Double Restriction Research Articles

Light bullets under conditions of third harmonics generation

Abstract An analytical study of the possibility of a two-color light bullet forming during generation of the third harmonics in a graded index waveguide with the focusing Kerr nonlinearity is carried out. It is shown that under conditions of phase and group matching, as well as the absence of group velocity dispersion at the third harmonic frequency, a stable light bullet can be formed under certain restrictions. This applies to the lower limit on the temporal duration of the light bullet and to the upper limit on its power. The most stringent condition is the double restriction on the transverse radius of the light bullet.

OsPUB75-OsHDA716 mediates deactivation and degradation of OsbZIP46 to negatively regulate drought tolerance in rice.

Histone deacetylases (HDACs) play crucial roles in plant stress responses via modification of histone as well as non-histone proteins; however, how HDAC-mediated deacetylation of non-histone substrates affects protein functions remains elusive. Here, we report that the Reduced Potassium Dependency3/Histone Deacetylase1 (RPD3/HDA1)-type histone deacetylase OsHDA716 and plant U-box (PUB) E3 ubiquitin ligase OsPUB75 form a complex to regulate rice drought response via deactivation and degradation of basic leucine zipper (bZIP) transcription factor OsbZIP46 in rice (Oryza sativa). OsHDA716 decreases ABA-induced drought tolerance, and mechanistic investigations showed that OsHDA716 interacts with and deacetylates OsbZIP46, a key regulator in ABA signaling and drought response, thus inhibiting its transcriptional activity. Furthermore, OsHDA716 recruits OsPUB75 to facilitate ubiquitination and degradation of deacetylated OsbZIP46. Therefore, the OsPUB75-OsHDA716 complex exerts double restrictions on the transcriptional activity and protein stability of OsbZIP46, leading to repression of downstream drought-responsive gene expression and consequently resulting in reduced drought tolerance. Conversely, OsbZIP46 acts as an upstream repressor to repress OsHDA716 expression, and therefore OsHDA716 and OsbZIP46 form an antagonistic pair to reciprocally inhibit each other. Genetic evidence showed that OsHDA716 works with OsbZIP46 in a common pathway to antagonistically regulate rice drought response, revealing that plants can fine-tune stress responses by the complex interplay between chromatin regulators and transcription factors. Our findings unveil an acetylation-dependent regulatory mechanism governing protein functions and shed light on the precise coordination of activity and stability of key transcription factors through a combination of different post-translational modifications.

Instrument-Based Estimation of Full Treatment Effects with Partial Compliers

Abstract The effect of the full treatment is a primary parameter of interest in policy evaluation, while often the effect of a subset of treatment is estimated. We partially identify the local average treatment effect of receiving full treatment (LAFTE) using an instrumental variable that may induce individuals into subsets of treatment (partial compliers). We show that partial compliers violate the standard exclusion restriction, necessary conditions on the absence of partial compliers are testable, and partial identification holds under a double exclusion restriction. We identify partial compliers in four applications and estimate informative bounds on the LAFTE in three of them.

Identification of geochemical anomalies in multibackground areas using the combined k-means clustering and residual contrast value method: A case study in a district in Hunan, China

Due to the complex characteristics of geological structures, identifying geochemical anomalies in valuable deposits using regional geochemical datasets of stream sediments is challenging. In this study, an effective combined method was proposed to solve the problem of anomaly identification in multibackground areas. First, samples were classified into different clusters through the k-means clustering method using major elements/minerals (such as SiO2 and Na2O) that can reflect the lithology and were chosen as classification indicators. Considering the double restriction of the contour coefficient and lithological background, each sample within the same cluster was considered to have the same background. Then, the residual value between each sample and the mean data of adjacent samples within the same cluster was calculated, and the original data of each sample were replaced with the ratio (a new parameter defined as the residual contrast value) of the residual value and the anomaly threshold obtained for the corresponding cluster. Finally, geochemical maps and anomaly maps were generated using the residual contrast values. A practical example involving a regional geochemical dataset of stream sediments in Hunan, China, was examined in detail to clarify the procedure. Moreover, a comparative analysis through success rate curves of the percentage of deposits correctly determined was performed between the traditional method, singularity method and new combined method. The results showed that the anomalies identified by the proposed method were closely associated with known deposits, and the residual contrast value, which considers the effects of the lithological background, random error, and structural anomalies, could eliminate the influence of lithology and enhance weak anomalies. Moreover, the geological significance of this method is clear, and the calculation procedure is simple. Thus, this method could be applied for identifying regional geochemical anomalies in multibackground areas and could be used as a guide for new exploration targets.

