of the roughly estimated warranty claim quantity is leading to also inability to understand defect trend behavior and its effect upcoming warranty ...claim quantity. This is where an equation model is derived by considering the previous actual warranty data, to represent warranty claim defect quantity impact. Taking into consideration, identified parameters which link with pricing and cost, it also includes the observation and monitoring of warranty trend from the existing actual warranty data, by plotting cumulative defect quantity over Vehicle Line-off Date, as well as plotting cumulative defect quantity over Vehicle Submission Date. Multiple Linear Regression is deployed to define the best Multiple Regression Equation. Predictors, response and predictors’ validations defined by using normality and probability test. The successfully developed equation model, takes into account the existing warranty data and trend, As a result, the equation model managed to provide forecasted warranty claim quantity, based on a complete 36-month warranty period cycle, which has a significant impact on a reliable and convincing figure – a key factor in warranty budgeting and accrual task.
We evaluate the third- and fourth-order baryon, charge and strangeness susceptibilities near a chiral critical point using the Nambu-Jona-Lasinio model. We identify robust qualitative behaviors of ...the susceptibilities along hypothetical freeze-out lines that agree with previous model studies. Quantitatively, baryon number fluctuations are the largest in magnitude and thus offer the strongest signal when freeze-out occurs farther away from a critical point. Charge and strangeness susceptibilities also diverge at a critical point, but the area where the divergence dominates is smaller, meaning freeze-out must occur closer to a critical point for a signal to be visible in these observables. In the case of strangeness, this is attributable to the relatively large strange-quark mass. Plotting the third- and fourth-order susceptibilities against each other along the freeze-out line exhibits clearly their nonmontonicity and robust features.
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