A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.

Because of the limited effectiveness of prevailing phylogenetic methods when applied to highly divergent protein sequences, the phylogenetic analysis problem remains challenging. Here, we propose a sequence-based evolutionary distance algorithm termed sequence distance (SD), which innovatively incorporates site-to-site correlation within protein sequences into the distance estimation. In protein superfamilies, SD can effectively distinguish evolutionary relationships both within and between protein families, producing phylogenetic trees that closely align with those based on structural information, even with sequence identity less than 20%. SD is highly correlated with the similarity of the protein structure, and can calculate evolutionary distances for thousands of protein pairs within seconds using a single CPU, which is significantly faster than most protein structure prediction methods that demand high computational resources and long run times. The development of SD will significantly advance phylogenetics, providing researchers with a more accurate and reliable tool for exploring evolutionary relationships.

HIV-1 tropism prediction by the XGboost and HMM methods.

Human Immunodeficiency Virus 1 (HIV-1) co-receptor usage, called tropism, is associated with disease progression towards AIDS. Furthermore, the recently developed and developing drugs against co-receptors CCR5 or CXCR4 open a new thought for HIV-1 therapy. Thus, knowledge about tropism is critical for illness diagnosis and regimen prescription. To improve tropism prediction accuracy, we developed two novel methods, the extreme gradient boosting based XGBpred and the hidden Markov model based HMMpred. Both XGBpred and HMMpred achieved higher specificities (72.56% and 72.09%) than the state-of-the-art methods Geno2pheno (61.6%) and G2p_str (68.60%) in a 10-fold cross validation test at the same sensitivity of 93.73%. Moreover, XGBpred had more outstanding performances (with AUCs 0.9483, 0.9464) than HMMpred (0.8829, 0.8774) on the Hivcopred and Newdb (created in this work) datasets containing larger proportions of hard-to-predict dual tropic samples in the X4-using tropic samples. Therefore, we recommend the use of our novel method XGBpred to predict tropism. The two methods and datasets are available via http://spg.med.tsinghua.edu.cn:23334/XGBpred/. In addition, our models identified that positions 5, 11, 13, 18, 22, 24, and 25 were correlated with HIV-1 tropism.

MiR-449 overexpression inhibits osteogenic differentiation of bone marrow mesenchymal stem cells via suppressing Sirt1/Fra-1 pathway in high glucose and free fatty acids microenvironment.

Diabetic osteoporosis is a chronic complication caused by diabetes mellitus, and However, the exact mechanism of diabetes mellitus-induced osteoporosis is still unknown. In this study, we investigate the effect of miR-449 on osteogenic differentiation and its underlying mechanism in human bone marrow-derived mesenchymal stem cells (hBMSCs) with high glucose (HG) and free fatty acids (FFA) treatment. Results showed that after culturing for 14 days, high glucose (HG) and free fatty acids (FFA) treatment dramatically decreased mineralization of human bone marrow-derived mesenchymal stem cells (hBMSCs) compared with cells treated with osteogenic medium (OM) alone. We also found that miR-449 expression was up-regulated during osteogenic differentiation of hBMSCs with HG and FFA treatment. Moreover, during osteogenic differentiation of hBMSCs with HG and FFA treatment, miR-449 mimics notably decreased the alkaline phosphatase (ALP) activity and the mRNA and protein expression levels of runt-related transcription factor 2 (Runx2), ALP, collagen I, osteocalcin (OCN), and bone sialoprotein (BSP), which was remarkably increased by miR-449 inhibitors. Furthermore, miR-449 directly targets Sirt1 by binding to its 3'-UTR. Sirt1 overexpression reverses the suppressive effect of miR-449 mimics on Fra-1 mRNA and protein expression, which was also alleviated by Fra-1 overexpression. In addition, Fra-1 overexpression alleviates the inhibitory effect of miR-449 mimics on the ALP activity and the mRNA and protein of Runx2, collagen I, OCN and BSP. Taken together, our results indicated that miR-449 overexpression inhibited osteogenic differentiation of HG-FFA-treated hBMSCs through the Sirt1/Fra-1 signal pathway. It is conceivable that modulating miR-449 might provide a new therapy for intervention in diabetic osteoporosis.

