Cross phenotype normalization of microarray data

The real-time system of the JT-60 has a cascade structure with the major and the minor control loops. The multi-variable feedback control is adopted in the major control loop in order to adjust non-linear effects which will appear in the high-/beta/region. By applying the concept of 'phase shift control' to the control program of the major control loop, a flexible tokamak discharge control is expected to be performed with taking account of machine protection.

The World Health Organization on March 11, 2020, declared Coronavirus Disease 2019 (Covid-19) a pandemic. Covid-19 is a disease caused by a new type of coronavirus, namely Sars-CoV-2, which affects the respiratory system. Until now, positive confirmed cases of Covid-19 in Indonesia are still occurring every day. This study aims to predict the addition of Covid-19 cases in Indonesia. The data is sourced from the public API page covid19.go.id in the form of an additional number of Covid-19 cases in Indonesia by 122 lines of data. Predictions are made using linear regression and polynomial regression methods as comparisons. Evaluation of the linear regression method obtains a value of R2 = 0.57, while the polynomial regression method obtains a value of R2 = 0.84. Based on these evaluations, the polynomial regression method yields better results than the linear regression method. The prediction of Covid-19 cases in Indonesia from January to March 2022 using the polynomial regression methods predicts that the addition of Covid-19 cases will rise again.

This article demonstrates the applicability of the algorithm of grid search to the determination of Mark–Houwink (MH) parameters. In the existing methods, the determination of MH parameters involves the use of linear or nonlinear regression. In the cases of using the algorithm of grid search to solve the linear regression problem for the determination of MH parameters, the values of the MH parameters obtained by the grid search method are the same as those obtained by the linear regression method, while in the cases when some nonlinear regression methods have to be used in the existing methods, using the algorithm of grid search can determine the parameters much more easily and accurately than using any nonlinear regression methods. In addition, the grid search method is very easy to understand and execute, and the accuracy of the results can be exhibited by the value of the least-square function. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 76: 481–487, 2000

BackgroundCross-validation techniques in genetic evaluations encounter limitations due to the unobservable nature of breeding values and the challenge of validating estimated breeding values (EBVs) against pre-corrected phenotypes, challenges which the Linear Regression (LR) method addresses as an alternative. Furthermore, beef cattle genetic evaluation programs confront challenges with connectedness among herds and pedigree errors. The objective of this work was to evaluate the LR method's performance under pedigree errors and weak connectedness typical in beef cattle genetic evaluations, through simulation.MethodsWe simulated a beef cattle population resembling the Argentinean Brangus, including a quantitative trait selected over six pseudo-generations with a heritability of 0.4. This study considered various scenarios, including: 25% and 40% pedigree errors (PE-25 and PE-40), weak and strong connectedness among herds (WCO and SCO, respectively), and a benchmark scenario (BEN) with complete pedigree and optimal herd connections.ResultsOver six pseudo-generations of selection, genetic gain was simulated to be under- and over-estimated in PE-40 and WCO, respectively, contrary to the BEN scenario which was unbiased. In genetic evaluations with PE-25 and PE-40, true biases of − 0.13 and − 0.18 genetic standard deviations were simulated, respectively. In the BEN scenario, the LR method accurately estimated bias, however, in PE-25 and PE-40 scenarios, it overestimated biases by 0.17 and 0.25 genetic standard deviations, respectively. In herds facing WCO, significant true bias due to confounding environmental and genetic effects was simulated, and the corresponding LR statistic failed to accurately estimate the magnitude and direction of this bias. On average, true dispersion values were close to one for BEN, PE-40, SCO and WCO, showing no significant inflation or deflation, and the values were accurately estimated by LR. However, PE-25 exhibited inflation of EBVs and was slightly underestimated by LR. Accuracies and reliabilities showed good agreement between true and LR estimated values for the scenarios evaluated.ConclusionsThe LR method demonstrated limitations in identifying biases induced by incomplete pedigrees, including scenarios with as much as 40% pedigree errors, or lack of connectedness, but it was effective in assessing dispersion, and population accuracies and reliabilities even in the challenging scenarios addressed.

