Analysis of ultra-sensitive fluorescence experiments

This work primarily investigates use of the neural network(NN) method to analyze spectral data collected in single molecule detection(SMD) and identification (SMI) ex-periments.. The 2-layer neural networks, with sigmoid as the activation function, are constructed and trained on a set of simulated data using back-propagation and the 6- learning rule. The trained networks are then used for identification of photon bursts in subsequent simulations. Results show that the NN method yields better identification of individual photon bursts than the traditional maximum likelihood estimation (MLE), particularly in cases where the fluorophores have disparate fluorescence quantum effi-ciencies, absorption cross-sections, or photodegradation efficiencies. In addition, this work reports several improvements over the prior version of the Monte Carlo simulation program. The improved version considers the fluorescence prob-ability as the convolution of the pure exponential decay function characterized by the fluorescence lifetime and the instrument impulse response function in the experiment. The setting of the time window is then implemented by monitoring the variation of signal and noise. A number of problems have been investigated by using the improved version. In particular, the effects of the number and widths of the bins within the time window on the precision of identification of molecules are studied. The results from the improved version of the simulation show that only a small number of bins (4-8) are required to achieve approximately 90% correct predictions with the NN method. Bin widths chosen in accordance with the intuitive algorithm, or equal bin widths, generally give better predictions. Experimental improvements are also reported in this work. In particular, the transit time of BODIBY-TR(D-6116) dye molecules in an SMD experiment was improved to less than 200 μ, and a circuit is implemented to accomplish fast and continuous data collection to be used in future single molecule identification experiments

Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients

A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca

Contactless Haptic Display Through Magnetic Field Control

Haptic rendering enables people to touch, perceive, and manipulate virtual objects in a virtual environment. Using six cascaded identical hollow disk electromagnets and a small permanent magnet attached to an operator's finger, this paper proposes and develops an untethered haptic interface through magnetic field control. The concentric hole inside the six cascaded electromagnets provides the workspace, where the 3D position of the permanent magnet is tracked with a Microsoft Kinect sensor. The driving currents of six cascaded electromagnets are calculated in real-time for generating the desired magnetic force. Offline data from an FEA (finite element analysis) based simulation, determines the relationship between the magnetic force, the driving currents, and the position of the permanent magnet. A set of experiments including the virtual object recognition experiment, the virtual surface identification experiment, and the user perception evaluation experiment were conducted to demonstrate the proposed system, where Microsoft HoloLens holographic glasses are used for visual rendering. The proposed magnetic haptic display leads to an untethered and non-contact interface for natural haptic rendering applications, which overcomes the constraints of mechanical linkages in tool-based traditional haptic devices

Improving Classification of Protein Interaction Articles Using Context Similarity-Based Feature Selection

Protein interaction article classification is a text classification task in the biological domain to determine which articles describe protein-protein interactions. Since the feature space in text classification is high-dimensional, feature selection is widely used for reducing the dimensionality of features to speed up computation without sacrificing classification performance. Many existing feature selection methods are based on the statistical measure of document frequency and term frequency. One potential drawback of these methods is that they treat features separately. Hence, first we design a similarity measure between the context information to take word cooccurrences and phrase chunks around the features into account. Then we introduce the similarity of context information to the importance measure of the features to substitute the document and term frequency. Hence we propose new context similarity-based feature selection methods. Their performance is evaluated on two protein interaction article collections and compared against the frequency-based methods. The experimental results reveal that the context similarity-based methods perform better in terms of the 1 measure and the dimension reduction rate. Benefiting from the context information surrounding the features, the proposed methods can select distinctive features effectively for protein interaction article classification

An efficient and robust exfoliated bentonite/Ag3PO4/AgBr plasmonic photocatalyst for degradation of parabens

