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Stress-induced DNA duplex destabilization (SIDD) analysis exploits the known structural and energetic properties of DNA to predict sites that are susceptible to strand separation under negative superhelical stress. When this approach was used to calculate the SIDD profile of the entire Escherichia coli K12 genome, it was found that strongly destabilized sites occur preferentially in intergenic regions that are either known or inferred to contain promoters, but rarely occur in coding regions. Here, we investigate whether the genes grouped in different functional categories have characteristic SIDD properties in their upstream flanks. We report that strong SIDD sites in the E. coli K12 genome are statistically significantly overrepresented in the upstream regions of genes encoding transcriptional regulators. In particular, the upstream regions of genes that directly respond to physiological and environmental stimuli are more destabilized than are those regions of genes that are not involved in these responses. Moreover, if a pathway is controlled by a transcriptional regulator whose gene has a destabilized 59 flank, then the genes (operons) in that pathway also usually contain strongly destabilized SIDD sites in their 59 flanks. We observe this statistically significant association of SIDD sites with upstream regions of genes functioning in transcription in 38 of 43 genomes of free-living bacteria, but in only four of 18 genomes of endosymbionts or obligate parasitic bacteria. These results suggest that strong SIDD sites 59 to participating genes may be involved in transcriptional responses to environmental changes, which are known to transiently alter superhelicity. We propose that these SIDD sites are active and necessary participants in superhelically mediated regulatory mechanisms governing changes in the global pattern of gene expression in prokaryotes in response to physiological or environmental changes. [ABSTRACT FROM AUTHOR]

In this paper, we propose a new algorithm based on a quantum walk search model to distinguish strongly similar graphs. Our algorithm computes a signature for each graph via the quantum walk search model and uses signatures to distinguish non-isomorphic graphs. Our method is less complex than those of previous works. In addition, our algorithm can be extended by raising the signature levels. The higher the level adopted, the stronger the distinguishing ability and the higher the complexity of the algorithm. Our algorithm was tested with standard benchmarks from four databases. We note that the weakest signature at level 1 can distinguish all similar graphs, with a time complexity of which that outperforms the previous best work except when it comes to strongly regular graphs (SRGs). Once the signature is raised to level 3, all SRGs tested can be distinguished successfully. In this case, the time complexity is , also better than the previous best work. [ABSTRACT FROM AUTHOR]

Boron is selectively implanted on the surface of an n-type silicon wafer to form a p-type area surrounded by an n-type area. The wafer is then put into a buffered oxide etch solution. It is found that the n-type area can be selectively etched without illumination, with an etching rate lower than 1 nm min[?]1, while the p-type area can be selectively etched under illumination with a much higher etching rate. The possible mechanism of the etching phenomenon is discussed. A simple fabrication process of silicon nanowires is proposed according to the above phenomenon. In this process only traditional micro-electromechanical system technology is used. Dimensions of the fabricated nanowire can be controlled well. A 50 nm wide and 50 nm thick silicon nanowire has been formed using this method. [ABSTRACT FROM AUTHOR]

Based on the law that the oxidation rate of Si decreases with the oxidation time, a method to fabricate a nanochannel is presented. In this method, the depth of the channel is precisely controlled by the oxidation time. Nanochannels are fabricated with depths of several tens of nanometers, width of 20 µm and lengths of several millimeters. SEM images show that the channel is fabricated well. It is shown that the flow rate increases linearly with the inlet pressure for water, NaCl solution and oil. Besides, the flow rate increases with the temperature. The capillary phenomenon is also observed in the nanochannel. [ABSTRACT FROM AUTHOR]

