Protein structural class prediction based on an improved statistical strategy

<p>Abstract</p> <p>Background</p> <p>A protein structural class (PSC) belongs to the most basic but important classification in protein structures. The prediction technique of protein structural class has been developing for decades. Two popular indices are the amino-acid-frequency (AAF) based, and amino-acid-arrangement (AAA) with long-term correlation (LTC) – based indices. They were proposed in many works. Both indices have its pros and cons. For example, the AAF index focuses on a statistical analysis, while the AAA-LTC emphasizes the long-term, biological significance. Unfortunately, the datasets used in previous work were not very reliable for a small number of sequences with a high-sequence similarity.</p> <p>Results</p> <p>By modifying a statistical strategy, we proposed a new index method that combines probability and information theory together with a long-term correlation. We also proposed a numerically and biologically reliable dataset included more than 5700 sequences with a low sequence similarity. The results showed that the proposed approach has its high accuracy. Comparing with amino acid composition (AAC) index using a distance method, the accuracy of our approach has a 16–20% improvement for re-substitution test and about 6–11% improvement for cross-validation test. The values were about 23% and 15% for the component coupled method (CCM).</p> <p>Conclusion</p> <p>A new index method, combining probability and information theory together with a long-term correlation was proposed in this paper. The statistical method was improved significantly based on our new index. The cross validation test was conducted, and the result show the proposed method has a great improvement.</p

The influence of protein free calf blood extract eye gel on dry eye after pterygium surgery

AIM: To investigate the influence of protein free calf blood extract eye gel on dry eye after pterygium surgery. <p>METHODS: Thirty six patients(40 eyes)with primary nasal pterygium were enrolled in this study, which were divided into study group and control group randomly, with 20 eyes in each group. All patients received pterygium excision and limbal stem cell autograft surgery and tobramicin dexamethasone eye drops after surgery. Patients of the study group received protein free calf blood extract eye gel while those of the control group received 0.1% sodium hyaluronate eye drops furthermore. Ocular surface disease index(OSDI)questionnaire, tear film break-up time(BUT)and Schirmer's Ⅰ test Ⅰ(SⅠt)were carried before and 3 months after surgery to evaluate the dry eye degree of the patients. <p>RESULTS: There was no statistical difference between the age, gender and size of the pterygium of the study and control groups preoperatively. There was no statistical difference between the OSDI(2.33±1.02 <i>vs</i> 2.32±0.93), BUT(8.80±2.48 <i>vs</i> 8.35±2.28)seconds and SⅠt(4.30±2.30 <i>vs</i> 4.40±2.44)of the two groups preoperatively. There was statistical difference between the OSDI(1.45±0.47 <i>vs</i> 1.81±0.60), BUT(11.20±2.07 <i>vs</i> 9.50±2.40)seconds and SⅠt(8.35±3.13 <i>vs</i> 6.35±2.18)of the two groups 3 months postoperatively, which was also different from that of the preoperative data correspondingly. <p>CONCLUSION: Protein free calf blood extract eye gel could reduce the dry eye after pterygium surgery

Engineering properties of vertical cutoff walls consisting of reactive magnesia-activated slag and bentonite: workability, strength and hydraulic conductivity

Soil–cement–bentonite (SCB) vertical cutoff walls are commonly used to control the flow of contaminated groundwater at polluted sites. However, conventional backfill consisting of ordinary portland cement (OPC) is associated with a relatively high CO2 footprint. Potential chemical interactions between OPC and bentonite could also undermine the long-term durability of SCB materials. This paper proposes an innovative backfill material for cutoff walls that is composed of MgO-activated ground granulated blast furnace slag (GGBS), bentonite, and soil. The OPC–soil, OPC–bentonite–soil, and OPC–GGBS–bentonite–soil backfill materials are also tested for comparison purposes. The workability of fresh backfills and unconfined compressive strength of aged backfills are investigated. The hydraulic conductivities of aged backfills permeated with tap water, Na2SO4, and Pb–Zn solutions are assessed. The unconfined compressive strength and hydraulic conductivity of the proposed backfill permeated with tap water are in the range of 230–520 kPa and 1.1×10−10  to  6.3×10−10  m/s after 90 days of curing, respectively, depending on the mix composition. The hydraulic conductivity of the proposed MgO–GGBS–bentonite–soil backfill permeated with sodium sulfate (Na2SO4) or lead–zinc (Pb–Zn) solution is well below the commonly used limit, while the OPC–bentonite–soil backfill shows a significant loss in impermeability. Environmental and economic analyses indicate that, compared with conventional backfill made from OPC–bentonite–soil mixtures, the proposed backfill reduces CO2 emissions by approximately 84.7%–85.1% and costs by 15.3%–16.9%. The environmental and economic advantages will promote the use of MgO-activated GGBS–bentonite mixtures in cutoff walls and lead to their increased application in land remediation projects

Effects of acute ammonia exposure and post-exposure recovery on nonspecific immunity in Clam Cyclina sinensis

This study aimed to assess the toxicity of ammonia on clam Cyclina sinensis and the post-exposure recovery. With increased exposure to TAN, the alkaline phosphatase (AKP) activities after exposure showed a trend of growing initially and subsequently decreasing, whereas the AKP activities after post-exposure recovery showed an increasing trend. The AKP activities after post-exposure recovery were significantly higher than those in control. The acid phosphatase (ACP) activities in T1 and T2 after post-exposure recovery were higher than those in the control, whereas the ACP activities in T3, T4, and T5 after post-exposure recovery were significantly higher than those in the control. The lysozyme (LZM) activities in T1 and T2 after exposure were significantly higher than those in control, whereas the LZM activities in T3, T4, and T5 after exposure were significantly lower than those in the control. Overall, ACP and LZM in the clams exposed to a low level of TAN (≤ 40 mg/L) can recover to the normal levels completely. However, a 48h recovery period scarcely seems adequate to compensate for AKP, ACP, and LZM activities in the clams exposed to a high level of TAN (> 40 mg/L)