Temperature dependence of circular DNA topological states

Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo simulation, we predict the temperature dependence of the linking number distribution of small circular DNAs. Our predictions are based on flexible defect excitations resulted from local melting or unstacking of DNA base pairs. We found that the reduced bending rigidity alone can lead to measurable changes of the variance of linking number distribution of short circular DNAs. If the defect is accompanied by local unwinding, the effect becomes much more prominent. The predictions can be easily investigated in experiments, providing a new method to study the micromechanics of sharply bent DNAs and the thermal stability of specific DNA sequences. Furthermore, the predictions are directly applicable to the studies of binding of DNA distorting proteins that can locally reduce DNA rigidity, form DNA kinks, or introduce local unwinding.Comment: 15 pages in preprint format, 4 figure

Relationship of rock microscopic parameters with the elastic modulus and strength

The microscopic damage of materials will induce changes in the macroscopic mechanical characteristics of rock material. When simulating engineering problems using the discrete element method, to explore the macroscopic mechanical response of rock material, the microscopic parameters that match the macro material characteristics must be obtained. In this paper, the influence of macroscopic mechanical properties of rock materials is studied through the variation of microscopic parameters, and the quantitative relation between macroscopic parameters of rock material is discussed. The results show that, (1) In accordance with the order of influencing factors, the parameters affecting the elastic modulus of the specimen are parallel bond elastic modulus, particle contact modulus, and parallel bond stiffness ratio. (2) The Poisson’s ratio of the specimen was most influenced by the parallel bond stiffness ratio, and their relation was nonlinear. The influence of parallel bond modulus and friction factor on the Poisson’s ratio was negatively correlated. (3) The effect of particle contact stiffness ratio, parallel bond stiffness ratio, and particle contact modulus on the uniaxial compressive strength was less than that of the particle friction factor

Crystallization and preliminary crystallographic analysis of the ADP-ribosyltransferase HopU1. Corrigendum

A correction to the article by Lin et al. [(2010). Acta Cryst. F66, 932–934]

Railway Safety Risk Assessment and Control Optimization Method Based on FTA-FPN: A Case Study of Chinese High-Speed Railway Station

In order to make safety risk assessment more accurately and more reasonably for high-speed railway station in China, this paper analyzes risk factors of fault tree and transfers the fault tree of risk accident into fuzzy petri net and then builds the FPN-FTA model by combining the dynamic weighting fuzzy petri net (FPN) and fault tree analysis (FTA) based on the latter. This paper simulates the FTA-FPN model with Stateflow of Matlab software. Then, it builds up a bi-objective risk control model, making the minimum safety risk level and minimum necessary cost as the objectives, and it designs discrete particle swarm optimization algorithm to solve the risk control model. Finally, this paper selects stampede accident of Shijiazhuang high-speed railway station as an example in case study for assessing stampede risk level and gets the risk control schemes for this station. The results verify the feasibility and validity of the model and algorithm. Document type: Articl

Study on order analysis for condition monitoring wind turbine gearbox

A complex 3-stage gearbox design, in which one planetary gear set at first stage and two sets of parallel gears at second and third stage, is conventionally applied on the large wind turbine configuration with Doubly Fed Induction Generator. In this variable-speed wind turbine, it is hard to directly apply conventional frequency analysis on condition monitoring of the gearbox planetary stage. Proper signal processing and analysis become crucial here for interpreting the conditions of gears and bearings. In this paper, order analysis is studied for condition monitoring the planetary stage of wind turbine gearbox. The approach takes advantage of angular resampling to achieve cyclo-stationary vibration signals and lessen the effects due to speed changes. One key element in the scheme is taking angular information to enable resampling the time-domain signals into angular-domain signals. A vibration signal model for gearbox planetary stage is firstly described, and the scheme is then tested on simulated signals to achieve fine frequency resolution. Time synchronous averaging is applied as a pre-processing technique to enhance the Signal to Noise Ratio (SNR) in order spectru

Parameter-Efficient Tuning Makes a Good Classification Head

In recent years, pretrained models revolutionized the paradigm of natural language understanding (NLU), where we append a randomly initialized classification head after the pretrained backbone, e.g. BERT, and finetune the whole model. As the pretrained backbone makes a major contribution to the improvement, we naturally expect a good pretrained classification head can also benefit the training. However, the final-layer output of the backbone, i.e. the input of the classification head, will change greatly during finetuning, making the usual head-only pretraining (LP-FT) ineffective. In this paper, we find that parameter-efficient tuning makes a good classification head, with which we can simply replace the randomly initialized heads for a stable performance gain. Our experiments demonstrate that the classification head jointly pretrained with parameter-efficient tuning consistently improves the performance on 9 tasks in GLUE and SuperGLUE.Comment: Accepted as a long paper to EMNLP 2022 Main Conferenc

Experience in prenatal ultrasound diagnosis of fetal microtia and associated abnormalities

