Implementing a two-layer feed-forward catalytic DNA circuit for enzyme-free and colorimetric detection of nucleic acids

In the present study, a highly sensitive and specific bio-sensing platform for enzyme-free and colorimetric detection of nucleic acids has been developed. The biosensor is composed of two DNA nanostructures and two fuel strands that construct the foundation of a feed-forward catalytic DNA circuit. Upon binding the target strand to a specific DNA nanostructure, the circuit is run in order that at the end a hemin-binding aptamer, with the ability to convert a colorless substrate into a colored substance is released. Based on this strategy, 4 pM of the target DNA can be easily detected in serum samples by naked eyes after only a two-hour incubation with the circuit; meanwhile, if the incubation time is extended to 3 h, the biosensor can detect 1 pM of the target DNA. Besides the elevated sensitivity, the circuit can truly discriminate a spurious target containing one nucleotide mismatch with high specificity. Overall, the enzyme-free catalytic DNA circuit can be used as a sensitive alternative method to enzyme-based biosensors for the specific and cost-effective detection of nucleic acids.     

Influence of crosslinker identity and position on gas-phase dissociation of lys-lys crosslinked peptides

A systematic study of the dissociation patterns of crosslinked peptides analyzed by tandem mass spectrometry is reported. A series of 11-mer peptides was designed around either a polyalanine or polyglycine scaffold with arginine at the C terminus. One or two lysine residues were included at various locations within the peptides to effect inter- or intra-molecular crosslinking, respectively. Crosslinked species were generated with four commonly used amine-specific chemical crosslinking reagents: disuccinimidyl suberate (DSS), disuccinimidyl tartarate (DST), dithiobis(succinimidylpropionate) (DSP), and disuccinimidyl glutarate (DSG). The influence of precursor charge state, location of crosslink, and specific crosslinking reagent on the MS/MS dissociation pattern was examined. Observed trends in the dissociation patterns obtained for these species will allow for improvements to software used in the automated interpretation of crosslinked peptide MS/MS data.     

A Caputo–Fabrizio Fractional-Order Model of HIV/AIDS with a Treatment Compartment: Sensitivity Analysis and Optimal Control Strategies

Although most of the early research studies on fractional-order systems were based on the Caputo or Riemann–Liouville fractional-order derivatives, it has recently been proven that these methods have some drawbacks. For instance, kernels of these methods have a singularity that occurs at the endpoint of an interval of definition. Thus, to overcome this issue, several new definitions of fractional derivatives have been introduced. The Caputo–Fabrizio fractional order is one of these nonsingular definitions. This paper is concerned with the analyses and design of an optimal control strategy for a Caputo–Fabrizio fractional-order model of the HIV/AIDS epidemic. The Caputo–Fabrizio fractional-order model of HIV/AIDS is considered to prevent the singularity problem, which is a real concern in the modeling of real-world systems and phenomena. Firstly, in order to find out how the population of each compartment can be controlled, sensitivity analyses were conducted. Based on the sensitivity analyses, the most effective agents in disease transmission and prevalence were selected as control inputs. In this way, a modified Caputo–Fabrizio fractional-order model of the HIV/AIDS epidemic is proposed. By changing the contact rate of susceptible and infectious people, the atraumatic restorative treatment rate of the treated compartment individuals, and the sexual habits of susceptible people, optimal control was designed. Lastly, simulation results that demonstrate the appropriate performance of the Caputo–Fabrizio fractional-order model and proposed control scheme are illustrated.     

Unique cascade ring-opening/cyclization reaction of azlactones and DBU or DBN: Synthesis of new pyrrolam A analogues

1-Azabicyclo[3.3.0]oct-3-en-2-one derivatives were synthesized efficiently through the facile cascade reaction of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) or 1,5-diazabicyclo[4.3.0]non-5-ene (DBN) with arylidene azlactones. This research provides a straightforward procedure for the synthesis of a novel class of multicyclic semi-alkaloids which shows good antimicrobial activity. Under catalyst-free, mild, and solventless condition, a wide range of fused tricyclic derivatives was obtained in high yields.     