Efficient visible-light-driven heterojunction photocatalysts have attracted broad interest owing to their promising adsorption and degradation performances in the removal of organic pollutants. In this study, a mesoporous exfoliated bentonite (EB)/Ag3PO4/AgBr (30%) photocatalyst was obtained by stripping and exfoliating bentonite as the support for loading Ag3PO4 and AgBr. The particle size ranges of Ag3PO4 and AgBr were about 10-30 nm and 5-10 nm, respectively. The exfoliated bentonite could greatly improve the dispersion and adsorption of Ag3PO4 and AgBr, and significantly enhance the stability of the material during paraben photodegradation. 0.2 g L-1 methylparaben (MPB) was completely decomposed over the EB/Ag3PO4/AgBr (30%) in 40 min under visible light irradiation. In addition, the photocatalytic activity of EB/Ag3PO4/AgBr (30%) remained at about 91% after five recycling runs manifesting that EB/Ag3PO4/AgBr (30%) possessed excellent stability. Radical quenching tests revealed that holes (h+) and hydroxyl radicals (·OH) were the major radicals. They attacked the side chain on the benzene ring of parabens, which were gradually oxidized to the intermediates, such as benzoic acid, 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, azelaic acid, and eventually became CO2 and H2O. The enhancement of photocatalytic activity and photo-stability could be ascribed to the stable structural characteristics, enlarged surface area, high absorption ability, and improved light absorption ability from loading Ag3PO4 onto EB. Meanwhile, the matched energy levels of Ag3PO4 and AgBr made the photoelectron-hole pairs separate and transfer effectively at the interfaces. As a result, the photocatalytic properties of EB/Ag3PO4/AgBr (30%) composites were enhanced. © 2020 The Royal Society of Chemistry

NDM-1-producing Enterobacteriaceae in a teaching hospital in Shanghai, China: IncX3-type plasmids may contribute to the dissemination of blaNDM-1

SummaryObjectivesTo provide the epidemiological dissemination and the genetic characteristics of blaNDM-1 in a teaching hospital in Shanghai, China.MethodsHere, the carbapenemase genes of 114 CRE isolates were evaluated by polymerase chain reaction (PCR). Clonal relatedness was assessed by pulsed-field gel electrophoresis (PFGE). Conjugation experiments and Southern blot hybridization were performed to determine the transferability of plasmids. Then plasmids were completely sequenced by the shotgun method.ResultsTwo Klebsiella pneumoniae strains (RJA1227 and RJF866) and one Raoultella planticola strain (RJA274) were identified as NDM-1 positive. The two K. pneumoniae isolates belonged to ST11 and exhibited highly similar PFGE patterns. Shotgun sequencing showed that plasmid pRJF866 (ca. 110kb) contained genes associated with the IncFII-FIB group and was highly similar to plasmid pKOX_NDM1. RJA274 (ca. 50kb) harbored blaNDM-1 on an IncX3 plasmid, which was nearly identical to plasmid pNDM-HN380 except that part of the ISAba125 element is missing.ConclusionThis is the first report of NDM-1-positive Enterobacteriaceae from Shanghai, China. IncX3 plasmids, reported in various species in the United Arab Emirates and China, may contribute to the dissemination of blaNDM-1.. More attention should be devoted to monitoring the dissemination of the NDM-1 gene due to its potential horizontal transfer via mobile genetic elements

Piperacillin-Tazobactam (TZP) Resistance in Escherichia coli Due to Hyperproduction of TEM-1 β-Lactamase Mediated by the Promoter Pa/Pb

