Coordinate Plots Research Articles

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

DNA-based identification methods, such as DNA metabarcoding, are increasingly used as biodiversity assessment tools in research and environmental management. Although powerful analysis software exists to process raw data, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, the need for easy-to-use, graphical user interface (GUI) software to analyze and visualize DNA metabarcoding data is growing. Here we present TaxonTableTools (TTT), a new platform-independent GUI that aims to fill this gap by providing simple, reproducible analysis and visualization workflows. The input format of TTT is a so-called "TaXon table". This data format can easily be generated within TTT from two common file formats that can be obtained using various published DNA metabarcoding pipelines: a read table and a taxonomy table. TTT offers a wide range of processing, filtering and analysis modules. The user can analyze and visualize basic statistics, such as read proportion per taxon, as well as more sophisticated visualizations such as interactive Krona charts for taxonomic data exploration, or complex parallel category diagrams to assess species distribution patterns. Venn diagrams can be calculated to compare taxon overlap among replicates, samples, or analysis methods. Various ecological analyses can be produced directly, including alpha or beta diversity estimates, rarefaction analyses, and principal coordinate or non-metric multidimensional scaling plots. The taxonomy of a data set can be validated via the Global Biodiversity Information Facility (GBIF) API to check for synonyms and spelling mistakes. Furthermore, geographical distribution data can be automatically downloaded from GBIF. Additionally, TTT offers a conversion tool for DNA metabarcoding data into formats required for traditional, taxonomy-based analyses performed by regulatory bioassessment programs. Beyond that, TTT is able to produce fully interactive html-based graphics that can be analyzed in any web browser. The software comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) or the Python package index (https://pypi.org/project/taxontabletools/).

Characterization of Caecal Microbiota in Broilers that Differ in Genetic Strain, Nutrition, and Development of Woody Breast

ObjectivesWoody breast (WB) meat from broilers has undesirable textural characteristics, including, crunchiness and stickiness. Genetic, nutritional, and environmental factors are associated with the mechanism of WB development. A diverse microbiota plays an important role on the growth performance and health of the host, and greater than 900 species of bacteria have been isolated in the gastrointestinal tract of chicken. However, minimal information is known about the microbiota in the guts of broilers that yield WB meat. Therefore, the objective of this research was to characterize and compare the bacterial diversity of caecal microbiota in broilers with normal and woody breast fillets.Materials and MethodsThe Institutional Animal Care and Use Committee of Mississippi State University (IACUC-16–542) reviewed and approved all protocols. One-day-old mixed sex broilers from two strains (A2 and B2) were raised in 32 pens in a chicken house. Birds of each strain were randomly assigned to 16 pens (15 birds per pen) and 8 pens were fed a control diet and 8 pens were fed an amino acid reduced diet (digestible lysine, total sulfur amino acids, and threonine reduced by 20% as compared to the control diet). After 8 wk of growth, 4 male broilers with normal breast (1 chick per pen) and 4 male broilers with WB (1 chick per pen) determined by palpation were selected for each treatment (breed × diet). The cecum samples were collected after birds were euthanized and bled. DNA was extracted and amplified using universal primers that target the V3∼4 regions of bacterial 16S rRNA for sequencing in Illumina MiSeq. Raw sequences were processed, and the quality was filtered using the default parameters of Quantitative Insights into Microbial Ecology (QIIME 2). Differences between species were assessed using the unpaired two-tailed Student t test assuming unequal variance at α = 0.05.ResultsData suggested that the most abundant phyla in all samples were Firmicutes, followed by Bacteroidetes and Proteobacteria. Accounting for both abundance and evenness of the species present in each sample (α diversity), results indicated that there was no difference (P > 0.05, pairwise Kruskal–Wallis test) in the diversity of gut microbiota between two phenotypes (normal vs. woody), two strains (A2 vs. B2) or two diets (control vs. reduced). However, principal coordinate analysis plots (β diversity) revealed that the samples were clustered based on the phenotype rather than by the strain or diet. These results revealed that the microbiota of each bird with normal breast was more similar to each other than the microbiota of birds with WB. Among all species (300–400) identified, no difference (P < 0.05) existed in bacterial abundance between the two genetic strains. However, 16 and 13 species were differentially abundant (P < 0.05) between normal and woody breast and between control and reduced diet treatments, respectively. In the ceca of WB birds Selenomonas bovis (12.6%) and Bacteroides plebeius (12.3%) were the top two predominant bacteria; however, the relative abundances of these two bacteria were only 5.1% and 1.2% in normal birds, respectively.ConclusionDifferences in the microbiome may be associated with the development of WB. Further studies are needed to investigate the potential mechanism and how to reduce broiler WB incidence by regulating their gut microbiota.