Variant calling and genotyping accuracy of ddRAD-seq: Comparison with 20X WGS in layers.

Whole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens. Until now, breeding companies have been using or developing SNP chips. Nevertheless, alternatives methods based on sequencing have been developed. Among these, reduced representation sequencing approaches can offer sequencing quality and cost-effectiveness by reducing the genomic regions covered by sequencing. The aim of this study was to evaluate the ability of double digested Restriction site Associated DNA sequencing (ddRAD-seq) to identify and genotype SNPs in laying hens, by comparison with a presumed reliable WGS approach. Firstly, the sensitivity and precision of variant calling and the genotyping reliability of ddRADseq were determined. Next, the SNP Call Rate (CRSNP) and mean depth of sequencing per SNP (DPSNP) were compared between both methods. Finally, the effect of multiple combinations of thresholds for these parameters on genotyping reliability and amount of remaining SNPs in ddRAD-seq was studied. In raw form, the ddRAD-seq identified 349,497 SNPs evenly distributed on the genome with a CRSNP of 0.55, a DPSNP of 11X and a mean genotyping reliability rate per SNP of 80%. Considering genomic regions covered by expected enzymatic fragments (EFs), the sensitivity of the ddRAD-seq was estimated at 32.4% and its precision at 96.4%. The low CRSNP and DPSNP values were explained by the detection of SNPs outside the EFs theoretically generated by the ddRAD-seq protocol. Indeed, SNPs outside the EFs had significantly lower CRSNP (0.25) and DPSNP (1X) values than SNPs within the EFs (0.7 and 17X, resp.). The study demonstrated the relationship between CRSNP, DPSNP, genotyping reliability and the number of SNPs retained, to provide a decision-support tool for defining filtration thresholds. Severe quality control over ddRAD-seq data allowed to retain a minimum of 40% of the SNPs with a CcR of 98%. Then, ddRAD-seq was defined as a suitable method for variant calling and genotyping in layers.

The Imprisonment and Escape of the Characters in The Cement Garden from the Perspective of Power Space

Under the interaction of space and power, characters in The Cement Garden are subject to the double restriction of the above-ground and underground spaces in their home, resulting in confused identity cognition, which leads to the characters’ incestuous behavior. From the perspective of power space, this paper explores the negative impact of family dysfunction on the soul and body of characters, as well as the initiative and necessity of individuals to develop a clear personal identity recognition through interaction with social space.

Construction, Identification, and Expression of Lactococcus lactis-Based Recombinant Vaccine for Echinococcus granulosus

To construct Lactococcus lactis (LL)-based recombinant LL-Eg95 (rLL-Eg95) vaccine for Echinococcus granulosus (Eg) and to examine its expression efficiency. Eg95 gene was obtained by PCR from the template of pCD-Eg95. Then, pMG36e was inserted in the Eg95 gene after double cleaving with restriction endonucleases XbaⅠ and HindⅢ to construct recombinant plasmid pMG36e-Eg95, which was transformed into E.coli BL2 (DE3) competent cells. The recombinant plasmid was extracted and identified by double restriction endonuclease digestion and was then electroporated into LL MG1363 to construct rLL-Eg95 vaccine. Then, the plamid was extracted and identified by PCR. Examination of the recombinant plasmid by double restriction endonuclease digestion showed that the segment was of the expected length. PCR showed that 471 base pairs of Eg95 gene were amplified when the plasmid extracted from roxithromycin-resistant recombinant LL was used as the template. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that the relative molecular mass of the Eg95 protein expressed was approximately 16.5×103 and that the amount of the expressed protein was 17% of the total bacterial proteins. Western blot findings suggested that the expressed protein could be recognized by mice serum infected with hydatid cyst. The rLL-Eg95 vaccine was successfully constructed, expressing Eg95 protein that has specific antigenicity.