Determinants of Thermostability in Serine Hydroxymethyltransferase Identified by Principal Component Analysis.

Protein thermostability has received growing attention in recent years. Little is known about the determinants of thermal resistance in individual protein families. However, it is known that the mechanism is family-dependent and not identical for all proteins. We present a multivariate statistical analysis to find the determinants of thermostability in one protein family, the serine hydroxymethyltransferase family. Based on principal component analysis, we identified three amino acid fragments as the potential determinants of thermostability. The correlation coefficients between all the putative fragments and the protein thermostability were significant according to multivariable linear regression. Within the fragments, four critical amino acid positions were identified, and they indicated the contributions of Leu, Val, Lys, Asp, Glu, and Phe to thermostability. Moreover, we analyzed the insertions/deletions of amino acids in the sequence, which showed that thermophilic SHMTs tend to insert or delete residues in the C-terminal domain rather than the N-terminal domain. Our study provided a promising approach to perform a preliminary search for the determinants of thermophilic proteins. It could be extended to other protein families to explore their own strategies for adapting to high temperature.

Establishing knowledge on the sequence arrangement pattern of nucleated protein folding.

The heat-tolerance mechanisms of (hyper)thermophilic proteins provide a unique opportunity to investigate the unsolved protein folding problem. In an attempt to determine whether the interval between residues in sequence might play a role in determining thermostability, we constructed a sequence interval-dependent value function to calculate the residue pair frequency. Additionally, we identified a new sequence arrangement pattern, where like-charged residues tend to be adjacently assembled, while unlike-charged residues are distributed over longer intervals, using statistical analysis of a large sequence database. This finding indicated that increasing the intervals between unlike-charged residues can increase protein thermostability, with the arrangement patterns of these charged residues serving as thermodynamically favorable nucleation points for protein folding. Additionally, we identified that the residue pairs K-E, R-E, L-V and V-V involving long sequence intervals play important roles involving increased protein thermostability. This work demonstrated a novel approach for considering sequence intervals as keys to understanding protein folding. Our findings of novel relationships between residue arrangement and protein thermostability can be used in industry and academia to aid the design of thermostable proteins.

Biomechanical Comparison of Expansive Pedicle Screw and Polymethylmethacrylate-augmented Pedicle Screw in Osteoporotic Synthetic Bone in Primary Implantation: An Experimental Study.

STUDY DESIGN: Expansive pedicle screws (EPS) and polymethylmethacrylate-augmented pedicle screws (PMMA-PS) were inserted into osteoporotic synthetic bones, which were then tested by radiographic and biomechanical examinations. OBJECTIVE: To compare the stability of EPS and PMMA-PS with that of a conventional pedicle screw (CPS) in an osteoporotic synthetic bone. SUMMARY OF BACKGROUND DATA: It is a significant challenge for orthopedic surgeons performing transpedicular fixation in the osteoporotic spine. Prior studies have suggested that both EPS and PMMA-PS can increase the screw stability effectively. However, there are no biomechanical comparisons of EPS and PMMA-PS, especially in primary spinal surgery in osteoporosis. METHODS: Thirty osteoporotic synthetic bone blocks were divided into 3 groups randomly. A pilot hole was prepared in advance in all samples by the same method. Then, the CPS was inserted directly into the pilot hole in the CPS group; the hole in the PMMA-PS group was first filled with polymethylmethacrylate (PMMA; 2.5 mL) and then inserted with CPS, and the EPS was inserted directly into the blocks in the EPS group. Twenty-four hours later, x-ray and computed tomography examination and axial pullout tests were performed on all samples; the block destructions were then recorded, and the hole diameters were measured. RESULTS: In the CPS group, the screw was surrounded directly by the synthetic bone without any other materials, whereas in the PMMA-PS group, the screw was totally wrapped up by PMMA, and the PMMA was evenly distributed in the synthetic bone around the screw, indicating obvious improvement of the local density around the track. In the EPS group, the anterior part of the EPS presented an obvious expansion in synthetic bone and formed an unguiform structure pressing the surrounding synthetic bone. Screw stabilities in both the PMMA-PS and the EPS groups were significantly enhanced compared with those in the CPS group, and the screw stability in the PMMA-PS group was significantly higher than that in the EPS group. After the pullout tests, the block destructions were the most severe in the PMMA-PS group and the lightest in the CPS group. Hole diameters in the PMMA-PS and the EPS groups were significantly larger than that in the CPS group, whereas the diameter of the hole in the PMMA-PS group was significantly greater than that in the EPS group. CONCLUSIONS: EPS can significantly increase the strength of screw fixation compared with CPS in osteoporotic synthetic bone. Although EPS shows a weaker fixation strength compared with PMMA-PS in the osteoporotic synthetic bone, it may still provide an alternative option to prevent screw loosening in the clinical treatment of osteoporosis.