Background: The strategy of using fecal microbiota transplantation (FMT) for refractory ulcerative colitis (UC) remains unclear if single FMT failed to induce remission. This study aimed to evaluate the efficacy and safety of a designed step-up FMT strategy for the steroid-dependent UC.Methods: Fifteen patients with steroid-dependent UC were enrolled, and treated with step-up FMT strategy. Follow-up clinical data was collected for a minimum of 3 months. Fecal microbiota composition before and post FMT of patients and related donors were analyzed by 16S rRNA sequencing.Results: Eight of fourteen (57.1 %) patients achieved clinical improvement and were able to discontinue steroids following step-up FMT. One patient was lost to follow-up. Among the 8 patients who responded, five (35.7 %) received one FMT therapy, one (7.1 %) received two FMTs, and two (14.2 %) received two FMTs plus a scheduled course of steroids. Four (28.6 %) of the 8 patients who responded maintained long-term remission during follow-up (3-18 months). Six patients (42.9 %) failed to meet the criteria of clinical improvement and maintained steroid dependence, though three experienced transient or partial improvement. Microbiota analysis showed that FMT altered the composition greatly, and a microbiota composition highly similar to that of the donor emerged in the patients with successful treatment. No severe adverse events occurred during treatment and follow-up.Conclusions: Step-up FMT strategy shows promise as a therapeutic strategy for patients with steroid-dependent UC, likely due to the successful restructuring of gut microbial composition.Trial Registration: ClinicalTrials.gov, Number NCT01790061. [ABSTRACT FROM AUTHOR]

Nano thin film transistor (TFT) is fabricated at the root of a beam, which becomes the maximum stress area when the beam is bent. In this process, a probe is used to bend the beam and produce GPa-order mechanical stress. The electrical characteristic of TFT under different GPa stress has been studied. Threshold voltage VT, relative drain current change ΔIds/IT, and transconductance gm present a nonlinear relationship with increasing GPa-order stress. Analyzed from experimental results, channel piezoresistivity effect below 1.82 GPa stress, energy valley splitting, large change of valence effective mass from 1.82 to 2.08 GPa, and interface effect above 2.08 GPa are the factors of nonlinear change of parameter with GPa-order mechanical stress. [ABSTRACT FROM AUTHOR]

In living cells, due to the selective permeability and complicated cellular environment, the uptake efficiency and fluorescence decay of organic dyes during dye-labeling may be influenced, which may eventually result in poor fluorescent imaging. In this work, a protocol of UCNs@mSiO2-(FA and Azo) core–shell nanocarriers was designed and prepared successfully. The core–shell nanocarriers were assembled from two parts, including a mesoporous silica shell surface modified by folate (FA) and azobenzene (Azo), and an upconverting nanocrystal (UCN) core. The mesoporous silica shell is used for loading organic dyes and conjugating folate which helps to enhance the cellular uptake of nanocarriers. The UCN core works as a transducer to convert near infrared (NIR) light to local UV and visible light to activate a back-and-forth wagging motion of azobenzene molecules on the surface, while the azobenzene acts as a molecular impeller for propelling the release of organic dyes. The nanocarriers of loading organic dyes can maintain the stability of the fluorescent imaging effect better than free organic dyes. The experimental results show that with the help of the nanoparticle, cell uptake efficiency of the model dyes of rhodamine and 4′, 6-diamidino-2-phenylindole (DAPI) was significantly improved. The release of dyes can only be triggered by NIR light exposure and their quantity is highly dependent on the duration of NIR light exposure, thus realizing NIR-regulated dye release spatiotemporally. Our work may open a novel avenue for precisely controlling UCN-based living cell imaging in biotechnology and diagnostics, as well as studying cell dynamics, cell–cell interactions, and tissue morphogenesis. [ABSTRACT FROM AUTHOR]

Nano-needles play important roles in nanoscale operations. However, current nano-needle fabrication is usually expensive and controling the sizes and angles is complicated. We have developed a simple and low cost silicon nano-needle fabrication method using traditional microelectromechanical system (MEMS) tetramethyl ammonium hydroxide (TMAH) etching techniques. We take advantage of the fact that the decrease of the silicon etch rate in TMAH solutions exhibits an inverse fourth power dependence on the boron doping concentration in our nano-needle fabrication. Silicon nano-needles, with high aspect ratio and sharp angles th as small as 2.9deg, are obtained, which could be used for bio-sensors and nano-handling procedures, such as penetrating living cells. An analytic model is proposed to explain the etching evolution of the experimental results, which is used to predict the needle angle, length, and etching time. Based on our method, nano-needles with small acute angle th can be obtained. [ABSTRACT FROM AUTHOR]