An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton (Gossypium spp.).

High-throughput chromosome conformation capture (Hi-C) technology has been applied to explore the chromatin interactions and shed light on the biological functions of three-dimensional genomic features. However, it remains challenging to guarantee the high quality of Hi-C library in plants and hence the reliable capture of chromatin structures, especially loops, due to insufficient fragmentation and low efficiency of proximity ligations. To overcome these deficiencies, we optimized the parameters of the Hi-C protocol, principally the cross-linking agents and endonuclease fragmentation strategy. The double cross-linkers (FA+DSG) and double restriction enzymes (DpnII+DdeI) were utilized. Thus, a systematic in situ Hi-C protocol was designed using plant tissues embedded with comprehensive quality controls to monitor the library construction. This upgraded method, termed Hi-C 3.0, was applied to cotton leaves for trial. In comparison with the conventional Hi-C 2.0, Hi-C 3.0 can obtain more than 50% valid contacts at a given sequencing depth to improve the signal-to-noise ratio. Hi-C 3.0 can furthermore enhance the capturing of loops almost as twice as that of Hi-C 2.0. In addition, Hi-C 3.0 showed higher efficiency of compartment detection and identified compartmentalization more accurately. In general, Hi-C 3.0 contributes to the advancement of the Hi-C method in plants by promoting its capability on decoding the chromatin organization.

Biopanning, Heterologous Expression, and Characterization of a Shark-Derived Single-Domain Antibody Fusion Protein against Pancreatic Lipase.

Nowadays, obesity severely impacts human health and is the fifth leading risk factor that leads to death globally. Pancreatic lipase (PL) inhibitors have attracted extensive attention owing to their role in effective prevention and treatment of obesity. Here, a shark-derived single-domain antibody fusion protein was used to inhibit PL for the first time. After biopanning, the heterologous expression system pET28a-SUMO-D2 was constructed using the method of double restriction enzyme digestion and T4 ligase to achieve the soluble expression of the PL-specific antibody gene D2. According to the calculation of protein concentration, the final expression of fusion protein PL-D2S was 1.183 mg per liter of Luria Bertani broth. The binding ability of the soluble fusion protein PL-D2S to PL was identified. Enzyme-linked immunosorbent assay results showed that the fusion protein PL-D2S exhibited a strong binding affinity to PL. The experimental results of PL inhibition of PL-D2S in vitro showed that the fusion protein could significantly inhibit the activity of PL, with an IC50 of 404 μg/mL. Our study shows that the fusion protein PL-D2S is a potential PL inhibitor to prevent and treat obesity.

Limitation of claims for creditors: causes and general rules of calculation

The paper is devoted to topical issues of the occurrence of accounts payable, its reflection in accounting and the procedure for calculating the statute of limitations for accounts payable. The researched topic is very relevant, because missing the statute of limitations can lead to dissatisfaction with the claim and the ability of the company to fulfill its obligations. The paper analyzes the normative-legislative base, on the basis of which the concept of statute of limitations, statute of limitations, types of statute of limitations is defined. In order to find out the statute of limitations in accounting, the forms of current payables were examined. Limitation periods were also established for each form of current payables. We found out that the statute of limitations also applies to labor disputes. It should be noted that Article 233 of the Labor Code of Ukraine establishes the statute of limitations for an employee's claim against the enterprise. It was investigated that according to the norms of the current legislation, not only the employee, but also the employer also has the right to apply to the court for recovery from the employee to maintain the material damage caused by the employee to the business entity. During the analysis of the Ukrainian legislature, it was found that the statute of limitations also applies to administrative legal relations. We have established that the Tax Code of Ukraine due to the expiration of the statute of limitations, the creditor debt can be considered bad debt. However, due to the fact that Ukraine currently has double restrictions on the expiry of the statute of limitations, these terms are being extended.