Inhibitors of Growth 1b Suppresses Peroxisome Proliferator-Activated Receptor-ß/δ Expression Through Downregulation of Hypoxia-Inducible Factor 1α in Osteoblast Differentiation.

Bone formation, a highly regulated developmental process, involves osteoblast differentiation, which is controlled by different important transcription factors. Recent evidence has suggested possible negative regulation of inhibitors of growth (ING) 1b on the osteoblast marker expression. The aim of this study is to examine the detailed mechanism by which the activity of ING1b inhibits osteoblast differentiation. In the current study, we investigated the function and mechanism by which ING1b inhibits osteoblast differentiation using C3H10T1/2 mesenchymal stem cells and MC3T3-E1 preosteoblasts. Real-time polymerase chain reaction and Western blotting showed that ING1b was decreased during osteoblast differentiation and ING1b overexpression markedly decreased alkaline phosphatase (ALP) activity, runt-related transcription factor 2 (Runx2) expression, and collagen type 1 synthesis, whereas ING1b silencing significantly upregulated ALP activity, Runx2 expression, and collagen type 1 synthesis. Further studies indicated that ING1b suppressed the expression of peroxisome proliferator-activated receptor (PPAR)-ß/δ in a hypoxia-inducible factor (HIF) 1α-dependent manner, while ING1b silencing significantly increased the expression of PPAR-ß/δ and HIF1α. Moreover, PPAR-ß/δ or HIF1α silencing significantly inhibited ALP activity, Runx2 expression, and collagen type 1 synthesis. These results demonstrated that ING1b is an important regulator of osteoblast differentiation and suppresses PPAR-ß/δ. Our study may provide additional insight into osteoblast differentiation and offer a potential new molecular target for osteoporosis.

HIV coreceptor tropism determination and mutational pattern identification.

In the early stages of infection, Human Immunodeficiency Virus Type 1 (HIV-1) generally selects CCR5 as the primary coreceptor for entering the host cell. As infection progresses, the virus evolves and may exhibit a coreceptor-switch to CXCR4. Accurate determination coreceptor usage and identification key mutational patterns associated tropism switch are essential for selection of appropriate therapies and understanding mechanism of coreceptor change. We developed a classifier composed of two coreceptor-specific weight matrices (CMs) based on a full-scale dataset. For this classifier, we found an AUC of 0.97, an accuracy of 95.21% and an MCC of 0.885 (sensitivity 92.92%; specificity 95.54%) in a ten-fold cross-validation, outperforming all other methods on an independent dataset (13% higher MCC value than geno2pheno and 15% higher MCC value than PSSM). A web server (http://spg.med.tsinghua.edu.cn/CM.html) based on our classifier was provided. Patterns of genetic mutations that occur along with coreceptor transitions were further identified based on the score of each sequence. Six pairs of one-AA mutational patterns and three pairs of two-AA mutational patterns were identified to associate with increasing propensity for X4 tropism. These mutational patterns offered new insights into the mechanism of coreceptor switch and aided in monitoring coreceptor switch.