A many-objective optimization model for construction scheduling

In recent years, the number of stakeholders of construction projects has significantly increased; this has required the simultaneous achievement of competing objectives, such as reductions in the time, cost, resources, and environmental impact of a project, for example. In order to achieve a balance between these objectives, several multiple-objective construction scheduling models have been reported in the literature. However, several challenges have been encountered, due to the complexities of modelling and visualizing more than three objectives simultaneously. Some of these challenges are addressed in this work via the development of a many-objective scheduling model (MOSM) based on a non-dominated sorting genetic algorithm for the simultaneous optimization of four objectives: time, cost, resources and environmental impact. Coordinate plots are used to visualize the trade-offs made between all four of these objectives. A weighted sum is introduced that offers the project team the freedom to choose an optimal solution, depending on the specific priorities of the project, and the practical application of the model is demonstrated via a case study. Our MOSM allows the optimal outcome to be achieved in construction projects with multiple objectives.

An evaluation method for the polishing and abrasion resistance of aggregate

The polishing resistance performance and abrasion resistance performance of aggregate affect the long-term skid resistance and durability of the pavement, but there is still a lack of a comprehensive evaluation method to evaluate the aggregate performance in all aspects. This paper presents a study to develop a comprehensive evaluation method based on the assessments of four types of common aggregates in pavement engineering. The Wehner/Schulze polishing test and Micro-Deval abrasion test are used to respectively analyse the polishing resistance performance and abrasion resistance performance of the four aggregates. A comprehensive method for evaluating aggregate properties is proposed based on a laboratory test, the slope of the linear fitting line of the test results and the distribution of the results in the coordinate plot can reflect the performance of different aggregates, thus the coordinate plot is separated into four quadrants, aggregates falling into different quadrants are evaluated as good, fair and poor, respectively, so that to provide reference for aggregate screening or aggregate blending in pavement engineering.

P672 Does the ileocecal valve functionally separate ileal and right-sided colon microbiota compositions?

there is current debate about a causal relation between retinoid treatment and inflammatory bowel disease (IBD). Patients have claimed that they developed acute intestinal inflammation during isotretinoin treatment or to develop inflammatory bowel disease (IBD) weeks or even years after cessation of the medication. We have previously shown that isotretinoin treatment has no adverse effects in two mouse models of inflammatory bowel disease [1]. Since the gut microbiota can metabolize retinoids, we investigated whether administration of retinoids might change the gut microbiota composition in a way that is favorable for the development of IBD. Methods: Balb/c mice were treated with isotretinoin (30mg/kg bodyweight) or vehicle orally for 2 weeks and kept for further 4 weeks to study potential direct and long-term effects. Fecal samples were collected before treatment, directly after the treatment period and four weeks later for analysis of gut microbiota composition by 16S rRNA gene sequencing on the GS-Flx 454 platform. Sequencing data were analyzed with the software QIIME to determine OTUs, calculate the relative abundance for each group and time point and to general principal coordinate analysis plots. Results: Principle coordinate analysis showed no formation of clusters neither depending on treatment nor on time point of investigation indicating no fundamental differences between the gut microbiota composition of isotretinoin or vehicle treated animals or between the different time points studied. Some differences with regard to alpha and beta diversity between the different treatment groups as well as between the different time points studied were observed and are currently under further investigation. Conclusions: Preliminary results with QIIME showed no substantial differences between isotretinoin and vehicle treated animals indicating that isotretinoin treatment had no fundamental effect on the composition of the murine gut microbiota. We are currently investigating the variations in alpha and beta diversity that were observed between groups exposed to isotretinoin and vehicle, as well as between the different time points.

Relative retention analysis in HPLC: The correlation between incremental relationships

It was shown that, in the absence of specific intramolecular interactions, residual silanol groups of reversed-phase sorbents should not affect the linearity of plots in the coordinates used in the method of relative retention analysis for pairs of substances. The validity of the method proposed previously for analysis of the selectivity of separation of substances was supported experimentally (based on the analysis of retention of substituted benzoates). The possibility of the extension of incremental relationships to the system consisting of three different substances was justified.

On linear concentration dependences of K'm, V' and 1/νi enzyme kinetic parameters

The most frequently occurring incorrect uses of the plots of intercepts, slopes and other coordinates for the determination of constants of enzyme activation Ka and of nontrivial inhibition K(IIi), K(Vi), K(Ii), were analyzed. The correct plots are shown. Calculations of the K(Ii) and K(IIi) constants of nontrivial types of enzyme inhibition using the corrected plots of the intercepts are given.