Performance Optimization for Decode and Forward Cooperative Cognitive Radio Networks

This paper considers the problem of optimizing the data rate of the cooperative cognitive system subject to the dual constraints of the interference threshold of primary users and power budget of secondary users. In particular, under a single constraint, the rate can reach its peak easily. But under the double restrictions, the peak rate problem becomes complicated and changeable. According to different interference conditions and power supplies, four scenarios are formulated: total interference threshold and total power budget, total interference threshold and separate power budget, separate interference threshold and total power budget, and separate interference threshold and separate power budget. Each scenario needs to be further divided into many situations for discussion due to the sheer particularity. Through careful comparison and classification, we summarize and formulate each situation one by one to achieve the optimal value of the rate. Extensive simulation results demonstrate that the proposed resource allocation policy represents the best compromise between enhancing the rate of the secondary users and satisfying the interference threshold requirements of the primary users.

Characterization of a sex-determining locus and development of early molecular assays in Telfairia occidentalisHook. F., a dioecious cucurbit

Although there exist over 7000 crop species, only a few are commercially valuable and grown on a large scale in monocultures worldwide. However, underutilised crops (also called orphan crops) have significant potential for food security and Telfairia occidentalis Hook. F. (Cucurbitaceae) is one such orphan crop grown in West Africa for its nutritious leaves, oil and protein-rich seeds. In this dioecious crop, farmers like to eliminate male plants and keep mostly females to increase their yield. However, they face the challenge of determining sex due to limited morphological differences between females and males before flowering. This study used double digested restriction site-associated DNA sequencing data (ddRADseq) to examine the genetic diversity within and among landraces of T. occidentalis, identify common sex-determining loci, and establish reliable assays to characterize the sex of immature plants in the vegetative state. To differentiate males from females of T. occidentalis, two molecular assays were thereupon developed based on polymerase chain reaction (PCR) to genotype sex-specific sequence variation either through restriction by Mfe1 or the direct use of sex-specific primers. Both assays require standard laboratory conditions to reach a certainty of 94.3% for females and 95.7% for males from the studied samples. With the inclusion of additional landraces, medium to largescale farms growing T. occidentalis as a crop can readily benefit from an early determination of the sex of plants.

Study of Magnetorheological Grease Flow in a Double Restriction Seal Configuration

Abstract This work presents an investigation of magnetohydrodynamic flow in a novel double restriction seal configuration using micro-Particle Image Velocimetry (µPIV). A conventional seal design has been modified to impart magnetic effects in the flow of magnetorheological grease, which is prepared with 5% by weight of carbonyl iron particles dispersed in NLGI 3 grade lithium-soap-based grease. Rectangular bar magnets are fitted on the seal to induce an external magnetic field strength greater than 0.8 T. The grease flows between two restrictions in the annular domain, and the velocity field is captured by a µPIV technique. Experimental results predict that flow velocities are considerably lower in the presence of the magnetic field. Carbonyl iron particles orient themselves in the direction of the magnetic field and form strong chains which increase the yield stress of the grease medium. Maximum velocities are obtained in the vicinity of the shaft. Further, a numerical model has been developed to predict the velocities at different locations in the annular grease domain at varying rotational speeds of the shaft.

Localization of TWISTED NEEDLES Locus on Linkage Map of Japanese Cedar (Cryptomeria japonica D. Don)

Sugi (Cryptomeria japonica D. Don) is an important forestry species in Japan. C. japonica ‘Spiralis’ is a mutant with twisted needles. The mutant is called Yore-sugi in Japan and is known as ‘Rasen’ in other countries. The twisted trait is regulated by a dominant gene called TWISTED NEEDLES, and it can be identified by observing the needles within 1 to 2 months after germination. The TWISTED NEEDLES gene may be useful for improving the efficiency of genome editing technology in C. japonica. In this study, we attempted to identify the linkage group of the TWISTED NEEDLES locus and investigate markers that sandwich this locus using the mapping family. First, we identified the linkage group containing the TWISTED NEEDLES locus based on the distortion from the expected segregation ratio using 32 mutant individuals of the mapping family. The segregation distortion showed that the TWISTED NEEDLES locus was located on the 11th linkage group (LG11). Next, a linkage map of LG11 was constructed based on genotype data from the single-nucleotide polymorphism (SNP) markers and double digested restriction site-associated DNA sequencing (ddRAD-seq) using 123 individuals of the MMY-1 family. On this map, six markers were located at the same position as the TWISTED NEEDLES locus. To investigate markers sandwiching the TWISTED NEEDLES locus, a partial linkage map around the TWISTED NEEDLES locus was constructed using 643 individuals of the MMY-1 family. The TWISTED NEEDLES locus was located in the 0.6 cM region between gSNP01822 and the other five markers (Contig_4705-179, Contig_4518-93, Contig_4398-118, gSNP04056, and Contig_4970-113).

