fREDUCE: Detection of degenerate regulatory elements using correlation with expression

<p>Abstract</p> <p>Background</p> <p>The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs.</p> <p>Results</p> <p>We present fREDUCE, a computational method specialized for the detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. fREDUCE is built upon the widely applied program REDUCE, which elicits motifs by global statistical correlation of motif counts with expression data. fREDUCE introduces several algorithmic refinements that allow efficient exhaustive searches of oligonucleotides with a specified number of degenerate IUPAC symbols. On yeast ChIP-chip benchmarks, fREDUCE correctly identified motifs and their degeneracies with accuracies greater than its predecessor REDUCE as well as other known motif-finding programs. We have also used fREDUCE to make novel motif predictions for transcription factors with poorly characterized binding sites.</p> <p>Conclusion</p> <p>We demonstrate that fREDUCE is a valuable tool for the prediction of degenerate transcription factor binding sites, especially from array datasets with weak signals that may elude other motif detection methods.</p

Experimental Study on Fractal Characteristics of Particle Size Distribution by Repeated Compaction of Road Recycling Crushed Stone

In order to investigate the compaction characteristics of graded crushed stone under repeated utilization, it is necessary to improve the utilization rate of road recycling crushed stone and maintain its strength and stability during recycling. In the present study, repeated compaction characteristic curves of graded crushed stone were developed using repeated compaction and screening of the graded crushed stone. The correlations between the fractal dimension of particle size distribution and repeated compaction times, water content, and dry density were analyzed. The experimental results indicate that both the maximum dry density and the optimal water content increase as the repeated compaction times increase. The fractal dimension of the particle size distribution of the graded crushed stone used in this test is 2.33 to 2.57. The obtained results show that as the fractal dimension increases, the maximum dry density of the graded crushed stone increases. At a constant repeated compaction time, the fractal dimension of the particle size distribution of graded crushed stone increased and then decreased as the water content increased. In summary, the compaction performance of the structural layer of graded crushed stone can be tuned by adjusting the fractal dimension of the particle size distribution of the recycled pavement structural layer in practical applications. Moreover, the optimal graded materials can be prepared under the guidance of the fractal dimension, thereby achieving an optimized working performance of the recycled pavement structural layer

Experimental Study on Fractal Characteristics of Particle Size Distribution by Repeated Compaction of Road Recycling Crushed Stone

In order to investigate the compaction characteristics of graded crushed stone under repeated utilization, it is necessary to improve the utilization rate of road recycling crushed stone and maintain its strength and stability during recycling. In the present study, repeated compaction characteristic curves of graded crushed stone were developed using repeated compaction and screening of the graded crushed stone. The correlations between the fractal dimension of particle size distribution and repeated compaction times, water content, and dry density were analyzed. The experimental results indicate that both the maximum dry density and the optimal water content increase as the repeated compaction times increase. The fractal dimension of the particle size distribution of the graded crushed stone used in this test is 2.33 to 2.57. The obtained results show that as the fractal dimension increases, the maximum dry density of the graded crushed stone increases. At a constant repeated compaction time, the fractal dimension of the particle size distribution of graded crushed stone increased and then decreased as the water content increased. In summary, the compaction performance of the structural layer of graded crushed stone can be tuned by adjusting the fractal dimension of the particle size distribution of the recycled pavement structural layer in practical applications. Moreover, the optimal graded materials can be prepared under the guidance of the fractal dimension, thereby achieving an optimized working performance of the recycled pavement structural layer

Experimental Study on Confined Compaction Deformation of Crushed Gangue under Different Water Content Conditions

To study the deformation characteristics of crushed gangue under different water content conditions, the confined compaction test of crushed gangue was carried out under five different water content conditions by using a universal material testing machine and a compaction device. The strain–stress relationship in the compaction process of crushed gangue and the crushing law of gangue particles were obtained through the test, and the effects of the axial stress, water content, and relative crushing rate on the compaction deformation of crushed gangue were analyzed. The results show that the confined compaction deformation process of crushed gangue can be divided into three stages: the rapid compaction stage, crushing compaction stage, and stable compaction stage. The strain–stress relationship can be described by the parameter logarithmic function and Chapman–Richards function, respectively. The maximum change in the compression modulus under different water content states ranged from 9.9 to 19.3 MPa, and the influence of the water content on the compression modulus was more significant with increasing axial stress. There is a good correlation between particle crushing and compaction deformation. The relative crushing rate increases with the increase in the axial strain, and the increasing rate of the relative crushing rate also gradually increases. The change law of the relative crushing rate and axial strain is different in dry and water-containing conditions

5-Methoxyflavone alleviates LPS-mediated lung injury by promoting Nrf2-mediated the suppression of NOX4/TLR4 axis in bronchial epithelial cells and M1 polarization in macrophages