Fully Developed Sliding of Rough Surfaces

Given the contact region between two bodies, the normal pressure distribution over the contact region, and the coefficient of friction, we seek to find all combinations of tangential forces and twisting moment (about the normal to the contact surface) for which fully developed sliding impends. As part of the solution we must determine the distribution of the surface tractions (shear stresses) and the location of the instantaneous center (IC) of the impending motion. New closed form solutions of the stated problem are found for circular contact patches with pressure distributions corresponding to (a): a flat stamp; and (b): elastic spheroids with Hertzian pressure distributions. For contact regions other than circular, no closed form solutions are known. We have developed numerical procedures to solve for arbitrary contact patches, with arbitrary distributions of normal pressure, and present carpet plots of tangential force components (Fx, Fy) and IC coordinates for the following cases: flat ellipsoidal stamps; ellipsoidal indenters (Hertzian pressure); and a non-Hertzian, nonelliptical contact of a rail and wheel. Level curves of twisting moment Mz versus tangential force components are provided. Given any two of the three quantities (Fx, Fy, Mz), the algorithms and the plots in this paper make it possible and convenient to find the remaining force or moment which will cause gross sliding to impend, for virtually arbitrary contact regions and arbitrary pressure distributions.

Classification of byzantine glass samples by principal component analysis

Nine samples of byzantine glass classified previously by cluster analysis are classified by principal component analysis (PCA). A visual inspection of plots in coordinates of the first two principal components gives essentially the same results as cluster analysis. In addition, PCA indicates relationships among the classification variables.

Three views of the annual phase map of the domestic cat,Felis catusL.

Abstract Longitudinal studies for a period of a year were conducted on five variables with eight normal adult male cats. The variables were adrenaline, noradrenaline, glucocorticoid hormones, body weight, and food intake. Body weight and food intake were determined once every two weeks for the period of a year, and the urinary content of adrenaline, noradrenaline and glucocorticoid hormones were determined once a month for the same period. The annual trend was viewed in three ways, by plotting the means, by a “cosinor‐like coordinate plot, and by a periodic regression technique. The results indicate that the periodic regression technique provided a good representation of the data in all cases, but the cosinor plot had limited applicability. In the special case when the annual sine curve accounted for all the trend, the cosinor and periodic regression technique are equivalent. Limitations of the cosinor representation involve the non‐sinusoidal shape of the data and the ubiquity of bimodal patterns, a ubi...

Colorimetric Performance of Non-Standard Television Receiver with Customer Adjustment

A method of comparing receivers on the basis of matching fleshtones is proposed. An algorithm for predicting the required chroma gain and phase adjustments to obtain this match is presented. An implementation of the algorithm on a personal proqrammable calculator is demonstrated, using five linked programs. Results of calculations for eight different receivers/monitors of interest are summarized in tables and coordinate plots. An extensive set of references on fleshtone reproduction is included.

A note on the static calibration of constant temperature hot wire anemometers

Uncertainties are shown to exist in the usual static methods for determining the sensitivity of hot wire anemometer systems to velocity fluctuations. These uncertainties arise from the erratic behaviour of the derivative of the curve which is obtained by attempting to linearize an imprecisely known function by the use of nonlinear coordinates. They apply equally to the 'electronic linearizer' method and the usual nonlinear coordinate calibration plots (for example plotting voltage squared against velocity to some power). These errors are additional to those already caused by possible inaccuracies in the data. Recently developed static methods have been tested but uncertainties still exist.

Stratigraphic Analysis of Diplogs: ABSTRACT

Recently, the diplog has been used to estimate stratigraphic conditions of the formations penetrated by a borehole. In particular, the diplog frequently can be utilized to predict the trend, direction of thickening, and movement of depositing currents in channel-and barrier-bar sandstones. Because of compaction and bifurcation, channel sands tend to be more complex and difficult to interpret using a diplog. However, barrier-bar sands commonly can be interpreted correctly from the diplog. Many thick sequences of fluvial sands do not exhibit channel-dip patterns. In some problems, the use of statistical analysis is useful. In many instances, the determination of the type of sand from a diplog in fluvial sequences will be difficult. Barrier-bar sands exhibit several different types of crossbedding depending on the relative importance of tides, longshore currents, and onshore winds in forming and modifying these deposits. The present interpretational techniques for this type of deposit use differential compaction of the overlying shales as a key to the analysis. The general interpretation of diplogs for stratigraphic information requires the use of statistical plots. The polar coordinate (modified Schmidt) and azimuth frequency plots especially are useful in the analysis of certain stratigraphic anomalies. End_of_Article - Last_Page 1832------------