Missing value imputation for gene expression data: computational techniques to recover missing data from available information

Microarray gene expression data generally suffers from missing value problem due to a variety of experimental reasons. Since the missing data points can adversely affect downstream analysis, many algorithms have been proposed to impute missing values. In this survey, we provide a comprehensive review of existing missing value imputation algorithms, focusing on their underlying algorithmic techniques and how they utilize local or global information from within the data, or their use of domain knowledge during imputation. In addition, we describe how the imputation results can be validated and the different ways to assess the performance of different imputation algorithms, as well as a discussion on some possible future research directions. It is hoped that this review will give the readers a good understanding of the current development in this field and inspire them to come up with the next generation of imputation algorithms.     

Systematic review and meta-analysis of the efficacy and safety of existing TNF blocking agents in treatment of rheumatoid arthritis

Background and Objectives

Five-tumour necrosis factor (TNF)-blockers (infliximab, etanercept, adalimumab, certolizumab pegol and golimumab) are available for treatment of rheumatoid arthritis. Only few clinical trials compare one TNF-blocker to another. Hence, a systematic review is required to indirectly compare the substances. The aim of our study is to estimate the efficacy and the safety of TNF-blockers in the treatment of rheumatoid arthritis (RA) and indirectly compare all five currently available blockers by combining the results from included randomized clinical trials (RCT).

Methods

A systematic literature review was conducted using databases including: MEDLINE, SCOPUS (including EMBASE), Cochrane library and electronic search alerts. Only articles reporting double-blind RCTs of TNF-blockers vs. placebo, with or without concomitant methotrexate (MTX), in treatment of RA were selected. Data collected were information of patients, interventions, controls, outcomes, study methods and eventual sources of bias.

Results

Forty-one articles reporting on 26 RCTs were included in the systematic review and meta-analysis. Five RCTs studied infliximab, seven etanercept, eight adalimumab, three golimumab and three certolizumab. TNF-blockers were more efficacious than placebo at all time points but were comparable to MTX. TNF-blocker and MTX combination was superior to either MTX or TNF-blocker alone. Increasing doses did not improve the efficacy. TNF-blockers were relatively safe compared to either MTX or placebo.

Conclusions

No single substance clearly rose above others in efficacy, but the results of the safety analyses suggest that etanercept might be the safest alternative. Interestingly, MTX performs nearly identically considering both efficacy and safety aspects with a margin of costs.     

ACR70-disease activity score remission achievement from switches between all the available biological agents in rheumatoid arthritis: a systematic review of the literature

Introduction  

The aim of our analysis was to compare the gaining of a major response (disease activity score [DAS] remission or American College of Rheumatology 70% improvement criteria [ACR70]) by switching between all the available biological therapies in rheumatoid arthritis.     

Cometabolism of trichloroethylene: concepts, limitations and available strategies for sustained biodegradation

Due to its toxicity and persistence in the environment, trichloroethylene (TCE) has become a major soil and groundwater contaminant in many countries. A group of aliphatic- and aromatic-degrading bacteria expressing nonspecific oxygenases have been reported to transform TCE through aerobic cometabolism in the presence of primary substrate such as methane, ammonia, propane, phenol, toluene or cumene. This paper reviews the fundamentals and results of TCE cometabolism from laboratory and field studies. The limitations associated with TCE cometabolism including the causes and effects of substrate and/or inducer utilization rate and depletion, enzyme inhibition and inactivation, and cytotoxicity during TCE oxidation among various TCE-degrading bacteria and enzymes are discussed. In addition, the potential strategies e.g. addition of primary substrate/inducer or external energy substrate, use of a two-stage reactor and application of cell immobilization for sustained TCE degradation are highlighted. The review summarizes important information on TCE cometabolism, which is necessary for developing efficient TCE bioremediation approaches.     

Rubella and rheumatoid arthritis: hyaluronic acid and susceptibility of cultured rheumatoid synovial cells to viruses.

Synovial cell lines were established from patients with rheumatoid arthritis (RA) and from normal human embryos. High levels of hyaluronic acid (HA) were produced by some RA cell lines, some of which were partially or completely resistant to infection with Newcastle disease virus (NDV), vesicular stomatitis virus (VSV), and rubella virus (RV). Normal fetal synovial cells lines were susceptible to NDV, VSV, and RV. Infection with virus became possible after treatment of RA cells with hyaluronidase to depolymerize HA, and HA prevented infection of normal synovial cells with VSV. These results provide evidence that HA and not chronic or latent viral infection is responsible for the lack of susceptibility of RA synovial cells to certain viruses.     

