Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme

BACKGROUND: Gene expression profiling has become a useful biological resource in recent years, and it plays an important role in a broad range of areas in biology. The raw gene expression data, usually in the form of large matrix, may contain missing values. The downstream analysis methods that postulate complete matrix input are thus not applicable. Several methods have been developed to solve this problem, such as K nearest neighbor impute method, Bayesian principal components analysis impute method, etc. In this paper, we introduce a novel imputing approach based on the Support Vector Regression (SVR) method. The proposed approach utilizes an orthogonal coding input scheme, which makes use of multi-missing values in one row of a certain gene expression profile and imputes the missing value into a much higher dimensional space, to obtain better performance. RESULTS: A comparative study of our method with the previously developed methods has been presented for the estimation of the missing values on six gene expression data sets. Among the three different input-vector coding schemes we tried, the orthogonal input coding scheme obtains the best estimation results with the minimum Normalized Root Mean Squared Error (NRMSE). The results also demonstrate that the SVR method has powerful estimation ability on different kinds of data sets with relatively small NRMSE. CONCLUSION: The SVR impute method shows better performance than, or at least comparable with, the previously developed methods in present research. The outstanding estimation ability of this impute method is partly due to the use of the most missing value information by incorporating orthogonal input coding scheme. In addition, the solid theoretical foundation of SVR method also helps in estimation of performance together with orthogonal input coding scheme. The promising estimation ability demonstrated in the results section suggests that the proposed approach provides a proper solution to the missing value estimation problem. The source code of the SVR method is available from for non-commercial use

Mycobacterial Interspersed Repetitive Unit Can Predict Drug Resistance of Mycobacterium tuberculosis in China

BackgroundRecently, Mycobacterial Interspersed Repetitive Unit (MIRU) was supposed to be associated with drug resistance in M.tuberculosis (MTB). However, whether the MIRU was related to drug resistance actually was still unknown. This research was conducted to explore that association.MethodsDrug susceptibility testing was used to evaluate the drug resistance of five anti-tuberculosis drug (isoniazid, INH; rifampicin, RFP; streptomycin, SM; ethambutol, EMB; and Paminosalicylicacid, PAS.). We tested the number of the repeat unite of MIRU (Mycobacterial Interspersed Repetitive Unit) locus based on PCR of miru-vntr genotyping. Then, through logistic regression, we evaluated the association between fifteen MIRU and the resistance. In addition, we explored the most suitable MIRU locus of identified MIRU loci for drug resistance through multivariate logistic regression.ResultsAmong these fifteen MIRU, we found several MIRU loci could predict the drug resistance well. For example ,ETRB and ETRC could predict INH resistance; MIRU20 was associated with EMB resistance; and QUB11a was a predictive factor of PSA. ConclusionOur results may provide candidate regions for future genetic studies and aid in the prediction for drug resistance of MTB

4,4′-Bipyridine–2-(carb­oxy­methyl­sulfan­yl)pyridine-3-carb­oxy­lic acid (1/1)

In the title co-crystal, C10H8N2·C8H7NO4S, the formate group is coplanar with the pyridyl ring of the acid [dihedral angle = 6.2 (7)°], while the carb­oxy­methyl­sulfanyl group makes a C—S—C—C torsion angle of 70.2 (1)° with the pyridine ring. The dihedral angle between the pyridyl rings of the 4,4′-bipyridine mol­ecule is 27.4 (1)°. The acid and the 4,4′-bipyridine mol­ecules are involved in hydrogen bonding via carb­oxy­lic O and pyridyl N atoms. The structure is further consolidated by inter­molecular C—H⋯O hydrogen bonds, generating a three-dimensional network

Diagnostic value of two dimensional shear wave elastography combined with texture analysis in early liver fibrosis.