Feed efficiency traits are important for reducing feeding costs while potentially decreasing the environmental impact of broiler production. This study aimed to compare the predictive ability of different genome-wide prediction models for residual feed intake (RFI) calculated with linear and non-linear regression techniques. We also evaluated the heritability of such RFI as well as their associations with body weight. Genotypes and phenotypes used in this study were recorded from 32,747 purebred broiler chickens of both sexes. The individual feed intake was monitored daily in floor-raised birds using a radio-frequency antenna system. RFI was computed as the residual term of total feed intake (FI) adjusted for the average metabolic weight (AMW), body weight gain (BWG), and sex. The following regression methods were used to compute RFI: multiple linear regression (MLR), generalized additive model using splines (GAM), support vector regression using a radial basis kernel (SVR), and two-hidden layer neural network (NN). The different RFI assessments were fitted jointly with body weight measured at the end of the feeding trial (FBW) using a two-trait mixed model. The effects of contemporary groups were fitted as fixed for both traits, whereas sex was also considered for FBW. RFI (computed with different regression techniques) was predicted using different genomic prediction models (BayesA, BayesB, BayesCπ, GBLUP, RKHS, and SVR). Genomic prediction accuracy (ACC) was assessed using a random forward validation scheme, in which data from previous generations were used for training the models while later generations were used to test predictions. The effect of the RFI computation method on ACC was tested using an unpaired Wilcoxon test. Sample variance observed for RFI ranged between 57,207.04 and 59,254.76, depending on the regression method used to compute it. Overall, the RFI sample variance was smaller for non-linear methods (NN, SVR, and GAM) compared with the linear model (MLR). The regression methods did not impact the genetic parameter estimates for RFI, which presented a heritability value around 0.32 ± 0.015 and genetic correlation with FBW ranging between 0.22 ± 0.04 and 0.25 ± 0.04. Prediction accuracy across genomic regression methods was slightly higher (P-value = 0.038) when RFI was computed with SVR (0.336 ± 0.023) compared with the MLR (0.329 ± 0.025), although this small difference would have little practical implications. No differences in terms of ACC were observed among the other regression methods used to compute RFI. Our preliminary results indicate that the regression technique used to compute RFI does not have major implications for this trait. Therefore, the MLR method is the preferred choice as it is simpler to implement, and it provides easy-to-interpret parameters.

The ability of accurate predictions of biological response (biological activity/property/toxicity) of a given chemical makes the quantitative structure‐activity/property/toxicity relationship (QSAR/QSPR/QSTR) models unique among the in silico tools. In addition, experimental data of selected species can also be used as an independent variable along with other structural as well as physicochemical variables to predict the response for different species formulating quantitative activity–activity relationship (QAAR)/quantitative structure–activity–activity relationship (QSAAR) approach. Irrespective of the models' type, the developed model's quality, and reliability need to be checked through multiple classical stringent validation metrics. Among the validation metrics, error-based metrics are more significant as the basic idea of a good predictive model is to improve the predictions' quality by lowering the predicted residuals for new query compounds. Following the concept, we have checked the predictive quality of the QSAR and QSAAR models employing kernel-weighted local polynomial regression (KwLPR) approach over the traditional linear and non-linear regression-based approaches tools such as multiple linear regression (MLR) and k nearest neighbors (kNN). Five datasets which were previously modeled using linear and non-linear regression method were considered to implement the KwPLR approach, followed by comparison of their validation metrics outcomes. For all five cases, the KwLPR based models reported better results over the traditional approaches. The present study's focus is not to develop a better or improved QSAR/QSAAR model over the previous ones, but to demonstrate the advantage, prediction power, and reliability of the KwLPR algorithm and establishing it as a novel, powerful cheminformatic tool. To facilitate the use of the KwLPR algorithm for QSAR/QSPR/QSTR/QSAAR modeling, the authors provide an in-house developed KwLPR.RMD script under the open-source R programming language.

Canopy water interception is a key parameter to study the hydrological cycle, water utilization efficiency, and energy balance in terrestrial ecosystems. Especially in sprinkler-irrigated farmlands, the canopy interception further influences field energy distribution and microclimate, then plant transpiration and photosynthesis, and finally crop yield and water productivity. To reduce the field damage and increase measurement accuracy under traditional canopy water interception measurement, UAVs equipped with multispectral cameras were used to extract in situ crop canopy information. Based on the correlation coefficient (r), vegetative indices that are sensitive to canopy interception were screened out and then used to develop canopy interception models using linear regression (LR), random forest (RF), and back propagation neural network (BPNN) methods, and lastly these models were evaluated by root mean square error (RMSE) and mean relative error (MRE). Results show the canopy water interception is first closely related to relative normalized difference vegetation index (R△NDVI) with r of 0.76. The first seven indices with r from high to low are R△NDVI, reflectance values of the blue band (Blue), reflectance values of the near-infrared band (Nir), three-band gradient difference vegetation index (TGDVI), difference vegetation index (DVI), normalized difference red edge index (NDRE), and soil-adjusted vegetation index (SAVI) were chosen to develop canopy interception models. All the developed linear regression models based on three indices (R△NDVI, Blue, and NDRE), the RF model, and the BPNN model performed well in canopy water interception estimation (r: 0.53–0.76, RMSE: 0.18–0.27 mm, MRE: 21–27%) when the interception is less than 1.4 mm. The three methods underestimate the canopy interception by 18–32% when interception is higher than 1.4 mm, which could be due to the saturation of NDVI when leaf area index is higher than 4.0. Because linear regression is easy to perform, then the linear regression method with NDVI is recommended for canopy interception estimation of sprinkler-irrigated winter wheat. The proposed linear regression method and the R△NDVI index can further be used to estimate the canopy water interception of other plants as well as forest canopy.