Library Document Resource Construction and Data Sharing Based on Semantic Web Technology

With the deepening of the reform and development of higher education, many colleges and universities have taken the merger as an opportunity to promote the leap-forward development of their schools. Some colleges and universities that have not merged have also taken the newly-built campus as a new growth point to promote the rapid development of their schools. The library’s collection structure reflects a library’s document support ability, and the formation of the collection structure depends on the accumulation of document resources. Based on semantic web technology, this paper studies the construction of library literature resources. Among the institutions that choose to give priority to the development of library literature resources in the development strategy of main literature resources, the proportion of long-term preservation practice has reached 65.23%, compared with 57.42% of all other institutions. Due to the small number of samples, we cannot make a simple statistical inference, but it may reflect from the other side that the institutions that pay attention to digital resources are slightly more active in implementing preservation activities than other institutions. Based on the semantic web technology, the integrity and continuity of important documents and characteristic resources were kept and we paid attention to the collection of publications and academic documents related to our school. Under the double restriction of document resources guarantee, the acquisition behavior of guarantee systems at all levels will gradually strengthen self-control, actively establish the concept of coordination and sharing, and gradually move from randomness to standardization.

Using multiple-fragment amplification combined with Gibson assembly to clone genes with site-directed mutations

In order to develop a simple and efficient site-directed mutagenesis solution, the Gibson assembly technique was used to clone the cyclin dependent kinase 4 gene with single or double site mutations, with the aim to simplify the overlap extension PCR. The gene fragments containing site mutations were amplified using a strategy similar to overlap extension PCR. Meanwhile, an empty plasmid was digested by double restriction endonucleases to generate a linearized vector with a short adaptor overlapping with the targeted gene fragments. The gene fragments were directly spliced with the linearized vector by Gibson assembly in an isothermal, single-reaction, creating a recombinant plasmid. After the recombinant plasmids were transformed into competent Escherichia coli DH5α, several clones were screened from each group. Through restriction analysis and DNA sequencing, it was found that the randomly selected clones were 100% target mutants. Since there was neither tedious multiple-round PCR amplification nor frequent DNA extraction operation, and there was no need to digest the original plasmid, this protocol circumvents many factors that may interfere with the conventional site-directed mutagenesis. Hence, genes with single or multiple mutations could be cloned easily and efficiently. In summary, the major defects associated with overlap extension PCR and rolling circle amplification were circumvented in this protocol, making it a good solution for site-directed mutagenesis.

A Multi-Mechanism Particle Swarm Optimization Algorithm Combining Hunger Games Search and Simulated Annealing

Particle Swarm Optimization (PSO) algorithm is a meta-heuristic algorithm inspired by the foraging behavior of birds, which has received a lot of attention from many scholars because of its simple principle and fast convergence rate. However, the traditional particle update mechanism limits the performance of the algorithm and makes it easy to fall into local extremums, leading to a reduced convergence rate at a later stage. In this paper, we propose a Multi-Mechanism Particle Swarm Optimization (HGSPSO) algorithm. The algorithm optimizes the position update formula of the particles by the Hunger Game Search (HGS) algorithm to accelerate the convergence speed at the later stage of the algorithm, and then the Simulated Annealing (SA) algorithm is introduced to dynamically update the inertia weights to balance the exploration and utilization of the algorithm to help the particles jump out of the local extrema. In addition, the double variational restrictions strategy is used to simultaneously restrict the velocity and position of the particles to avoid particle transgressions. We tested the proposed algorithm with five compare algorithms on 20 benchmark functions in 30, 50, 100, and 1000 dimensions using Eclipse Kepler Release software. The experimental results show that HGSPSO shows significant superiority in all four evaluation metrics and five assessment schemes.