Strong and Weak Solutions to Second Order Differential Inclusions Governed by Monotone Operators

In this paper we introduce the concept of a weak solution for second order differential inclusions of the form u″(t) ∈ Au(t) + f(t), where A is a maximal monotone operator in a Hilbert space H. We prove existence and uniqueness of weak solutions to two point boundary value problems associated with such kind of equations. Furthermore, existence of (strong and weak) solutions to the equation above which are bounded on the positive half axis is proved under the optimal condition tf(t) ∈ L ¹(0, ∞; H), thus solving a long-standing open problem (for details, see our comments in Section 3 of the paper). Our treatment regarding weak solutions is similar to the corresponding theory related to the first order differential inclusions of the form f(t) ∈ u′(t) + Au(t) which has already been well developed.     

Row–column interaction models,with an R implementation

We propose a family of models called row–column interaction models (RCIMs) for two-way table responses. RCIMs apply some link function to a parameter (such as the cell mean) to equal a row effect plus a column effect plus an optional interaction modelled as a reduced-rank regression. What sets this work apart from others is that our framework incorporates a very wide range of statistical models, e.g., (1) log-link with Poisson counts is Goodman’s RC model, (2) identity-link with a double exponential distribution is median polish, (3) logit-link with Bernoulli responses is a Rasch model, (4) identity-link with normal errors is two-way ANOVA with one observation per cell but allowing semi-complex modelling of interactions of the form  \(\mathbf{A}\mathbf{C}^T\) , (5) exponential-link with normal responses are quasi-variances. Proposed here also is a least significant difference plot augmentation of quasi-variances. Being a special case of RCIMs, quasi-variances are naturally extended from the \(M=1\) linear/additive predictor  \(\eta \) case (within the exponential family) to the \(M>1\) case (vector generalized linear model families). A rank-1 Goodman’s RC model is also shown to estimate the site scores and optimums of an equal-tolerances Poisson unconstrained quadratic ordination. New functions within the VGAM R package are described with examples. Altogether, RCIMs facilitate the analysis of matrix responses of many data types, therefore are potentially useful to many areas of applied statistics.     

Effects of substrate on surface morphology, crystallinity, and photoluminescence properties of sputtered ZnO nano films

Effects of substrate on crystallinity, surface morphology, and luminescence properties of radio frequency sputtered zinc oxide (ZnO) thin films were investigated. A variety of materials such as Si (100), Si (111), Al₂O₃, quartz, and silicon carbide (SiC) wafers were examined as substrates for deposition of ZnO thin films. The results showed smooth and uniform growth of c-axis orientation films. The thickness of the layers was about 50 nm. The average grain sizes of films were about 10, 13, and 12 nm for Si (111), quartz, and SiC samples, respectively. The deposited film on Al₂O₃ showed the largest grain size, about 500 nm. Grazing incidence x-ray diffraction patterns of the samples revealed that sputtered layers on Al₂O₃ and quartz had better crystallinity with higher peak at (002) orientation compared to Si and SiC substrates. Moreover, the Al₂O₃ sample exhibited a weak peak at position of (100) planes of ZnO too. The photoluminescence spectra of the samples showed a typical luminescence behavior with a broad UV band, including a main peak at around 388 nm and a weak shoulder peak at around 381 nm, corresponding with bound excitonic recombination and free excitonic recombination, respectively. The luminescence peak revealed that the intensity of UV emission is not necessarily dependent on the grain sizes and the micro-structural quality of ZnO films.     

Enhancement of catalytic activity of titanosilicalite-1 - sulfated zirconia combination towards epoxidation of 1-octene with aqueous hydrogen peroxide

Summary Titanosilicalite-1 (TS-1) in combination with sulfated zirconia efficiently catalyzes the epoxidation of 1-octene with aqueous hydrogen peroxide. The presence of both octahedral zirconium and sulfate species in the catalysts enhances the epoxidation rates.