Cyclic Behavior of Reinforced High Strain-Hardening UHPC under Axial Tension

The cyclic tensile behavior of steel-reinforced high strain-hardening ultrahigh-performance concrete (HSHUHPC) was investigated in this paper. In the experimental program, 12 HSHUHPC specimens concentrically placed in a single steel reinforcement under cyclic uniaxial tension were tested, accompanied by acoustic emission (AE) source locating technology, and 4 identical specimens under monotonic uniaxial tension were tested as references. The experimental variables mainly include the loading pattern, the diameter of the embedded steel rebar, and the level of target strain at each cycle. The tensile responses of the steel-reinforced HSHUHPC specimens were evaluated using multiple performance measures, including the failure pattern, load–strain response, residual strain, stiffness degradation, and the tension-stiffening behavior. The test results showed that the enhanced bond strength due to the inclusion of steel fibers transformed the failure pattern of the steel-reinforced HSHUHPC into a single, localized macro-crack in conjunction with a sprinkling of narrow and closely spaced micro-cracks, which intensified the strain concentration in the embedded steel rebar. Besides, it was observed that the larger the diameter of the embedded steel rebar, the smaller the maximum accumulative tensile strain under cyclic tension, which indicated that the larger the diameter of the embedded steel rebar, the greater the contribution to the tensile stiffness of steel-reinforced HSHUHPC specimens in the elastic–plastic stage. In addition, it was found that a larger embedded steel rebar appeared to reduce the tension-stiffening effect (peak tensile strength) of the HSHUHPC. Moreover, the residual strain and the stiffness of the steel-reinforced HSHUHPC were reduced by increasing the number of cycles and finally tended toward stability. Nevertheless, different target strain rates in each cycle resulted in different eventual cumulative tensile strain rates; hence the rules about failure pattern, residual strain, and loading stiffness were divergent. Finally, the relationship between the accumulative tensile strain and the loading stiffness degradation ratio under cyclic tension was proposed and the tension-stiffening effect was analyzed.

Broad Purpose Vector for Site-Directed Insertional Mutagenesis in Bifidobacterium breve

Members of the genus Bifidobacterium are notoriously recalcitrant to genetic manipulation due to their extensive and variable repertoire of Restriction-Modification (R-M) systems. Non-replicating plasmids are currently employed to achieve insertional mutagenesis in Bifidobacterium. One of the limitations of using such insertion vectors is the presence within their sequence of various restriction sites, making them sensitive to the activity of endogenous restriction endonucleases encoded by the target strain. For this reason, vectors have been developed with the aim of methylating and protecting the vector using a methylase-positive Escherichia coli strain, in some cases containing a cloned bifidobacterial methylase. Here, we present a mutagenesis approach based on a modified and synthetically produced version of the suicide vector pORI28 (named pFREM28), where all known restriction sites targeted by Bifidobacterium breve R-M systems were removed by base substitution (thus preserving the codon usage). After validating the integrity of the erythromycin marker, the vector was successfully employed to target an α-galactosidase gene responsible for raffinose metabolism, an alcohol dehydrogenase gene responsible for mannitol utilization and a gene encoding a priming glycosyltransferase responsible for exopolysaccharides (EPS) production in B. breve. The advantage of using this modified approach is the reduction of the amount of time, effort and resources required to generate site-directed mutants in B. breve and a similar approach may be employed to target other (bifido)bacterial species.

barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection

Background Tracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including previously utilized tester strains. Recent work has shown that genomic insertion of short identification tags, called “barcodes” here, allows detection of chromosomally tagged strains by real-time PCR. Manual design of these barcodes is feasible for small sets, but expansion of the technique to larger pools of distinct and well-functioning assays would be significantly aided by software-guided design. Results Here we introduce barCoder, a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode “modules” that consist of binding sites for primers and probes, and appropriate spacer sequences. Each module is designed to yield optimal PCR amplification and unique identification. Optimal amplification includes metrics such as ideal melting temperature and G+C content, appropriate spacing, and minimal stem-loop formation; unique identification includes low BLAST hits against the target organism, previously generated barcode modules, and databases (such as NCBI). We tested the ability of our algorithm to suggest appropriate barcodes by generating 12 modules for Bacillus thuringiensis serovar kurstaki—a simulant for the potential biowarfare agent Bacillus anthracis—and three each for other potential target organisms with variable G+C content. Real-time PCR detection assays directed at barcodes were specific and yielded minimal cross-reactivity with a panel of near-neighbor and potential contaminant materials. Conclusions The barCoder algorithm facilitates the generation of synthetically barcoded biological simulants by (a) eliminating the task of creating modules by hand, (b) minimizing optimization of PCR assays, and (c) reducing effort wasted on non-unique barcode modules.

Periodic training of creeping solids

We consider disordered solids in which the microscopic elements can deform plastically in response to stresses on them. We show that by driving the system periodically, this plasticity can be exploited to train in desired elastic properties, both in the global moduli and in local “allosteric” interactions. Periodic driving can couple an applied “source” strain to a “target” strain over a path in the energy landscape. This coupling allows control of the system’s response, even at large strains well into the nonlinear regime, where it can be difficult to achieve control simply by design.

barCoder: a tool to generate unique, orthogonal genetic tags for qPCR detection

BackgroundTracking dispersal of microbial populations in the environment requires specific detection methods that discriminate between the target strain and all potential natural and artificial interferents, including previously utilized tester strains. Recent work has shown that genomic insertion of short identification tags, called “barcodes” here, allows detection of chromosomally tagged strains by real-time PCR. Manual design of these barcodes is feasible for small sets, but expansion of the technique to larger pools of distinct and well-functioning assays would be significantly aided by software-guided design.ResultsHere we introduce barCoder, a bioinformatics tool that facilitates the process of creating sets of uniquely identifiable barcoded strains. barCoder utilizes the genomic sequence of the target strain and a set of user-specified PCR parameters to generate a list of suggested barcode “modules” that consist of binding sites for primers and probes and appropriate spacer sequences. Each module is designed to yield optimal PCR amplification and unique identification. Optimal amplification includes metrics such as ideal Tm and G+C-content, appropriate spacing, and minimal stem-loop formation; unique identification includes low BLAST hits against the target organism, previously generated barcode modules, and databases, such as NCBI. We tested the ability of our algorithm to suggest appropriate barcodes by generating 12 modules for Bacillus thuringiensis serovar kurstaki, a simulant for the potential biowarfare agent Bacillus anthracis, and three each for other potential target organisms with variable G+C content. Real-time PCR detection assays directed at barcodes were specific and yielded minimal cross-reactivity with a panel of near-neighbor and potential contaminant materials.ConclusionsThe barCoder algorithm facilitates the generation of barcoded biological simulants by (a) eliminating the task of creating modules by hand, (b) minimizing optimization of PCR assays, and (c) reducing effort wasted on non-unique barcode modules.

Prediction of the Work-Hardening Exponent for 3104 Aluminum Sheets with Different Grain Sizes

A practical approach to predict the yield strength and work-hardening exponent (n value) to evaluate the deep-drawing performance of annealed 3104 aluminum sheets is presented in the present work by only measuring and analyzing the grain size of the sheet. The various grain sizes were obtained through the different annealing treatment and then the evolution of the n value under different strains and the yield strength of annealed 3104 aluminum sheet were evaluated. Results showed that the n value and yield strength vary greatly with the grain size. A mathematical model relating grain size d, work-hardening exponent n, target strain ε, and yield strength Rp0.2 was developed in the present work. Within the studied grain size range d (12–29 μm), the n value generally increased with d in a strain-dependent manner, such that n = 0.1875 − 85.03 × exp [ − d / 1.94 ] when the ε was less than 0.5%, but n = 0.3 − 0.15 d − 1 / 2 when the ε was greater than 2%. On the other hand, the n value was found to depend on the target strain ε as n = 0.276 − A 1 × exp [ − e / 1.0435 ] , where A1 varies with d and its value is in the range of 0.132–0.364. In addition, the relationship between Rp0.2 and d followed the Hall-Petch equation ( R p 0.2 = 36.273 + 139.8 × d − 1 / 2 ).

