Computational identification of rare codons of Escherichia coli based on codon pairs preference

<p>Abstract</p> <p>Background</p> <p>Codon bias is believed to play an important role in the control of gene expression. In <it>Escherichia coli</it>, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engineering operations. Previous studies have confirmed the existence of codon pair's preference in many genomes, but the underlying cause of this bias has not been well established. Here we focus on the patterns of rarely-used synonymous codons. A novel method was introduced to identify the rare codons merely by codon pair bias in <it>Escherichia coli</it>.</p> <p>Results</p> <p>In <it>Escherichia coli</it>, we defined the "rare codon pairs" by calculating the frequency of occurrence of all codon pairs in coding sequences. Rare codons which are disliked in genes could make great contributions to forming rare codon pairs. Meanwhile our investigation showed that many of these rare codon pairs contain termination codons and the recognized sites of restriction enzymes. Furthermore, a new index (F_rare) was developed. Through comparison with the classical indices we found a significant negative correlation between F_rareand the indices which depend on reference datasets.</p> <p>Conclusions</p> <p>Our approach suggests that we can identify rare codons by studying the context in which a codon lies. Also, the frequency of rare codons (F_rare) could be a useful index of codon bias regardless of the lack of expression abundance information.</p

Disseminated tuberculosis in a child during the COVID-19 pandemic: a case report and literature review

BackgroundDisseminated tuberculosis is an uncommon but devastating form of tuberculosis, possibly developing with the immune response of patients. COVID-19 infection may produce an immunosuppressive effect with possible implications for tuberculosis dissemination.Case presentationA 17-year-old female patient with a history of tuberculous pleurisy presented to the hospital with a high fever and life-threatening dyspnea after contracting a COVID-19 infection. Her condition deteriorated rapidly with grand mal epilepsy and acute gastrointestinal bleeding with a grossly depressed CD4 T-cell count, which was indicative of her profoundly immunosuppressed state. After identifying Mycobacterium tuberculosis in her cerebrospinal fluid and a subcutaneous abscess in her left lower back, she was diagnosed with disseminated tuberculosis involving both lungs, the central nervous system, the terminal ileum, the liver, bilateral adnexal tissue, and subcutaneous soft tissue in accordance with the chest and abdominal CT. Empirical treatment was initiated with dexamethasone (5 mg/day) and an anti-tuberculosis regimen of isoniazid, rifampicin, pyrazinamide, amikacin, and meropenem, which was replaced with faropenem after she left the hospital. The therapeutic effect was considered satisfied in the second month of follow-up.ConclusionTo the best of our knowledge, we report the first case report of disseminated tuberculosis after COVID-19 infection. Tuberculosis may disseminate and progress during the COVID-19 pandemic, requiring more significant studies to provide better diagnosis and treatment options for the co-infection

Transport of intense ion beams in plasmas: collimation and energy-loss reduction

We compare the transport properties of a well-characterized hydrogen plasma for low and high current ion beams. The energy-loss of low current beams can be well understood, within the framework of current stopping power models. However, for high current proton beams, significant energy-loss reduction and collimation is observed in the experiment. We have developed a new particle-in-cell code, which includes both collective electromagnetic effects and collisional interactions. Our simulations indicate that resistive magnetic fields, induced by the transport of an intense proton beam, act to collimate the proton beam and simultaneously deplete the local plasma density along the beam path. This in turn causes the energy-loss reduction detected in the experiment

Observation of whistler wave instability driven by temperature anisotropy of energetic electrons on EXL-50 spherical torus

Electromagnetic modes in the frequency range of 30-120MHz were observed in electron cyclotron wave (ECW) steady state plasmas on the ENN XuanLong-50 (EXL-50) spherical torus. These modes were found to have multiple bands of frequencies proportional to the Alfv\'en velocity. This indicates that the observed mode frequencies satisfy the dispersion relation of whistler waves. In addition, suppression of the whistler waves by the synergistic effect of Lower Hybrid Wave (LHW) and ECW was also observed. This suggests that the whistler waves were driven by temperature anisotropy of energetic electrons. These are the first such observations (not runaway discharge) made in magnetically confined toroidal plasmas and may have important implications for studying wave-particle interactions, RF wave current driver, and runaway electron control in future fusion devices

