Particle swarm optimization in constrained maximum likelihood estimation a case study

The aim of paper is to apply two types of particle swarm optimization, global best andlocal best PSO to a constrained maximum likelihood estimation problem in pseudotime anal-ysis, a sub-field in bioinformatics. The results have shown that particle swarm optimizationis extremely useful and efficient when the optimization problem is non-differentiable and non-convex so that analytical solution can not be derived and gradient-based methods can not beapplied.Comment: 11 pages, 7 figure

Chloride Ion Erosion of Pre-Stressed Concrete Bridges in Cold Regions

The erosion of chloride ions in concrete bridges will accelerate the corrosion of reinforcement, which is an important reason for the decline of bridge durability. The erosion process of chloride ion, especially deicing salt solution in cold regions, is complex and has many influencing factors. It is very important to use accurate and effective methods to analyze the chloride ion erosion process in concrete. In this study, the pre-stressed concrete bridge retired in the cold region was taken as the research object, and the specimens from the whole bridge are obtained by the method of core drilling sampling. The concentration of chloride ion was measured at different depths of the specimens. The process of chloride ion erosion was simulated in two-dimensional space through COMSOL multi-physical field simulation, and compared with the measured results. The simulation method proposed in this paper has good reliability and accuracy

Recent Progress of Remediating Heavy Metal Contaminated Soil Using Layered Double Hydroxides as Super-Stable Mineralizer

Heavy metal contamination in soil, which is harmful to both ecosystem and mankind, has attracted worldwide attention from the academic and industrial communities. However, the most-widely used remediation technologies such as electrochemistry, elution, and phytoremediation. suffer from either secondary pollution, long cycle time or high cost. In contrast, in situ mineralization technology shows great potential due to its universality, durability and economical efficiency. As such, the development of mineralizers with both high efficiency and low-cost is the core of in situmineralization. In 2021, the concept of ‘Super-Stable Mineralization’ was proposed for the first time by Kong et al.[1] The layered double hydroxides (denoted as LDHs), with the unique host–guest intercalated structure and multiple interactions between the host laminate and the guest anions, are considered as an ideal class of materials for super-stable mineralization. In this review, we systematically summarize the application of LDHs in the treatment of heavy metal contaminated soil from the view of: 1) the structure–activity relationship of LDHs in in situ mineralization, 2) the advantages of LDHs in mineralizing heavy metals, 3) the scale-up preparation of LDHs-based mineralizers and 4) the practical application of LDHs in treating contaminated soil. At last, we highlight the challenges and opportunities for the rational design of LDH-based mineralizer in the future

Visual and non-visual image tweet dataset

doi:10.25540/T4RP-938

Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime.

MotivationModeling single-cell gene expression trends along cell pseudotime is a crucial analysis for exploring biological processes. Most existing methods rely on nonparametric regression models for their flexibility; however, nonparametric models often provide trends too complex to interpret. Other existing methods use interpretable but restrictive models. Since model interpretability and flexibility are both indispensable for understanding biological processes, the single-cell field needs a model that improves the interpretability and largely maintains the flexibility of nonparametric regression models.ResultsHere, we propose the single-cell generalized trend model (scGTM) for capturing a gene's expression trend, which may be monotone, hill-shaped or valley-shaped, along cell pseudotime. The scGTM has three advantages: (i) it can capture non-monotonic trends that are easy to interpret, (ii) its parameters are biologically interpretable and trend informative, and (iii) it can flexibly accommodate common distributions for modeling gene expression counts. To tackle the complex optimization problems, we use the particle swarm optimization algorithm to find the constrained maximum likelihood estimates for the scGTM parameters. As an application, we analyze several single-cell gene expression datasets using the scGTM and show that scGTM can capture interpretable gene expression trends along cell pseudotime and reveal molecular insights underlying biological processes.Availability and implementationThe Python package scGTM is open-access and available at https://github.com/ElvisCuiHan/scGTM.Supplementary informationSupplementary data are available at Bioinformatics online

Role of 5-HT3 receptor on food intake in fed and fasted mice.

Many studies have shown that 5-hydroxytryptamine (5-HT) receptor subtypes are involved in the regulation of feeding behavior. However, the relative contribution of 5-HT3 receptor remains unclear. The present study was aimed to investigate the role of 5-HT3 receptor in control of feeding behavior in fed and fasted mice.Food intake and expression of c-Fos, tyrosine hydroxylase (TH), proopiomelanocortin (POMC) and 5-HT in the brain were examined after acute treatment with 5-HT3 receptor agonist SR-57227 alone or in combination with 5-HT3 receptor antagonist ondansetron. Food intake was significantly inhibited within 3 h after acute treatment with SR 57227 in fasted mice but not fed mice, and this inhibition was blocked by ondansetron. Immunohistochemical study revealed that fasting-induced c-Fos expression was further enhanced by SR 57227 in the brainstem and the hypothalamus, and this enhancement was also blocked by ondansetron. Furthermore, the fasting-induced downregulation of POMC expression in the hypothalamus and the TH expression in the brain stem was blocked by SR 57227 in the fasted mice, and this effect of SR 57227 was also antagonized by ondansetron.Taken together, our findings suggest that the effect of SR 57227 on the control of feeding behavior in fasted mice may be, at least partially, related to the c-Fos expression in hypothalamus and brain stem, as well as POMC system in the hypothalamus and the TH system in the brain stem

POMC/β-actin ratio,normalized to control, in hypothalamus and bran stem of fed and fasted mice.

<p>Con: control group; SR: SR 57227 (10 mg/kg, i.p.); On: ondansetron (3 mg/kg, i.p.). POMC: Pro-opiomelanocortin. Values are means ± SEM (n = 8–10). #, P < 0.05 vs. non-fasting control group; **, P < 0.01 vs. fasting control group.</p

TH/β-actin ratio,normalized to control, in hypothalamus and bran stem of fed and fasted mice.

<p>Con: control group; SR: SR 57227 (10 mg/kg, i.p.); On: ondansetron (3 mg/kg, i.p.). TH: tyrosine hydroxylase. Values are means ± SEM (n = 8–10). #, P < 0.05 vs. non-fasting control group; *, P < 0.05 vs. fasting control group.</p

Effects of acute SR 57227 on cumulative food intake in fed and fasted mice.

<p>SR: SR 57227 (1, 3 and 10 mg/kg, i.p.); On: ondansetron (3 mg/kg, i.p.). Values are means ± SEM (n = 8–10). #, P < 0.05; ##, P < 0.01 vs. non-fasting group; *, P <0.05; **, P < 0.01 vs. fasting group.</p