Comparative study of red yeast rice with high monacolin K, low citrinin concentration and pigments in white rice and brown rice

Growth pigments and metabolites of monacolin K and citrinin were compared for Monascus purpureus during 14-day solid-state ermentation on white rice and brown rice (Chai-Nart cultivar). Monascus purpureus IFRPD 4046 was selected as the target strain which produced the ighesth monacolin K content and the lowest citrinin content. Optimum fermentation conditions regarding moisture content, temperature and fermentation time were determined. A comparative study showed that monacolin K production in white rice was about twice higher than in brown rice. At the optimum conditions, concentrations of monacolin K dried at 55°C to constant weight were 132.98 and 66.48 mg/100 g in white rice and brown rice, respectively while citrinin was not detected. Results revealed that the IFRPD 4046 strain has a potential to produce red yeast rice with higher monacolin K in white rice than<br />in brown rice with low citrinin content.

RefSeq database growth influences the accuracy of k-mer-based species identification

ABSTRACTAccurate species-level taxonomic classification and profiling of complex microbial communities remains a challenge due to homologous regions shared among closely related species and a sparse representation of non-human associated microbes in the database. Although the database undoubtedly has a strong influence on the sensitivity of taxonomic classifiers and profilers, to date, no study has carefully explored this topic on historical RefSeq releases and explored its impact on accuracy. In this study, we examined the influence of the database, over time, on k-mer based sequence classification and profiling. We present three major findings: (i) database growth over time resulted in more classified reads, but fewer species-level classifications and more species-level misclassifications; (ii) Bayesian re-estimation of abundance helped to recover species-level classifications when the exact target strain was present; and (iii) Bayesian reestimation struggled when the database lacked the target strain, resulting in a notable decrease in accuracy. In summary, our findings suggest that the growth of RefSeq over time has strongly influenced the accuracy of k-mer based classification and profiling methods, resulting in different classification results depending on the particular database used. These results suggest a need for new algorithms specially adapted for large genome collections and better measures of classification uncertainty.

Morphological and growth responses of two green algal strains to toxic Microcystis are dependent on the cultivation growth phase of filtrate and target strain

Allelopathic interactions amongst phytoplankton are considered an important factor contributing to species competition and succession in aquatic ecosystems, but their mechanisms in plankton dynamics are poorly described. In this study, whether toxic Microcystis aeruginosa could affect the growth of Chlorella vulgaris and Kirchneriella sp. was examined according to filtrate experiments at different cultivation phases. Results indicated that M. aeruginosa filtrate significantly influenced the growth and morphological characteristics of the two target green algae, which were dependent on the cultivation growth phase of filtrate and target strain. At the beginning of the experiment, the formation of a large C. vulgaris colony was induced by M. aeruginosa filtrate. The effects of filtrate in the stationary phase (SP) was more significant than that of the exponential phase (EP). Subsequently, the colonies gradually broke into small colonies or single cells. The growth rate of C. vulgaris was finally promoted in the filtrate treatment. For Kirchneriella sp., the colonies formed and remained in M. aeruginosa filtrate under EP until the end of the experiment. Smaller colonies were observed in Kirchneriella sp. by M. aeruginosa filtrate under SP than those in the control, and larger colonies were not detected. The growth rate of Kirchneriella sp. was inhibited in the filtrate of EP but was promoted in SP. This study provided new insights into the interaction between the morphological responses and growth effects of algae and proposed a new theoretical basis for algal succession in aquatic ecosystems.