Development of a screening method for adulteration detection in coconut milk via mid-infrared spectroscopy: A study of linear and nonlinear regression method

The aim of this study was to determine the adsorption capacity of the smectite clays (from the overburden of the lignite deposit in Belchatow) for two anionic dyes, i.e. Reactive Blue 81 (RB-81) and Direct Blue 74 (DB-74). Additionally, the influence of the thermal and chemical (acid and alkali) clay modifications on the amount of bonded dyes was investigated. The adsorption capacity of the clay (natural and modified) was different for studied dyes and depended on the initial concentration and modification type. All the modified clays adsorbed the dyes at pH>pHPZC as the negatively charged surfaces of their particles (in accordance with the formula: AOH ↔ AO- + H+) prevented the formation of electrostatic bonds between the anionic dyes and the clay surface. The dyes were mainly bound with the hydrogen bonds forming between the donor groups in the dyes and the acceptor groups (-SiO and -Al2OH) in the clays. The coefficients in the adsorption isotherms were estimated with the linear and non-linear regression. The linear regression method was found that the Freundlich and Dubinin-Radushkevich isotherms described the dye sorption much better than the Langmuir model. On the other hand, all three models described well the experimental data in the non-linear regression method. Furthermore, the 1/n value (<1) obtained from the Freundlich equation for all the dye-sorbent systems indicated the favorable sorption.

Publication bias is a serious problem in meta-analysis. Various methods have been developed to detect the presence of publication bias in meta-analysis. These methods have been assessed and compared in many dichotomous studies utilizing the log-odds ratio as the measure of effect. This paper evaluates and compares the performance of three popular methods, namely the Egger’s linear regression method, the Begg and Mazumdar’s rank correlation method and the Duvall and Tweedie’s trim and fill method, on meta-analysis of continuous data. The data comprised simulated meta-analyses with different levels of primary studies in the absence and presence of induced publication bias. The performance of these methods were measured through the power and type 1 error rate for the tests. The results suggest the trim and fill method to be superior in terms of its ability to detect publication bias when it exists, even in presence of only 5% unpublished studies. However this method is not recommended for large meta-analysis as it produces high rate of false-positive results. Both linear regression and rank correlation method performed relatively well in moderate bias but should be avoided in small meta-analysis as their power is very low in this data.

One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. Here we describe T-profiler, a tool that uses the t-test to score changes in the average activity of predefined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif or location on the same chromosome. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can upload their microarray data for analysis on the web at .

This paper formulates and tests a mathematical model for the prediction of historical average daily maximum and minimum temperatures. First, the model is derived based on a physical understanding of the problem. Then some available weather data are analyzed by three traditional regression methods, namely, a nonlinear regression method, a linear regression method, and a Fourier transform method. Using the coefficients obtained by these analyses, temperatures are predicted for an independent test set and the root-mean-square errors (rms) determined. In an alternative approach, an artificial neural network (ANN) is trained using the same weather data. The trained ANN is made to predict the temperatures for the test set and its rms determined. The variation of rms values with the change in ANN structure is also observed. A comparative study shows that the ANN is a general tool for data analysis and capable of producing results comparable in accuracy to those obtained by the more conventional methods.

Spotted cDNA microarrays are emerging as a powerful and cost-effective tool for large-scale analysis of gene expression. Microarrays can be used to measure the relative quantities of specific mRNAs in two or more tissue samples for thousands of genes simultaneously. While the power of this technology has been recognized, many open questions remain about appropriate analysis of microarray data. One question is how to make valid estimates of the relative expression for genes that are not biased by ancillary sources of variation. Recognizing that there is inherent "noise" in microarray data, how does one estimate the error variation associated with an estimated change in expression, i.e., how does one construct the error bars? We demonstrate that ANOVA methods can be used to normalize microarray data and provide estimates of changes in gene expression that are corrected for potential confounding effects. This approach establishes a framework for the general analysis and interpretation of microarray data.

A study on coating properties of an epoxy system hardened with maleinized castor oil

It is envisaged that magnetisation might alter the sorption behaviours of magnetised biochars due to some variation in the physicochemical properties from their precursor. This study evaluated the adsorption behaviours of a coconut shell biochar produced at 600 °C, CSB600, and its magnetised pair, MCSB600, in the adsorption of methylene blue (MB) from aqueous solutions. Langmuir, Freundlich and Redlich-Peterson isotherm models were used to describe the experimental isotherm using linear and nonlinear regression methods to determine the best fit for MB adsorption from the batch experiments conducted. The Langmuir model proved to be the best fit to explain the experimental data as it had the highest R² (0.9684 and 0.9855) from linear regression and the lowest hybrid fractional error function, HYBRID (4.58, 1.145) and marquardt’s percent standard deviation, MPSD (10.61, 5.04) error function values from the nonlinear regression methods with maximum monolayer adsorption capacities of 5.590 and 5.229 mg/g for CSB600 and MCSB600 respectively. The magnetised biochar exhibited similar adsorption characteristics to what was observed for the non-magnetised biochar and only about 6.46% lower MB adsorption capacity was recorded. A p-value of 0.088 obtained suggested the isotherms were similar and therefore, magnetisation did not affect the adsorption of MB.