BACKGROUND: Staging diagnosis of liver fibrosis is a prerequisite for timely diagnosis and therapy in patients with chronic hepatitis B. In recent years, ultrasound elastography has become an important method for clinical noninvasive assessment of liver fibrosis stage, but its diagnostic value for early liver fibrosis still needs to be further improved. In this study, the texture analysis was carried out on the basis of two dimensional shear wave elastography (2D-SWE), and the feasibility of 2D-SWE plus texture analysis in the diagnosis of early liver fibrosis was discussed. AIM: To assess the diagnostic value of 2D-SWE combined with textural analysis in liver fibrosis staging. METHODS: This study recruited 46 patients with chronic hepatitis B. Patients underwent 2D-SWE and texture analysis; Young\u27s modulus values and textural patterns were obtained, respectively. Textural pattern was analyzed with regard to contrast, correlation, angular second moment (ASM), and homogeneity. Pathological results of biopsy specimens were the gold standard; comparison and assessment of the diagnosis efficiency were conducted for 2D-SWE, texture analysis and their combination. RESULTS: 2D-SWE displayed diagnosis efficiency in early fibrosis, significant fibrosis, severe fibrosis, and early cirrhosis (AUC \u3e 0.7, P \u3c 0.05) with respective AUC values of 0.823 (0.678-0.921), 0.808 (0.662-0.911), 0.920 (0.798-0.980), and 0.855 (0.716-0.943). Contrast and homogeneity displayed independent diagnosis efficiency in liver fibrosis stage (AUC \u3e 0.7, P \u3c 0.05), whereas correlation and ASM showed limited values. AUC of contrast and homogeneity were respectively 0.906 (0.779-0.973), 0.835 (0.693-0.930), 0.807 (0.660-0.910) and 0.925 (0.805-0.983), 0.789 (0.639-0.897), 0.736 (0.582-0.858), 0.705 (0.549-0.883) and 0.798 (0.650-0.904) in four liver fibrosis stages, which exhibited equivalence to 2D-SWE in diagnostic efficiency (P \u3e 0.05). Combined diagnosis (PRE) displayed diagnostic efficiency (AUC \u3e 0.7, P \u3c 0.01) for all fibrosis stages with respective AUC of 0.952 (0.841-0.994), 0.896 (0.766-0.967), 0.978 (0.881-0.999), 0.947 (0.835-0.992). The combined diagnosis showed higher diagnosis efficiency over 2D-SWE in early liver fibrosis (P \u3c 0.05), whereas no significant differences were observed in other comparisons (P \u3e 0.05). CONCLUSION: Texture analysis was capable of diagnosing liver fibrosis stage, combined diagnosis had obvious advantages in early liver fibrosis, liver fibrosis stage might be related to the hepatic tissue hardness distribution

Magnetic and transport properties of n-type Fe-doped In2O3 ferromagnetic thin films

Room temperature ferromagnetism was observed in n-type Fe-doped In2O3 thin films deposited on c-cut sapphire substrates by pulsed laser deposition. Structure, magnetism, composition, and transport studies indicated that Fe occupied the In sites of the In2O3 lattice rather than formed any metallic Fe or other magnetic impurity phases. Magnetic moments of films were proved to be intrinsic and showed to have a strong dependence on the carrier densities which depended on the Fe concentration and its valance state as well as oxygen pressure.Comment: Accepted in Applied Physics Letter

Downregulation of KLF8 expression by shRNA induces inhibition of cell proliferation in CAL27 human oral cancer cells

Objectives: KLF8 is a member of KLF transcription factors which play an important tolr in oncogenesis. It is barely expressed in normal human epithelial cells but highly overexpressed in several types of human cancer cell lines. In the present study, we investigate the role of KLF8 in oral cancer and the effects of KLF8 knockdown via lentivirus mediated siRNA infection in human adenosquamos carcinoma CAL 27 cells. Study Design: We developed a vector-based siRNA expression system that can induce RNAi in CAL 27 oral cancer cells. Downregulation of KLF8 was confirmed by evaluating GFP expressions, RT-PCR and western blot analysis. Finally, the effects of KLF8 downregulation were analyzed by MTT assay and colony formation assays. Results: The expression levels of KLF8 mRNA and proteins are reduced in CAL 27 cells that transfected with 21- nt siRNA against KLF8. Lentivirus-mediated silencing of KLF8 reduces cell proliferation and colonies number, thereby indicating the role of KLF8 in cell proliferation and tumorigenesis. Conclusions: These results strongly suggest that KLF8 is essential for growth of CAL 27 cancer cells. A better understanding of KLF8 function and processing may provide novel insights into the clinical therapy of oral cancer

Multi-Player and Multi-Choice Quantum Game

We investigate a multi-player and multi-choice quantum game. We start from two-player and two-choice game and the result is better than its classical version. Then we extend it to N-player and N-choice cases. In the quantum domain, we provide a strategy with which players can always avoid the worst outcome. Also, by changing the value of the parameter of the initial state, the probabilities for players to obtain the best payoff will be much higher that in its classical version.Comment: 4 pages, 1 figur