TEM-1, mediated by plasmid and transposon, is the most commonly encountered β-lactamase in Gram-negative bacteria. Four different promoters upstream of blaTEM-related genes have been identified: the weak P3 promoter, and the strong promoters Pa/Pb, P4, and P5. In this study, we investigated the genetic basis of a clinical strain of Escherichia coli (RJ904), which was found to be resistant to BLBLIs (β-lactam/β-lactamase inhibitors), including amoxicillin-clavulanate, ticarcillin-clavulanate (TCC), and piperacillin-tazobactam (TZP) but sensitive to third-generation cephalosporins. The conjugation test and S1-nuclease pulsed-field gel electrophoresis (S1-PFGE) demonstrated that transfer of this resistance was mediated by a ca. 100 kb plasmid. The transformant with TZP resistance was screened out with the shortgun cloning. Sequence analysis revealed that the recombinant plasmid contained a blaTEM-1b gene with the strong promoter Pa/Pb. Different plasmids were cloned based on the clone vector pACYC184 with the insertion of the blaTEM-1b gene with promoters Pa/Pb or P3. Susceptibility to TZP was determined by the E-test, agar dilution, and broth microdilution. The level of blaTEM-1b-specific transcription was determined by quantitative real-time PCR. Substitution of Pa/Pb for P3 resulted in a 128-fold decline of the MIC value of TZP, from >1024 mg/L to 8 mg/L, and a significantly lower blaTEM-1b expression level. Hyperproduction of TEM-1 β-lactamase mediated by the promoter Pa/Pb was responsible for high resistance to TZP in E. coli. Our data show possible risks of resistance development in association with the clinical use of TZP. The blaTEM promoter modifications should be considered for whole genome whole-genome sequencing-inferred bacterial antimicrobial susceptibility testing

Impaired reverse cholesterol transport and hepatic steatosis contribute to pathogenesis of high fat dietinduced hyperlipidemia in murine models

Purpose: To investigate the pathogenesis of high fat diet (HFD)-induced hyperlipidemia (HLP) in mice, rats and hamsters and to comparatively evaluate their sensitivity to HFD.Methods: Mice, rats and hamsters were fed with high-fat diet formulation (HFD, n = 8) or a control diet (control, n = 8) for 4 weeks. Changes in body weight, relative liver weight, serum lipid profile, expressions of hepatic marker gene of lipid metabolism and liver morphology were observed in three hyperlipidemic models.Results: Elevated total cholesterol (TC), triglyceride, low density lipoprotein-cholesterol (LDL-C) and high density lipoprotein-cholesterol (HDL-C) levels and body weight were observed in all hyperlipidemic animals (p < 0.05), while hepatic steatosis was manifested in rat and hamster HLP models, and increased hepatic TC level was only seen (p < 0.05) in hamster HLP model. Suppression of HMG-CoA reductase and up-regulation of lipoproteinlipase were observed in all HFD groups. Hepatic gene expression of LDLR, CYP7A1, LCAT, SR-B1, and ApoA I, which are a response to reverse cholesterol transport (RCT), were inhibited by HFD in the three models. Among these models, simultaneous suppression of HMG-CR, LCAT, LDLR and SR-BI and elevated LPL were features of the hamster model.Conclusion: As the results show, impaired RCT and excessive fat accumulation are major contributors to pathogenesis of HFD-induced murine HLP. Thus, the hamster model is more appropriate for hyperlipidemia research.Keywords: Hyperlipidemic model, Murine, Hamster, mRNA, Reverse cholesterol transport, High-fat diet, Pathogenesi

A Novel Approach to Molecular Recognition Surface of Magnetic Nanoparticles Based on Host–Guest Effect

A novel route has been developed to prepared β-cyclodextrin (β-CD) functionalized magnetic nanoparticles (MNPs). The MNPs were first modified with monotosyl-poly(ethylene glycol) (PEG) silane and then tosyl units were displaced by amino-β-CD through the nucleophilic substitution reaction. The monotosyl-PEG silane was synthesized by modifying a PEG diol to form the corresponding monotosyl-PEG, followed by a reaction with 3-isocyanatopropyltriethoxysilane (IPTS). The success of the synthesis of the monotosyl-PEG silane was confirmed with1H NMR and Fourier transform infrared (FTIR) spectroscopy. The analysis of FTIR spectroscopy and X-ray photoelectron spectroscopy (XPS) confirmed the immobilization of β-CD onto MNPs. Transmission electron microscopy (TEM) indicated that the β-CD functionalized MNPs were mostly present as individual nonclustered units in water. The number of β-CD molecules immobilized on each MNP was about 240 according to the thermogravimetric analysis (TGA) results. The as-prepared β-CD functionalized MNPs were used to detect dopamine with the assistance of a magnet