PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions (PPIs) are crucial for almost all cellular processes, including metabolic cycles, DNA transcription and replication, and signaling cascades. Given the importance of PPIs, several methods have been developed to detect them. Since the experimental methods are time-consuming and expensive, developing computational methods for effectively identifying PPIs is of great practical significance.</p> <p>Findings</p> <p>Most previous methods were developed for predicting PPIs in only one species, and do not account for probability estimations. In this work, a relatively comprehensive prediction system was developed, based on a support vector machine (SVM), for predicting PPIs in five organisms, specifically humans, yeast, <it>Drosophila</it>, <it>Escherichia coli</it>, and <it>Caenorhabditis elegans</it>. This PPI predictor includes the probability of its prediction in the output, so it can be used to assess the confidence of each SVM prediction by the probability assignment. Using a probability of 0.5 as the threshold for assigning class labels, the method had an average accuracy for detecting protein interactions of 90.67% for humans, 88.99% for yeast, 90.09% for <it>Drosophila</it>, 92.73% for <it>E. coli</it>, and 97.51% for <it>C. elegans</it>. Moreover, among the correctly predicted pairs, more than 80% were predicted with a high probability of ≥0.8, indicating that this tool could predict novel PPIs with high confidence.</p> <p>Conclusions</p> <p>Based on this work, a web-based system, Pred_PPI, was constructed for predicting PPIs from the five organisms. Users can predict novel PPIs and obtain a probability value about the prediction using this tool. Pred_PPI is freely available at <url>http://cic.scu.edu.cn/bioinformatics/predict_ppi/default.html</url>.</p

Analysis of risk factors for benign prostate enlargement with prostate calcification

The occurrence of benign prostatic hyperplasia (BPH) accompanied by calcification can reduce the quality of life and treatment effectiveness of patients. This study focuses on middle-aged and elderly patients in physical examination centers, and divides them into a control group and a study group based on their condition. By comparing the general information and serum indicators of the subjects, descriptive analysis methods are used to analyze the risk factors for prostate hyperplasia accompanied by calcification. Among 700 male physical examinations, there were 305 patients with benign prostate enlargement, with a prevalence rate of 43.57%. There were 290 patients with prostate calcification, accounting for 41.43%. Among them, there were 203 patients with prostate calcification in BPH, accounting for 66.56%. Multivariate logistic regression analysis showed that age, education and culture, diabetes, hypertension, uric acid (UA) and blood urea nitrogen (BUN) are independent risk factors for prostate calcification, while height is the protective factor. The prevalence rate of BPH and BPH with prostate calcification is high in middle-aged and elderly men. Although the cause of calcification is still unclear, age, education, occupation, diabetes, hypertension, UA, BUN and prostate-specific antigen (PSA) indicators are closely related to the disease. Therefore, early intervention should be carried out according to the above risk factors to prevent the occurrence of the disease as soon as possible

Financial Development and Total Factor Productivity Growth: Evidence from China

In this article, we estimate the effect of China’s regional financial development on total factor productivity (TFP) growth using large provincial panel data for the years 1990 to 2009. Using the nonparametric stochastic frontier data envelopment approach, we analyze how financial development is related to efficiency improvement and technological progress, the two components of TFP. The study shows that Chinese financial development plays a significant role in promoting TFP growth via technological progress rather than efficiency change. The faster the financial development takes place, the better it could correct the mismatch of resource allocation, thus promoting TFP growth. The results imply that China needs to both further optimize the allocation of financial resources and perfect the regional financial system

A Four Quadrature Signals’ Generator with Precise Phase Adjustment

A four-way quadrature signals generator with precise phase modulation is presented. It consists of a phase precision regulator and a frequency divider. The phase precision regulator generates two programmable currents by controlling the conduction of the tail current sources and then changes the currents into two bias voltages which are superimposed on the clock signals to adjust the phase difference of the four quadrature signals generated by the frequency divider, making the phase difference of 90 degrees. The four quadrature signals’ generator with precise phase modulation has been implemented in a 0.18 μm mixed-signal and RF 1P6M CMOS technology. The size of the chip including the pads is 675 μm⁎690 μm. The circuit uses a supply voltage of 1.8 V, a bias current of 7.2 μA, and the bits of phase-setting input level n=6 in the design. The measured results of the four orthogonal signals’ phase error can reach ±0.1°, and the phase modulation range can reach ±3.6°

A Four Quadrature Signals&apos; Generator with Precise Phase Adjustment

A four-way quadrature signals generator with precise phase modulation is presented. It consists of a phase precision regulator and a frequency divider. The phase precision regulator generates two programmable currents by controlling the conduction of the tail current sources and then changes the currents into two bias voltages which are superimposed on the clock signals to adjust the phase difference of the four quadrature signals generated by the frequency divider, making the phase difference of 90 degrees. The four quadrature signals&apos; generator with precise phase modulation has been implemented in a 0.18 m mixed-signal and RF 1P6M CMOS technology. The size of the chip including the pads is 675 m * 690 m. The circuit uses a supply voltage of 1.8 V, a bias current of 7.2 A, and the bits of phase-setting input level = 6 in the design. The measured results of the four orthogonal signals&apos; phase error can reach ±0.1 ∘ , and the phase modulation range can reach ±3.6 ∘