Solenoid-free current drive via ECRH in EXL-50 spherical torus plasmas

As a new spherical tokamak (ST) designed to simplify engineering requirements of a possible future fusion power source, the EXL-50 experiment features a low aspect ratio (A) vacuum vessel (VV), encircling a central post assembly containing the toroidal field coil conductors without a central solenoid. Multiple electron cyclotron resonance heating (ECRH) resonances are located within the VV to improve current drive effectiveness. Copious energetic electrons are produced and measured with hard X-ray detectors, carry the bulk of the plasma current ranging from 50kA to 150kA, which is maintained for more than 1s duration. It is observed that over one Ampere current can be maintained per Watt of ECRH power issued from the 28-GHz gyrotrons. The plasma current reaches Ip>80kA for high density (>5e18me-2) discharge with 150kW ECHR heating. An analysis was carried out combining reconstructed multi-fluid equilibrium, guiding-center orbits of energetic electrons, and resonant heating mechanisms. It is verified that in EXL-50 a broadly distributed current of energetic electrons creates smaller closed magnetic-flux surfaces of low aspect ratio that in turn confine the thermal plasma electrons and ions and participate in maintaining the equilibrium force-balance

Anomalous stopping of laser-accelerated intense proton beam in dense ionized matter

Ultrahigh-intensity lasers (10$^{18}$-10$^{22}$W/cm$^{2}$) have opened up new perspectives in many fields of research and application [1-5]. By irradiating a thin foil, an ultrahigh accelerating field (10$^{12}$ V/m) can be formed and multi-MeV ions with unprecedentedly high intensity (10$^{10}$A/cm$^2$) in short time scale ($\sim$ps) are produced [6-14]. Such beams provide new options in radiography [15], high-yield neutron sources [16], high-energy-density-matter generation [17], and ion fast ignition [18,19]. An accurate understanding of the nonlinear behavior of beam transport in matter is crucial for all these applications. We report here the first experimental evidence of anomalous stopping of a laser-generated high-current proton beam in well-characterized dense ionized matter. The observed stopping power is one order of magnitude higher than single-particle slowing-down theory predictions. We attribute this phenomenon to collective effects where the intense beam drives an decelerating electric field approaching 1GV/m in the dense ionized matter. This finding will have considerable impact on the future path to inertial fusion energy.Comment: 8 pages, 4 figure

Dynamic recrystallization behavior and microstructure evolution of high-strength low-alloy steel during hot deformation

The dynamic recrystallization (DRX) behavior and microstructure evolution of the high-strength low-alloy (HSLA) steel were studied by isothermal compression experiments at temperatures ranging from 850 to 1150 °C and strain rates ranging from 0.01 to 10 s−1 with a true strain of 0.8. The true stress-strain curves show that the flow stress increases with increasing strain rate and decreasing deformation temperature. The constitutive equation of the HSLA steel was established based on the peak stress, and the deformation activation energy was calculated to be 414.263 kJ/mol. Processing maps corresponding to different true strains were constructed based on the dynamic material model. High strain rates and low deformation temperatures are more likely to lead to flow instability. The microstructure deformed at low temperatures and high strain rates mainly consists of elongated initial grains. The DRX nucleation mechanism of the HSLA steel was explained. Many fine grains nucleate at the initial grain boundaries, forming a necklace structure. The serrated or bulged grain boundaries are the beginning of DRX. In addition, the DRX volume fraction model was established, and the DRX grain size was analyzed. High temperatures and low strain rates promote the nucleation and growth of the DRX

Parallelization of elastic bunch graph matching (EBGM) algorithm for fast face recognition

This paper presents a parallel method for EBGM face recognition. Compared with other methods such as principal component analysis (PCA) and linear discriminant analysis (LDA), EBGM has the advantage of higher accuracy, however, with more computational time and memory usage, which also mean less practicability. We propose a parallel method for EBGM by balancing the unit of images. We distribute the training process and allot the probing images to all processors equally, and then the recognition process is carried out in all processors simultaneously by communicating with each other. The experimental result on Message Passing Interface (MPI) platform shows that the speedup and efficiency maintain excellent with different problem size and the number of processors. Moreover, memory usage also decreases on each processor. © 2013 IEEE