Protein-protein interaction based on pairwise similarity

<p>Abstract</p> <p>Background</p> <p>Protein-protein interaction (PPI) is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS) method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines.</p> <p>Results</p> <p>To assess the ability of the proposed method to recognize the difference between "<it>interacted</it>" and "<it>non-interacted</it>" proteins pairs, we applied it on different datasets from the available yeast <it>saccharomyces cerevisiae </it>protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction.</p> <p>Conclusion</p> <p>Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.</p

Enhanced Nitrogen Removal of Steel Rolling Wastewater by Constructed Wetland Combined with Sulfur Autotrophic Denitrification

Constructed wetlands (CWs), an ecological treatment technology, is suitable for advanced treatment, but has an unsatisfying denitrification performance for steel rolling wastewater with low C/N ratio. This study combined sulfur autotrophic denitrification (SAD) with conventional constructed horizontal subsurface flow wetlands to treat steel rolling wastewater, exploring the feasibility of applying SAD to enhance the denitrification performance of CWs. The reactor consists of two sections, one filled with manganese sand and gravel (HFC) and another filled with ceramic, sulfur, and lime (HFSAD). Results showed that HFC had a good performance on removing turbidity, DO, COD, and TP, while the average removal efficiency of total nitrogen (TN) in HFC was just 25.6%. On this basis, HFSAD could remove 45.6% of TN subsequently, whose denitrification rate was 4–6 times as high as that of HFC. Increasing hydraulic retention time could improve removal efficiency of contaminants in HFC and HFSAD in different degrees. The analysis of microbial community structure, observation results of fillers and monitored sulfate all provided proofs for the occurrence of SAD. CWs combined with SAD can be applied in the treatment of steel rolling wastewater with low carbon, which can provide reference for ecological wastewater treatment, water saving, and recycling in iron and steel enterprises

Characteristics of Atmospheric Deposition during the Period of Algal Bloom Formation in Urban Water Bodies

Urban water bodies are limited by poor mobility, small surface areas, and little water supply; thus, they are sensitive to atmospheric nutrient inputs, especially during the optimal period of algae growth. This study investigated the impact of atmospheric deposition on the Quyang urban water body in Shanghai. Observations that coupled atmospheric organic matter, nitrogen and phosphorous and the actual urban water body (nutrient availability and Chlorophyll-a concentrations (Chl-a)) were conducted during spring and summer. Atmospheric total organic carbon (TOC), total nitrogen (TN), ammonia (N-NH4+) and total phosphorus (TP) deposition ranged from 35&#8211;81, 3&#8211;40, 0.79&#8211;20.40 and 0.78&#8211;0.25 mg m&#8722;2 d&#8722;1, respectively. The soluble N/P molar ratios of the bulk deposition (ranging from 56&#8211;636) were well above the Redfield ratio (N/P = 16). Nutrient inputs from atmospheric deposition have been suggested to be a strong factor for increasing the likelihood of P limitation in the water bodies. The actual loads to small, shallow urban water bodies were assessed and found to be ~50, 130, 130 (the N-fixation contributes to the atmospheric deposition inputs especially during the spring), and 80% of TOC, TN, N-NH4+, and TP, respectively, representing nutrients transferred into the water phase. The maximum primary production (evaluated as Chl-a) stock resulting in a 2-m-deep water column from the above inputs ranged from 2.54&#8211;7.98 mg Chl-a m&#8722;3. As a continuous source of nutrients, atmospheric deposition should not be underestimated as a driving force for urban water body eutrophication, and it potentially influences primary production, especially during the optimal algae growth period

Prediction of Life Cycle Carbon Emissions of Sponge City Projects: A Case Study in Shanghai, China

In recent years, China has been vigorously carrying out the planning and implementation of Sponge City. Since the implementation of Sponge City projects involves substantial materials and energy consumption, it is significant to account corresponding carbon emissions and sinks. The existed studies about carbon emission of stormwater management measures, however, are not able to take the whole life cycle and different facilities into consideration. Therefore, this study develops a comprehensive accounting model based on Intergovernmental Panel on Climate Change (IPCC) guidelines and life cycle assessment (LCA) method to predict carbon emissions and carbon sinks of Sponge City projects more comprehensively and accurately. The model is applied to an actual residential community in Shanghai as a case study. Results show that the total indirect carbon emission is estimated to be 774,277 kg CO2 eq during a 30-year lifespan, among which carbon emissions from operation and maintenance phases are 2570 kg CO2 eq/year and 7309 kg CO2 eq/year, respectively, both directly proportional to the service life of the facilities. Three kinds of achievable carbon sinks are carbon sequestration in green space (5450 kg CO2 eq/year), carbon sink from rainwater utilization (15,379 kg CO2 eq/year) and carbon sink from runoff pollutant removal (19,552 kg CO2 eq/year). Carbon neutrality is expected to be reached after approximately 19 years. The established carbon emission accounting model can contribute to better planning and construction of Sponge City in China and enhance further energy conservation and carbon emission reduction