Local Treatment of Osteoporotic Sheep Vertebral Body With Calcium Sulfate for Decreasing the Potential Fracture Risk: Microstructural and Biomechanical Evaluations.

STUDY DESIGN: In this study, calcium sulfate (CS) was injected through pedicle into the osteoporotic vertebral body in vivo in sheep, and micro-computed tomography analysis, histologic observation, and biomechanical test were performed. OBJECTIVE: To investigate the improvement on microstructure and biomechanical performance of lumbar vertebrae augmented with CS in osteoporotic sheep. SUMMARY OF BACKGROUND DATA: The present treatments for osteoporosis relies on systemic medications intended to increase the bone mineral density (BMD). Although effective, these time-consuming medications provide little protection from fracture in the "early period" after initiation of therapy. In this regard, the strategy of local treatment is to target specific areas of the skeletal system that are prone to osteoporotic fractures. However, there is little or no research focused on local treatment of osteoporotic vertebrae with CS. METHODS: Eight female sheep were induced to osteoporosis with bilateral ovariectomy and methylprednisolone administration for 12 months. After successful establishment of an osteoporotic model, lumbar vertebrae (L1-L4) in every sheep were randomly divided into 2 groups: CS group and control group (2 vertebrae in each group in every sheep). CS was injected into the vertebral body transpedicularly in the CS group and no treatments were performed in the control group. Three months later, all sheep were killed and all L1-L4 vertebrae were harvested. Thereafter, microstructure and biomechanical performance of the cancellous bone of the vertebral body were assessed through micro-computed tomography analysis, histologic observation, and biomechanical test, respectively. RESULTS: After a 12-month induction with ovariectomy and methylprednisolone administration, the mean BMD of the sheep lumbar vertebrae significantly decreased (>25%) compared with the value before induction, which demonstrated successful establishment of osteoporosis. Three months after injection of CS, CS was completely degraded without any remains in bone tissue and the quality of bone tissue (amount and density of the bone tissue) in the CS group was significantly higher than that in the control group. The ultimate load, stiffness, and energy absorption in the CS group were all significantly higher than those in the control group. CONCLUSIONS: The preliminary data suggest that local injection of CS can significantly improve the amount, density, and biomechanical performance of the bone trabeculae in osteoporotic vertebra. The local injection of CS could also be used as a new method to improve the physical microstructure and augment the mechanical properties in "high-risk" vertebral bodies, decreasing the potential fracture risk of patients with osteoporosis. The strict inclusion and exclusion criteria should be performed before treatment.

An Improved Method for Predicting Linear B-cell Epitope Using Deep Maxout Networks.

To establish a relation between an protein amino acid sequence and its tendencies to generate antibody response, and to investigate an improved in silico method for linear B-cell epitope (LBE) prediction. We present a sequence-based LBE predictor developed using deep maxout network (DMN) with dropout training techniques. A graphics processing unit (GPU) was used to reduce the training time of the model. A 10-fold cross-validation test on a large, non-redundant and experimentally verified dataset (Lbtope_Fixed_ non_redundant) was performed to evaluate the performance. DMN-LBE achieved an accuracy of 68.33% and an area under the receiver operating characteristic curve (AUC) of 0.743, outperforming other prediction methods in the field. A web server, DMN-LBE, of the improved prediction model has been provided for public free use. We anticipate that DMN-LBE will be beneficial to vaccine development, antibody production, disease diagnosis, and therapy.

Reactive oxygen species induce cell death via Akt signaling in rat osteoblast-like cell line ROS 17/2.8.

In bones, osteoblasts are responsible for bone formation. The cell death of osteoblasts may cause a series of bone diseases and lead to bone loss, such as osteoarthrosis, hyperparathyroidism, and Paget's disease. Reactive oxygen species (ROS) are reported as a main factor for osteoblast cell death and further several bone diseases. However, the detailed mechanism is still largely unknown. Here, we found that ROS could induce cell death of rat osteoblast-like cell line ROS 17/2.8 via Akt (protein kinase B). Also, the mammalian target of rapamycin signaling was involved in this process. Our findings could help to reveal the cellular mechanism of osteoblast cell death, which is served for the pursuit of clinical treatment targets of relative bone diseases.

