Robust ridge regression for estimating the effects of correlated gene expressions on phenotypic traits

Statistical packages such as edgeR and DESeq are intended to detect genes that are relevant to phenotypic traits and diseases. A few studies have also modeled the relationships between gene expressions and traits. In the presence of multicollinearity and outliers, which are unavoidable in genetic data, the robust ridge regression estimator can be applied with the trait value as the response variable and the gene expressions as explanatory variables. In some simulation scenarios, the robust ridge estimator is resistant to outliers and less susceptible to multicollinearity than the ordinary least-squares (OLS) estimator. This study investigated the reliability of the robust ridge estimator, in a scenario where the explanatory variables have tail-dependence and negative binomial distributions, by comparing its performance to that of OLS using vine copula to model the tail-dependence among gene expressions. The robust ridge estimator and OLS were both applied to an ecological dataset. First, statistical analysis was used to compare RNA sequencing data between two treatments; then, 15 differentially expressed genes were selected. Next, the regression parameter estimates of robust ridge and OLS for the effects of the 15 contigs (explanatory variables) on trait values (response variables) were compared. Robust ridge regression was found to detect fewer positive and negative slopes than OLS regression. These results indicate that robust ridge regression can be successfully applied for RNA sequencing analysis to estimate the effect of trait-associated genes using real data, and holds great promise as a tool for modeling the association between RNA expression and phenotypic traits.     

Effect of exposure test conditions on leaching behavior of inorganic contaminants from recycled materials for roadbeds

Throughout the utilization of recycled materials, weathering factors such as humidity, gas composition and temperature have the potential to change the material properties and enhance the release of inorganic contaminants. In this research, the effects of weathering factors on recycled gravel materials for roadbeds were evaluated by applying three kinds of accelerating exposure tests: freezing–melting cycle test, carbonation test, and dry–humid cycle test. The effects of exposure tests were determined by X-ray diffraction (XRD) analysis and serial batch leaching test, making it possible to identify the change in release mechanisms. Sixteen elements, mainly metals, were investigated. Tested samples were molten slag from municipal solid waste, molten slag from automobile shredded residue, and crushed natural stone.After the exposure tests, the increase of cumulative release in the leaching test was generally less than 2.0 times that of the samples without the exposure test. Among the three test conditions, freezing–melting showed a slightly higher effect of enhancing the release of constituents. XRD analysis showed no change in chemical species. From these results, it was determined that the stony samples were stable enough so that their properties were not significantly changed by the exposure tests.     

Fate of metals contained in waste electrical and electronic equipment in a municipal waste treatment process

In Japan, waste electrical and electronic equipment (WEEE) that is not covered by the recycling laws are treated as municipal solid waste. A part of common metals are recovered during the treatment; however, other metals are rarely recovered and their destinations are not clear. This study investigated the distribution ratios and substance flows of 55 metals contained in WEEE during municipal waste treatment using shredding and separation techniques at a Japanese municipal waste treatment plant. The results revealed that more than half of Cu and most of Al contained in WEEE end up in landfills or dissipate under the current municipal waste treatment system. Among the other metals contained in WEEE, at least 70% of the mass was distributed to the small-grain fraction through the shredding and separation and is to be landfilled. Most kinds of metals were concentrated several fold in the small-grain fraction through the process and therefore the small-grain fraction may be a next target for recovery of metals in terms of both metal content and amount. Separate collection and pre-sorting of small digital products can work as effective way for reducing precious metals and less common metals to be landfilled to some extent; however, much of the total masses of those metals would still end up in landfills and it is also important to consider how to recover and utilize metals contained in other WEEE such as audio/video equipment.     

A trade-off between prey- and predator-induced polyphenisms in larvae of the salamander Hynobius retardatus

Organisms in natural habitats participate in complex ecological interactions that include competition, predation, and foraging. Under natural aquatic environmental conditions, amphibian larvae can simultaneously receive multiple signals from conspecifics, predators, and prey, implying that predator-induced morphological defenses can occur in prey and that prey-induced offensive morphological traits may develop in predators. Although multiple adaptive plasticity, such as inducible defenses and inducible offensive traits, can be expected to have not only ecological but also evolutionary implications, few empirical studies report on species having such plasticity. The broad-headed larval morph of Hynobius retardatus, which is induced by crowding with heterospecific anuran (Rana pirica) larvae, is a representative example of prey-induced polyphenism. The morph is one of two distinct morphs that have been identified in this species; the other is the typical morph. In this paper, we report that typical larval morphs of Hynobius can respond rapidly to a predatory environment and show conspicuous predator-induced plasticity of larval tail depth, but that broad-headed morphs cannot respond similarly to a predation threat. Our findings support the hypothesis that induction or maintenance of adaptive plasticity (e.g., predator-induced polyphenism) trades off against other adaptive plastic responses (e.g., prey-induced polyphenism). For a species to retain both an ability to forage for larger prey and an ability to more effectively resist predation makes sense in light of the range of environments that many salamander larvae experience in nature. Our results suggest that the salamander larvae clearly discriminate between cues from prey and those from predators and accurately respond to each cue; that is, they adjust their phenotype to the current environment.     

Development of dioxin toxicity evaluation method in human milk by enzyme-linked immunosorbent assay--assay validation for human milk

In this study, the development of a toxicity evaluation method for dioxins in human milk by enzyme-linked immunosorbent assay (ELISA) was reported. A total of 17 human milk samples were tested by ELISA and by gas chromatography/mass spectrometry (GC/MS) to assess whether the ELISA performed on samples obtained from primiparas could be considered as reliable enough for identifying a dioxins contamination in human milk. The concept of toxicity equivalent quantity (TEQ) screening was validated by comparing TEQ values for a set of human milk samples to the ELISA responses predicted for those samples. A fairly good correlation (r=0.920) between immunoassay and GC/MS was achieved for human milk. This ELISA should be useful for biological samples monitoring.     

Degradation of Poly(acrylic acid)s with Phenolic Side-Chains by Manganese Peroxidase from White Rot Fungi

Poly(acrylic acid)s (PAAs) with various functional groups, such as phenolic hydroxyl, amino, and aldehyde groups, in the side-chains were treated with manganese peroxidase (MnP) prepared from the culture of lignin-degrading white rot fungi. While no change in the M_w of PAA without a functional group was observed after a 24-h MnP treatment, the M_w␣of␣PAA␣with p-aminophenol as side-chains decreased from 90,000 to 59,000, and that with␣o-aminophenol from 70,000 to 26,000. MnP treatment also decreased the M_w of PAA with a p-aminoaniline or aldehyde group. Furthermore, the MnP treatment generated a significant depolymerization of the cross-linked PAA with p-aminophenol from an insoluble polymer to water soluble products. These results suggest that functional groups generating radicals can act as elemental devices and induce degradation of the PAA main chain.     

High-rate anaerobic digestion of sewage sludge by membrane separation solubilization coupled with UASB process

Journal of Material Cycles and Waste Management - Conventional anaerobic digestion (AD) process was often slow and thus required a large digestion tank. Upflow anaerobic sludge blanket (UASB)...