Matrix pencils completions under double rank restrictions

In this paper we study the General Matrix Pencil Completion Problem under double rank restrictions. Considered rank restrictions are not structural, hence the obtained results deal with full sets of Kronecker invariants of the involved matrix pencils, and they generalize many of the existing results in the literature, for example [1, 5, 7, 9, 11, 12, 21, 24, 45, 46]. Main methods consist of combining the celebrated S?-Thompson?s result [1, 39, 44] with novel results on rank restrictions in completions of matrix pencils. All of the obtained results are explicit and constructive.

Making the Shift from Research to Commercial Orchards: A Case Study in Aphid-Peach Tree Interactions as Affected by Nitrogen and Water Supplies.

Simple SummaryCommercial orchards are amongst the most intensively sprayed crops, and alternative methods have to be found to replace pesticides. Limiting water and nitrogen (N) supply has shown to be effective in reducing aphid infestations under controlled conditions. To evaluate how far these techniques could be transferred to orchards subject to production constraints, an experiment was performed in a commercial orchard planted with two varieties differing in precocity and vigour. Limiting supplies of both water and N to trees was shown to reduce the severity of aphid infestation (green peach aphid, mealy plum aphid, and leaf curl aphid), although reducing only water supply was less effective. At shoot level, the composition and development of the infested shoots were only slightly affected by treatment, thereby indicating that aphids colonize shoots of similar condition, whose numbers are modulated by nutrition treatments. These results were consistent with variety and year. Limiting water and N supplies contributes not only to the control of aphid infestations, but also reduces nitrate leaching and the use of water, the consumption of which will inevitably need to a decrease due to climate change. However, the efficiency of aphid control could be enhanced by complementing these practices by other techniques such as adapted pruning or changes to ground cover.Peach orchards are intensively sprayed crops, and alternative methods must be found to replace pesticides. We intend here to evaluate if limiting water and nitrogen (N) supply could be effective in controlling aphid infestation in commercial orchards. N and water supply were therefore either unrestricted or restricted by 30% only for water, or for both water and N, in 2018 and 2019 on trees of two contrasting varieties. Natural infestations (green peach aphid, mealy plum aphid, leaf curl aphid) were monitored regularly at tree and shoot level. Infested and control shoots were compared for their development during the infestation period, their apex concentrations of total N, amino acids, non-structural carbohydrates, and polyphenols at infestation peak. At tree level, limiting both water and N supplies decreased the proportion of infested shoots by 30%, and the number of trees hosting the most harmful specie by 20 to 50%. Limiting only N supplies had almost no effect on infestation severity. At shoot level, the apex N concentration of infested shoots was stable (around 3.2% dry weight) and was found to be independent of treatment, variety, and year. The remaining biochemical variables were not affected by infestation status but by variety and year. Shoot development was only slightly affected by treatment. Aphids colonized the most vigorous shoots, being those with longer apical ramifications in 2018 and higher growth rates in 2019, in comparison with the controls. The differences were, respectively, 40 and 55%. It was concluded that a double restriction in water and N could limit, but not control, aphid infestations in commercial orchards.

Performance and automation of ancient DNA capture with RNA hyRAD probes

DNA hybridization‐capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analysing ancient DNA (aDNA) extracts, which are often dominated by exogenous environmental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design‐free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic restriction of fresh DNA extracts to produce RNA probes that cover only a fraction of the genome and can serve as baits for capturing homologous fragments from aDNA libraries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5‐fold on‐target enrichment for aDNA extracts showing extremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%–30%), while the fraction of endogenous reads mapping on‐ and off‐target was relatively insensitive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on‐target coverage up to 3.6‐fold. Additionally, we used methylation‐sensitive restriction enzymes to produce probes targeting hypomethylated regions, which improved data quality by reducing post‐mortem DNA damage and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture processing. Overall, our work establishes hyRAD as a cost‐effective strategy to recover a set of shared orthologous variants across multiple ancient samples.