Evaluation of the comprehensive efficiency of the interception pipeline in the urban rainwater pipe network for the initial rainwater collection and storage

Urban runoff pollution has become one of the important limiting factors hindering the continuous improvement of water environment. In the process of drainage system reconstruction, the evaluation of interception pipeline for the collection and storage efficiency of initial rainwater is an important work. Therefore, this study uses the analytic hierarchy process to establish an evaluation system and method containing 4 first-level indicators and 10 second-level indicators to evaluate the comprehensive efficiency of the interception pipeline for initial rainwater collection and storage. Taking the interception pipeline in a drainage system in Shanghai as a case study, the established evaluation method was adopted to evaluate it, and the comprehensive indexes under the rainfall return periods of 0.5 year, 1 year, 3 years and 5 years were calculated. The results indicated that the evaluation method could be well applied to the effectiveness evaluation of intercepting pipelines in drainage systems, and could provide technical support for the planning and design of urban runoff pollution control projects in the future

Feasibility and Carbon Footprint Analysis of Lime-Dried Sludge for Cement Production

Cement manufacturing and the treatment of sludge are considered both energy-intensive industries and major greenhouse gas (GHG) emitters. However, there are still few studies on comprehensive carbon footprint analysis for adding municipal sludge in the cement production. In this study, the lime-dried sludge blended with calcium oxide at the mass mixing ratio of 10% was utilized as raw material for the preparation of Portland cement. The chemical and physical properties of sludge were analyzed. A set of carbon footprint calculation methods of lime-drying treatment of sludge and reuse in cement kilns was then established to explore the feasibility of coprocessing lime-dried sludge in cement kilns. The results showed lime-dried sludge containing CaO, SiO2, Al2O3, and Fe2O3 was ideal for cement production as raw material. However, the water content of lime-dried sludge should be strictly limited. The lime-drying process presented the biggest carbon emission (962.1 kg CO2-eq/t sludge), accounting for 89.0% of total emissions. In the clinker-production phase, the lime-dried sludge as raw material substitute and energy source gained carbon credit of 578.8 and 214.2 kg CO2-eq/t sludge, respectively. The sludge used for producing cement clinker could reduce carbon emissions by 38.5% to 51.7%. The addition ratio of lime and stacking time in the sludge lime-drying process could greatly affect the carbon footprint of coprocessing lime-dried sludge in cement kiln

Research progress and application exploration of techniques to remove emerging contaminants from water environment

Emerging contaminants in water have attracted more and more attention from scholars and the public. Various technologies have been gradually studied and applied to remove emerging contaminants in water, including adsorption technology based on carbon materials, membrane separation technology, advanced oxidation technology and constructed wetland. In this paper, the research progress of these technologies is reviewed, especially for photocatalysis, a promising technology, which is analyzed in detail. Immobilization is an important means for photocatalytic technology to be applied in engineering. In this paper, four existing immobilization methods of photocatalytic materials are analyzed, and the existing research is prospected. More in-depth research is urgently needed, and exploratory research aimed at application is encouraged. This study can provide some ideas and reference for the treatment of emerging contaminants in water

Occurrence and risk assessment of emerging contaminants in a water reclamation and ecological reuse project.

Water reclamation and ecological reuse is gradually becoming a popular solution to address the high pollutant loads and insufficient ecological flow of many urban rivers. However, emerging contaminants in water reuse system and associated human health and ecological risks need to be assessed. This study determined the occurrence and human health and ecological risk assessments of 35 emerging contaminants during one year, including 5 types of persistent organic pollutants (POPs), 5 pharmaceutical and personal care products (PPCPs), 7 endocrine disrupting chemicals (EDCs) and 18 disinfection by-products (DBPs), in a wastewater treatment plant (WWTP) and receiving rivers, as well as an unimpacted river for comparison. Results showed that most of PPCPs and EDCs, especially antibiotics, triclosan, estrogens and bisphenol A, occurred frequently at relatively high concentrations, and they were removed from 20.5% to 88.7% with a mean of 58.9% via WWTP. The highest potential noncarcinogenic and carcinogenic risks in different reuse scenarios were assessed using maximal detected concentrations, all below the acceptable risk limits, with the highest total combined risk value of 9.21 × 10-9 and 9.98 × 10-7, respectively. Ecological risk assessment was conducted using risk quotient (RQ) method and indicated that several PPCPs, EDCs and haloacetonitriles (HANs) pose high risk (RQ &gt; 1) to aquatic ecology in the rivers, with the highest RQ up to 83.8. The study suggested that ecological risks need to be urgently addressed by updating and optimizing the process in WWTPs to strengthen the removal efficiencies of emerging contaminants. The study can serve as a reference for safer water reuse in the future, while further studies could be conducted on the health risk of specific groups of people, exposure parameters in water reuse, as well as more emerging contaminants