EPMLR: sequence-based linear B-cell epitope prediction method using multiple linear regression.

BACKGROUND: B-cell epitopes have been studied extensively due to their immunological applications, such as peptide-based vaccine development, antibody production, and disease diagnosis and therapy. Despite several decades of research, the accurate prediction of linear B-cell epitopes has remained a challenging task. RESULTS: In this work, based on the antigen's primary sequence information, a novel linear B-cell epitope prediction model was developed using the multiple linear regression (MLR). A 10-fold cross-validation test on a large non-redundant dataset was performed to evaluate the performance of our model. To alleviate the problem caused by the noise of negative dataset, 300 experiments utilizing 300 sub-datasets were performed. We achieved overall sensitivity of 81.8%, precision of 64.1% and area under the receiver operating characteristic curve (AUC) of 0.728. CONCLUSIONS: We have presented a reliable method for the identification of linear B cell epitope using antigen's primary sequence information. Moreover, a web server EPMLR has been developed for linear B-cell epitope prediction: http://www.bioinfo.tsinghua.edu.cn/epitope/EPMLR/ .

High-accuracy identification of incident HIV-1 infections using a sequence clustering based diversity measure.

Accurate estimates of HIV-1 incidence are essential for monitoring epidemic trends and evaluating intervention efforts. However, the long asymptomatic stage of HIV-1 infection makes it difficult to effectively distinguish incident infections from chronic ones. Current incidence assays based on serology or viral sequence diversity are both still lacking in accuracy. In the present work, a sequence clustering based diversity (SCBD) assay was devised by utilizing the fact that viral sequences derived from each transmitted/founder (T/F) strain tend to cluster together at early stage, and that only the intra-cluster diversity is correlated with the time since HIV-1 infection. The dot-matrix pairwise alignment was used to eliminate the disproportional impact of insertion/deletions (indels) and recombination events, and so was the proportion of clusterable sequences (Pc) as an index to identify late chronic infections with declined viral genetic diversity. Tested on a dataset containing 398 incident and 163 chronic infection cases collected from the Los Alamos HIV database (last modified 2/8/2012), our SCBD method achieved 99.5% sensitivity and 98.8% specificity, with an overall accuracy of 99.3%. Further analysis and evaluation also suggested its performance was not affected by host factors such as the viral subtypes and transmission routes. The SCBD method demonstrated the potential of sequencing based techniques to become useful for identifying incident infections. Its use may be most advantageous for settings with low to moderate incidence relative to available resources. The online service is available at http://www.bioinfo.tsinghua.edu.cn:8080/SCBD/index.jsp.

Single level anterior interbody fusion and fixation in the treatment of thoracolumbar fractures.

BACKGROUND: Many surgical methods are available for repairing thoracolumbar fractures including short-segment internal fixation with posterior pedicle screws and anterior decompression and reduction. However, most methods are associated with significant surgical trauma and long postoperative recovery. The purpose of this study was to describe anterior single level interbody fusion and fixation for the repair of thoracolumbar fractures which may reduce surgical trauma and help speed recovery. METHODS: A group of 21 patients who underwent single level anterior interbody fusion and fixation from June 2006 to June 2011 were compared with a group of 21 patients who underwent double level anterior interbody fusion and fixation during the same period. The groups were compared with regard to operation time, intraoperative blood loss, fracture healing time, ratio of pre- to postoperative endplate height between adjacent vertebrae, Cobb angle in the sagittal plane, recovery of neural function, and internal fusion failure. RESULTS: The 2 groups were similar with the exception of fracture location (P=0.017). The patients who underwent the single level procedure had a shorter operation time (P < 0.001), less blood loss (P < 0.001), and shorter follow-up (P < 0.001). Both groups had significant improvement in Cobb angle at 1 week and 1 year after surgery, but there was no significant difference between the groups. Both groups also exhibited improvement in neurological function, and the difference in improvement between the groups was not significant. CONCLUSIONS: Single level intervertebral fusion and internal fixation for thoracolumbar fractures provides as satisfactory an outcome as the traditional approach, double level anterior interbody fusion and fixation, and reduces the degree of surgical trauma.