Determination of the Agricultural Eco-Compensation Standards in Ecological Fragile Poverty Areas Based on Emergy Synthesis

Eco-compensation is an important mechanism when applying the theory of ecosystem services to practical development, which translates the external and non-market value of the environment into real financial incentives for local actors. Scientifically formulating feasible and credible compensation standards is the most critical and key step to adjusting the benefits received by environment protectors and beneficiaries. The Inner Mongolia agro-pastoral zone is an important ecological area with an undeveloped economy in Northern China. The implementation of eco-compensation policies contributes to ecological restoration and poverty alleviation. Taking Horqin Left Back Banner, Inner Mongolia, China as a study case, a quantitative model of a non-point source pollution eco-compensation program was established by using emergy synthesis&#8212;a thermodynamics-based method in ecological economic systems&#8212;to create a comprehensive eco-compensation standard. The results showed that the eco-compensation amounts for non-point source pollution were generally below 10% of the regional gross domestic product (GDP). A 11&#8722;20% reduction in fertilizer would be accepted according to the field investigation and the optimal eco-compensation strategy reduced the phosphate fertilizer application by 20% with a compensation standard of $379.63/ha/year, which was similar to the farmers&#8217; willingness to accept compensation. For the accurate creation of a non-point source pollution eco-compensation program, the emergy synthesis overcomes the inconsistency in the quantification of the material flow, ecological flow, and economic flow, guaranteeing the sustainable implementation of non-point source pollution eco-compensation projects

Reliable and Efficient Anytime Skeleton Learning

Skeleton Learning (SL) is the task for learning an undirected graph from the input data that captures their dependency relations. SL plays a pivotal role in causal learning and has attracted growing attention in the research community lately. Due to the high time complexity, anytime SL has emerged which learns a skeleton incrementally and improves it overtime. In this paper, we first propose and advocate the reliability requirement for anytime SL to be practically useful. Reliability requires the intermediately learned skeleton to have precision and persistency. We also present REAL, a novel Reliable and Efficient Anytime Learning algorithm of skeleton. Specifically, we point out that the commonly existing Functional Dependency (FD) among variables could make the learned skeleton violate faithfulness assumption, thus we propose a theory to resolve such incompatibility. Based on this, REAL conducts SL on a reduced set of variables with guaranteed correctness thus drastically improves efficiency. Furthermore, it employs a novel edge-insertion and best-first strategy in anytime fashion for skeleton growing to achieve high reliability and efficiency. We prove that the skeleton learned by REAL converges to the correct skeleton under standard assumptions. Thorough experiments were conducted on both benchmark and real-world datasets demonstrate that REAL significantly outperforms the other state-of-the-art algorithms

Fatty Acid Profiles and Nutritional Evaluation of Fresh Sweet-Waxy Corn from Three Regions of China

Fresh corn is a kind of herbaceous plant with rich nutritive value and a reasonable composition of fatty acids; however, there is little research on methods for the systemic nutritional evaluation of fatty acids in fresh corn. The aim of the present study was to conduct a comparative analysis of the fatty acid profiles of Chinese Huangnuo 9 sweet-waxy corn from the provinces of Inner Mongolia, Jilin, and Heilongjiang by gas chromatography; to establish a nutritional evaluation system according to the impacts of nutrients from fatty acids on human health; and finally, to evaluate, compare and rank fresh sweet-waxy corn grown in different regions. Tocopherols were detected by liquid chromatography in order to demonstrate the anti-oxidation activity of fresh corn&rsquo;s fatty acids. The fatty acid contents and compositions of the 12 samples from the three regions are significantly different from each other. The nutrient value of the fatty acids in fresh corn was analyzed by factor analysis and a linear structural relation model, followed by the fitting and appraising of the model. The studied fresh sweet-waxy corn 1-4 from Inner Mongolia had the highest &gamma;-tocopherol content and the closest saturated fatty acid:monounsaturated fatty acid:polyunsaturated fatty acid rate to the recommended value. The fatty acid profiles of sweet-waxy corns 2-1, 2-2, and 2-3 were the most diverse, and the comprehensive evaluation result of fresh corn 2-4 was the best; its total fatty acid content was the highest. Fresh corn 3-1 in Heilongjiang had the highest unsaturated fatty acids and lower values in its atherosclerosis index and thrombosis index, which suggested the strongest anti-atherosclerosis and anti-thrombotic ability. This work will give a reference to guide dietary choices and provide data support for dietary recommendations for residents