ObjectivePrenatal ultrasound features, associated anomalies and genetic abnormalities of microtia cases were analyzed to explore the feasibility and value of prenatal ultrasound for the diagnosis of microtia.MethodsThe ultrasonographic features, associated anomalies, chromosome examination results and follow-up results of 81 fetuses with congenital microtia were analyzed retrospectively.ResultsAmong the 81 fetuses with microtia diagnosed after birth, 2 cases were missed diagnosis on prenatal ultrasound, and 1 case was diagnosed as unilateral microtia by prenatal ultrasound but was found to be bilateral microtia after birth. Microtia was accompanied by an accessory auricle in 4 cases (4.94%) and low-set ears in 7 cases (8.64%). 22 cases (27.16%) were complicated with other structural anomalies, including 11 cases (13.58%) of cardiac anomalies, 7 cases (8.64%) of ultrasonographic soft marker anomalies, 6 cases (7.41%) of facial anomalies, 6 cases (7.41%) of nervous system anomalies, 3 cases (3.70%) of urogenital system anomalies, 3 cases (3.70%) of digestive tract anomalies and 2 cases (2.47%) of limb anomalies. Chromosome karyotype analysis and gene detection were performed in 44 cases. Trisomy 18, trisomy 13, trisomy 21, pericentric inversion of chromosome 9, partial loss of heterozygosity on chromosome 14, 22q11 microdeletion and a normal karyotype were found in 2 cases, 2 cases, 3 cases, 1 case, 1 case, 1 case, and 34 cases, respectively.ConclusionIn summary, microtia is often accompanied by congenital defects of other organs and structures, especially the heart and face, and prenatal ultrasound diagnosis of microtia and associated anomalies is of important clinical significance

Indole-3-acetate induces apoptosis and stimulates phosphorylation of p65NF-κB in 143B and HOS osteosarcoma cells

Purpose: To investigate the effect of indole-3-acetate (IAA) on the proliferation of 143B and HOS osteosarcoma cells, and its mechanism of action.Methods: Indole-3-acetate (IAA)-induced changes in cell proliferation and apoptosis were investigated using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay and flow cytometry, respectively. The effects of IAA on expressions of mRNAs for phosphatase and tensin homolog (PTEN), fas ligand (FasL), and fas receptor (FasR) were evaluated using western blot assay.Results: Early apoptosis in 143B cell cultures due to addition of IAA (5 μM) was 34.67 %, relative to 2.82 % in untreated cultures. In HOS cells, IAA caused 39.21 % apoptosis, relative to 3.53 % apoptosis in control. The addition of IAA to the cell cultures significantly enhanced the expressions of mRNAs for PTEN, FasL and FasR, compared to untreated cells (p < 0.05). Western blot analysis showed that IAA caused a significant decrease in the level of IκBα expression in both cell lines (p < 0.05). In 143B and HOS cells, treatment with IAA led to accumulation of higher levels of NF-κB in the nucleus than in the cytosol. The levels of cytosolic NF-κB, and nuclear lamin B1 in IAA-treated cells were lower than the corresponding levels in untreated cells.Conclusion: These results indicate that IAA inhibits proliferation, and induces apoptosis in 143B and HOS cells via activation of NF-κB, and its translocation to the nucleus. Therefore, IAA may be a useful drug target in the treatment of osteosarcoma.Keywords: Indole-3-acetate, Phosphatase, Fas receptor, Translocation, Proliferation, Tumoricidal activit

Differential miRNA expression in Rehmannia glutinosa plants subjected to continuous cropping

<p>Abstract</p> <p>Background</p> <p>The productivity of the medicinally significant perennial herb <it>Rehmannia glutinosa </it>is severely affected after the first year of cropping. While there is some information available describing the physiological and environmental causes of this yield decline, there is as yet no data regarding the changes in gene expression which occur when the species is continuously cropped.</p> <p>Results</p> <p>Using a massively parallel (Solexa) DNA sequencing platform, it was possible to identify and quantify the abundance of a large number of <it>R. glutinosa </it>miRNAs. We contrasted the miRNA content of first year crop plants with that of second year crop ones, and were able to show that of 89 conserved (belonging to 25 families) and six novel miRNAs (six families), 29 of the former and three of the latter were differentially expressed. The three novel miRNAs were predicted to target seven genes, and the 29 conserved ones 308 genes. The potential targets of 32 of these differentially expressed miRNAs involved in the main transcription regulation, plant development and signal transduction. A functional analysis of the differentially expressed miRNAs suggested that several of the proposed targets could be directly or indirectly responsible for the development of the tuberous root.</p> <p>Conclusion</p> <p>We have compared differential miRNAs expression in the first year crop (FP) <it>R. glutinosa </it>plants and second year crop (SP) ones. The outcome identifies some potential leads for understanding the molecular basis of the processes underlying the difficulty of maintaining the productivity of continuously cropped <it>R. glutinosa</it>.</p