PDGF-regulated miRNA-138 inhibits the osteogenic differentiation of mesenchymal stem cells.

Differentiation-specific microRNAs may play a critical role in MSC differentiation, and they can be altered by PDGF signaling. We propose that PDGF modulates MSC differentiation by regulating microRNA expression. Therefore, we investigated whether PDGF treatment could alter the expression profile of miRNAs in MSCs. Furthermore, we assessed the osteoblast phenotype of MSCs after inducing osteogenic differentiation. We found that PDGF treatment significantly inhibits the osteogenic differentiation of MSCs and that miR-138 gene transcription is controlled by PDGF signaling. Our results confirm that miR-138 inhibits the osteogenic differentiation of MSCs and suppresses the phosphorylation of FAK, ERK1/2, and Runx2. Furthermore, our study clearly demonstrates that downregulation of Runx2 by miR-138 is critical for the PDGF-mediated inhibition of osteogenic differentiation of MSCs. These findings indicate that inhibition of miR-138 function in MSCs, either by treatment with anti-miR-138 or by overexpression of the miR-138 target sequence (miRNA sponge), could represent a potential therapeutic strategy for the treatment of bone homeostasis disorders caused by activation of the PDGF pathway.

C/EBP-α, involvement of a novel transcription factor in leptin-induced VCAM-1 production in mouse chondrocytes.

Leptin and vascular cell adhesion molecules-1 (VCAM-1) are two important mediators in obesity-related osteoarthritis, while the molecular mechanism linking leptin to VCAM-1 production is still obscure. Here we show that leptin upregulates VCAM-1 mRNA and protein levels in a time- and dose-dependent manner. Mechanistically, leptin induces VCAM-1 promoter activity by increasing the expression of C/EBP-α and facilitating its binding to a newly identified element in the VCAM-1 gene. Gain or loss of function studies reveal a regulatory role of C/EBP-α on VCAM-1 expression. Finally, elevated plasma leptin level correlates to increased C/EBP-α and VCAM-1 production in chondrocytes from obese mice.

Comparison of 2 kinds of pedicle screws in primary spinal instrumentation: biomechanical and interfacial evaluations in sheep vertebrae in vitro.

STUDY DESIGN: Expansive pedicle screw (EPS) and polymethylmethacrylate-augmented pedicle screw (PMMA-PS) were inserted in sheep vertebrae in vitro and were evaluated by performing biomechanical tests, radiographic examinations and histological observations. OBJECTIVE: The objective of the study was to compare the biomechanical and interfacial performances of EPS and PMMA-PS in sheep lumbar vertebrae in vitro. SUMMARY OF BACKGROUND DATA: It is a great challenge for orthopedic surgeons performing transpedicular fixation in the osteoporotic spine. It was reported that either the EPS or PMMA-PS could increase the screw stability. However, there are no studies comparing the 2 kinds of screws especially in primary spinal instrumentation. METHODS: A total of 60 sheep lumbar vertebrae were randomly divided into 3 groups. A pilot hole was made in advance in all samples using the same method. Thereafter, the conventional pedicle screw (CPS) was inserted directly into the pilot hole in the CPS group; the hole in PMMA-PS group was first filled with polymethylmethacrylate (PMMA; 1.0 mL) and then inserted with CPS; and the EPS was inserted directly into the vertebrae in EPS group. After a period of 24 hours, biomechanical tests were performed to evaluate screw stability, and x-ray examination, micro-computerized tomography analysis, and histologic observation were performed to evaluate the interface between screw and bone. RESULTS: Compared with the stability of CPS, those of EPS and PMMA-PS were significantly enhanced. However, no significant differences were detected between the stabilities of EPS and PMMA-PS. The PMMA surrounding the screw blocked direct contact between bone and screw and formed a "screw-PMMA-bone" interface in the PMMA-PS group. There was a "screw-bone" interface in both CPS and EPS groups. Nevertheless, the expanded anterior part of EPS formed a claw-like structure pressing the surrounding bone trabeculae, which made the local bone tissue more compacted and denser than that in the CPS group. CONCLUSIONS: EPS can enhance the screw stability as markedly as the traditional PMMA-PS in primary surgery, and EPS can form a better immediate interface between screw and bone compared with PMMA-PS. EPS also can effectively avoid thermal injury, leakage, and compression caused by PMMA. A great feasibility was proved in this study to perform comparisons between the 2 kinds of pedicle screws in osteoporotic sheep vertebrae in vivo in the further research. In conclusion, we propose that EPS has a great application potential in augmentation of screw stability in the clinic.