Abstract Background Acute lung injury (ALI) arises from sepsis or bacterial infection, which are life-threatening respiratory disorders that cause the leading cause of death worldwide. 5-Methoxyflavone, a methylated flavonoid, is gaining increased attention for its various health benefits. In the current study, we investigated the potential effects of 5-methoxyflavone against LPS-mediated ALI and elucidated the corresponding possible mechanism. Methods A mouse model with ALI was established by intratracheal instillation of LPS, and lung pathological changes, signaling pathway related proteins and apoptosis in lung tissues were estimated by H&E staining, immunofluorescence and TUNEL assay, respectively. Cell viability was evaluated by MTT assay; protein levels of pro-inflammatory mediators were measured by ELISA assay; levels of ROS and M1 macrophage polarization were assayed by flow cytometry; the expression of Nrf2 signaling, NOX4/TLR4 axis and P-STAT1 were detected by western blotting. Results Our results showed that 5-methoxyflavone treatment inhibited LPS-induced expression of NOX4 and TLR4 as well as the activation of downstream signaling (NF-κB and P38 MAPK), which was accompanied by markedly decreased ROS levels and pro-inflammatory cytokines (IL-6, TNF-α, MCP-1, and IL-8) in BEAS-2B cells. Moreover, we revealed that these effects of 5-methoxyflavone were related to its Nrf2 activating property, and blockade of Nrf2 prevented its inhibitory effects on NOX4/TLR4/NF-κB/P38 MAPK signaling, thus abrogating the anti-inflammatory effects of 5-methoxyflavone. Besides, the Nrf2 activating property of 5-methoxyflavone in RAW264.7 cells led to inhibition of LPS/IFN-γ-mediated STAT1 signaling, resulting in suppression of LPS/IFN-γ-induced M1 macrophage polarization and the repolarization of M2 macrophages to M1. In a mouse model of LPS-induced ALI, 5-methoxyflavone administration ameliorated LPS-mediated lung pathological changes, the increased lung index (lung/body weight ratio), and epithelial cell apoptosis. Meanwhile, we found 5-methoxyflavone effectively suppressed the hyperactive signaling pathways and the production of excessive pro-inflammatory mediators. Moreover, 5-methoxyflavone reduced LPS-mediated M1 macrophage polarization associated with elevated P-STAT1 activation in the lung tissues. In addition, 5-methoxyflavone improved the survival of LPS-challenged mice. Conclusion These results indicated that 5-methoxyflavone might be suitable for the development of a novel drug for ALI therapeutic

Performance of LiTaO₃ Crystals and Thin Films and Their Application

Lithium tantalate (LiTaO3, or LT) crystal is widely used in optical applications, infrared detection, and acoustic surface wave devices because of its excellent piezoelectric, pyroelectric, and nonlinear optical properties. In this paper, we discuss the defect structure of LT; the preparation method for LT; the influence of doping on LT; and LT’s application in optical, acoustic, and electrical devices. We mainly analyzed the structure and physical properties of LT crystal, the preparation of LT crystal and LT thin films, the periodic polarization of LT crystal, the reduction of LT wafers, and the application potential of LT crystals in lasers and acoustic surface filters according to the most recent research. We also provide an overview of future research directions for LT in the fields of acoustics, optics, and other fields. The applications of LT in 5G, 6G, SAW filters, nonlinear optical devices, and waveguides are expected to provide additional breakthroughs

Miniature All-Silica Microbubble-Based Fiber Optic Fabry-Perot Pressure Sensor with Pressure Leading-In Tube

A novel all-silica fiber optic Fabry-Perot (FP) pressure sensor with pressure leading-in tube based on microbubble structure is developed and experimentally demonstrated. The FP cavity is formed by fixing the end face of the single-mode fiber (SMF) parallel to the outer surface of the microbubble, in which the microbubble with a diameter of about 318 μm is constructed at the end of silica hollow tube. When external pressure is transmitted on the inner surface of the microbubble by the pressure leading-in tube, the FP cavity length changes with the diameter of microbubble. Experimental results show that such a sensor has a linear sensitivity of approximately 4.84 nm/MPa at room temperature over the pressure range of 1.1 MPa; the sensor has a very low temperature coefficient of approximately 2 pm/°C from room temperature to 600°C. The sensor has advantages of extremely low temperature coefficient, compact structure, and small size, which has potential applications for measuring pressure in high-temperature environment

FREDUCE: Detection of degenerate regulatory elements using correlation with expression-0

<p><b>Copyright information:</b></p><p>Taken from "fREDUCE: Detection of degenerate regulatory elements using correlation with expression"</p><p>http://www.biomedcentral.com/1471-2105/8/399</p><p>BMC Bioinformatics 2007;8():399-399.</p><p>Published online 17 Oct 2007</p><p>PMCID:PMC2174516.</p><p></p>tring, we compute a pseudo-Pearson coefficient, which is an estimate and upper bound on the true Pearson coefficient. After the vast majority of motifs are filtered out using the pseudo-Pearson value, we then compute true Pearson coefficients for the remaining motifs and select the top motif. The residual expression value is then used to iteratively derive subsequent motifs