Use of Finite Point Method for Wave Propagation in Nonhomogeneous Unbounded Domains

Wave propagation in an unbounded domain surrounding the stimulation resource is one of the important issues for engineers. Past literature is mainly concentrated on the modelling and estimation of the wave propagation in partially layered, homogeneous, and unbounded domains with harmonic properties. In this study, a new approach based on the Finite Point Method (FPM) has been introduced to analyze and solve the problems of wave propagation in any nonhomogeneous unbounded domain. The proposed method has the ability to use the domain properties by coordinate as an input. Therefore, there is no restriction in the form of the domain properties, such as being periodical as in the case of existing similar numerical methods. The proposed method can model the boundary points between phases with trace of errors and the results of this method satisfy both conditions of decay and radiation

Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity

This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques

Unusually Long Palindromes Are Abundant in Mitochondrial Control Regions of Insects and Nematodes

BACKGROUND: Palindromes are known to be involved in a variety of biological processes. In the present investigation we carried out a comprehensive analysis of palindromes in the mitochondrial control regions (CRs) of several animal groups to study their frequency, distribution and architecture to gain insights into the origin of replication of mtDNA. METHODOLOGY/PRINCIPAL FINDINGS: Many species of Arthropoda, Nematoda, Mollusca and Annelida harbor palindromes and inverted repeats (IRs) in their CRs. Lower animals like cnidarians and higher animal groups like chordates are almost devoid of palindromes and IRs. The study revealed that palindrome occurrence is positively correlated with the AT content of CRs, and that IRs are likely to give rise to longer palindromes. CONCLUSIONS/SIGNIFICANCE: The present study attempts to explain possible reasons and gives in silico evidence for absence of palindromes and IRs from CR of vertebrate mtDNA and acquisition and retention of the same in insects. Study of CRs of different animal phyla uncovered unique architecture of this locus, be it high abundance of long palindromes and IRs in CRs of Insecta and Nematoda, or short IRs of 10–20 nucleotides with a spacer region of 12–14 bases in subphylum Chelicerata, or nearly complete of absence of any long palindromes and IRs in Vertebrata, Cnidaria and Echinodermata

Recovering complete and draft population genomes from metagenome datasets

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution

Alzheimer disease models and human neuropathology: similarities and differences

Animal models aim to replicate the symptoms, the lesions or the cause(s) of Alzheimer disease. Numerous mouse transgenic lines have now succeeded in partially reproducing its lesions: the extracellular deposits of Aβ peptide and the intracellular accumulation of tau protein. Mutated human APP transgenes result in the deposition of Aβ peptide, similar but not identical to the Aβ peptide of human senile plaque. Amyloid angiopathy is common. Besides the deposition of Aβ, axon dystrophy and alteration of dendrites have been observed. All of the mutations cause an increase in Aβ 42 levels, except for the Arctic mutation, which alters the Aβ sequence itself. Overexpressing wild-type APP alone (as in the murine models of human trisomy 21) causes no Aβ deposition in most mouse lines. Doubly (APP × mutated PS1) transgenic mice develop the lesions earlier. Transgenic mice in which BACE1 has been knocked out or overexpressed have been produced, as well as lines with altered expression of neprilysin, the main degrading enzyme of Aβ. The APP transgenic mice have raised new questions concerning the mechanisms of neuronal loss, the accumulation of Aβ in the cell body of the neurons, inflammation and gliosis, and the dendritic alterations. They have allowed some insight to be gained into the kinetics of the changes. The connection between the symptoms, the lesions and the increase in Aβ oligomers has been found to be difficult to unravel. Neurofibrillary tangles are only found in mouse lines that overexpress mutated tau or human tau on a murine tau −/− background. A triply transgenic model (mutated APP, PS1 and tau) recapitulates the alterations seen in AD but its physiological relevance may be discussed. A number of modulators of Aβ or of tau accumulation have been tested. A transgenic model may be analyzed at three levels at least (symptoms, lesions, cause of the disease), and a reading key is proposed to summarize this analysis

Electrokinetic stabilization of soft clay

Electrokinetic is the movement of ions, charged solid particles and water between two electrodes under the influence of an electrical field. Electrokinetic can be applied to the fields such as stabilization of soft soils and slopes, decontamination of pollutants, and sealing and leak-detection system of geomembrane, etc. The aim of this study was to evaluate the use of electrokinetic as an effective method to strengthen the soft clay soil with high compressibility. An in situ soil treatment technique using the principles of electrokinetic was tested using laboratory experimental models. The effectiveness of this approach in stabilizing and improving the physical properties of soft clay was tested and examined. In the study, soil specimens were compacted in glass tanks to reproduce in-situ density and in-situ water content. Mild steel electrodes were inserted into the soil and a direct current was passed through the soil under a constant potential gradient of 35–60 Volts for a period of 14 days. Distilled water and saturated lime solutions were introduced to the soil from anode to cathodes over the testing period. The physical and index properties of the soft clay were tested before and after the electrokinetics stabilization and the results were discussed. Test results indicated that introducing lime into the soil by electrokinetic method reduced the plasticity index of the soil and resulted in a lower compressibility of the soft clay. Treatment of soil by electrokinetic method enabled the measurement of the compressive strength of the soil which resulted in an increase in soil’s strength

Electrokinetic stabilization of soft clay

Electrokinetic is the movement of ions, charged solid particles and water between two electrodes under the influence of an electrical field. Electrokinetic can be applied to the fields such as stabilization of soft soils and slopes, decontamination of pollutants, and sealing and leak-detection system of geomembrane, etc. The aim of this study was to evaluate the use of electrokinetic as an effective method to strengthen the soft clay soil with high compressibility. An in situ soil treatment technique using the principles of electrokinetic was tested using laboratory experimental models. The effectiveness of this approach in stabilizing and improving the physical properties of soft clay was tested and examined. In the study, soil specimens were compacted in glass tanks to reproduce in-situ density and in-situ water content. Mild steel electrodes were inserted into the soil and a direct current was passed through the soil under a constant potential gradient of 35–60 Volts for a period of 14 days. Distilled water and saturated lime solutions were introduced to the soil from anode to cathodes over the testing period. The physical and index properties of the soft clay were tested before and after the electrokinetics stabilization and the results were discussed. Test results indicated that introducing lime into the soil by electrokinetic method reduced the plasticity index of the soil and resulted in a lower compressibility of the soft clay. Treatment of soil by electrokinetic method enabled the measurement of the compressive strength of the soil which resulted in an increase in soil’s strength