Comparison of expansive pedicle screw and polymethylmethacrylate-augmented pedicle screw in osteoporotic sheep lumbar vertebrae: biomechanical and interfacial evaluations.

BACKGROUND: It was reported that expansive pedicle screw (EPS) and polymethylmethacrylate-augmented pedicle screw (PMMA-PS) could be used to increase screw stability in osteoporosis. However, there are no studies comparing the two kinds of screws in vivo. Thus, we aimed to compare biomechanical and interfacial performances of EPS and PMMA-PS in osteoporotic sheep spine. METHODOLOGY/PRINCIPAL FINDINGS: After successful induction of osteoporotic sheep, lumbar vertebrae in each sheep were randomly divided into three groups. The conventional pedicle screw (CPS) was inserted directly into vertebrae in CPS group; PMMA was injected prior to insertion of CPS in PMMA-PS group; and the EPS was inserted in EPS group. Sheep were killed and biomechanical tests, micro-CT analysis and histological observation were performed at both 6 and 12 weeks post-operation. At 6-week and 12-week, screw stabilities in EPS and PMMA-PS groups were significantly higher than that in CPS group, but there were no significant differences between EPS and PMMA-PS groups at two study periods. The screw stability in EPS group at 12-week was significantly higher than that at 6-week. The bone trabeculae around the expanding anterior part of EPS were more and denser than that in CPS group at 6-week and 12-week. PMMA was found without any degradation and absorption forming non-biological "screw-PMMA-bone" interface in PMMA-PS group, however, more and more bone trabeculae surrounded anterior part of EPS improving local bone quality and formed biological "screw-bone" interface. CONCLUSIONS/SIGNIFICANCE: EPS can markedly enhance screw stability with a similar effect to the traditional method of screw augmentation with PMMA in initial surgery in osteoporosis. EPS can form better biological interface between screw and bone than PMMA-PS. In addition, EPS have no risk of thermal injury, leakage and compression caused by PMMA. We propose EPS has a great application potential in augmentation of screw stability in osteoporosis in clinic.

Accurate prediction of protein structural class.

Because of the increasing gap between the data from sequencing and structural genomics, the accurate prediction of the structural class of a protein domain solely from the primary sequence has remained a challenging problem in structural biology. Traditional sequence-based predictors generally select several sequence features and then feed them directly into a classification program to identify the structural class. The current best sequence-based predictor achieved an overall accuracy of 74.1% when tested on a widely used, non-homologous benchmark dataset 25PDB. In the present work, we built a multiple linear regression (MLR) model to convert the 440-dimensional (440D) sequence feature vector extracted from the Position Specific Scoring Matrix (PSSM) of a protein domain to a 4-dimensinal (4D) structural feature vector, which could then be used to predict the four major structural classes. We performed 10-fold cross-validation and jackknife tests of the method on a large non-homologous dataset containing 8,244 domains distributed among the four major classes. The performance of our approach outperformed all of the existing sequence-based methods and had an overall accuracy of 83.1%, which is even higher than the results of those predicted secondary structure-based methods.