Pharmacological intervention strategies for affecting telomerase activity: future prospects to treat cancer and degenerative disease

Telomerase enzyme is a ribonucleoprotein maintaining the length of the telomeres by adding G-rich repeats to the end of the eukaryotic chromosomes. Normal human somatic cells, cultured in vitro, have a strictly limited proliferative potential undergoing senescence after about 50-70 population doublings. In contrast, most of the tumor cells have unlimited replicative potential. Although the mechanisms of immortalization are not understood completely at a genetic level, the key role of the telomere/telomerase system in the process is clear. The DNA replication machinery is not able to replicate fully the DNA at the very end of the chromosomes; therefore, about 50-200 nucleotides are lost during each of the replication cycles resulting in a gradual decrease of telomere length. Critically short telomere induces senescence, subsequent crisis and cell death. In tumor cells, however, the telomerase enzyme prevents the formation of critically short telomeres, adding GGTTAG repeats to the 3' end of the chromosomes immortalizing the cells. Immortality is one of the hallmarks of cancer. Besides the catalytic activity dependent telomere maintenance, catalytic activity-independent effects of telomerase may also be involved in the regulation of cell cycle. The telomere/telomerase system offers two possibilities to intervene the proliferative activity of the cell: (1) inhibition the telomere maintenance by inhibiting the telomerase activity; (2) activating the residual telomerase enzyme or inducing telomerase expression. Whilst the former approach could abolish the limitless replicative potential of malignant cells, the activation of telomerase might be utilized for treating degenerative diseases. Here, we review the current status of telomerase therapeutics, summarizing the activities of those pharmacological agents which either inhibit or activate the enzyme. We also discuss the future opportunities and challenges of research on pharmacological intervention of telomerase activity.     

Skilled care at birth in the developing world: progress to date and strategies for expanding coverage

Skilled attendance at delivery is one of the key indicators to reflect progress toward the Millennium Development Goal of improving maternal health. This paper assesses global progress in the use of skilled attendants at delivery and identifies factors that could assist in achieving Millennium Development Goals for maternal health. National data covering a substantial proportion of all developing country births were used for the estimation of trends and key differentials in skilled assistance at delivery. Between 1990 and 2000, the percentage of births with a skilled attendant increased from 45% to 54% in developing countries, primarily as a result of an increasing use of doctors. A substantial proportion of antenatal care users do not deliver with a skilled attendant. Delivery care use among antenatal care users is highly correlated with wealth. Women aged 35 and above, who are at greatest risk of maternal death, are the least likely to receive professional delivery care. Births in mid-level facilities appear to be a strategy that has been overlooked. More effective strategies are needed to promote skilled attendance at birth during antenatal care, particularly among poor women. Specific interventions are also needed to encourage older and high parity mothers to seek professional care at delivery.     

Engineering surfaces for bioconjugation: developing strategies and quantifying the extent of the reactions

This study presents two-step and multistep reactions for modifying the surface of plasma-functionalized poly(tetrafluoroethylene) (PTFE) surfaces for subsequent conjugation of biologically relevant molecules. First, PTFE films were treated by a radiofrequency glow discharge (RFGD) ammonia plasma to introduce amino groups on the fluoropolymer surface. This plasma treatment is well optimized and allows the incorporation of a relative surface concentration of approximately 2-3.5% of amino groups, as assessed by chemical derivatization followed by X-ray photoelectron spectroscopy (XPS). In a second step, these amino groups were further reacted with various chemical reagents to provide the surface with chemical functionalities such as maleimides, carboxylic acids, acetals, aldehydes, and thiols, that could be used later on to conjugate a wide variety of biologically relevant molecules such as proteins, DNA, drugs, etc. In the present study, glutaric and cis-aconitic anhydrides were evaluated for their capability to provide carboxylic functions to the PTFE plasma-treated surface. Bromoacetaldehyde diethylacetal was reacted with the aminated PTFE surface, providing a diethylacetal function, which is a latent form of aldehyde functionality. Reactions with cross-linkers such as sulfo-succinimidyl derivatives (sulfo-SMCC, sulfo-SMPB) were evaluated to provide a highly reactive maleimide function suitable for further chemical reactions with thiolated molecules. Traut reagent (2-iminothiolane) was also conjugated to introduce a thiol group onto the fluoropolymer surface. PTFE-modified surfaces were analyzed by XPS with a particular attention to quantify the extent of the reactions that occurred on the polymer. Finally, surface immobilization of fibronectin performed using either glutaric anhydride or sulfo-SMPB activators demonstrated the importance of selecting the appropriate conjugation strategy to retain the protein biological activity.     

CD4 and CD8 T cells in susceptibility/protection to collagen-induced arthritis in HLA-DQ8-transgenic mice: implications for rheumatoid arthritis

To investigate the role of CD4 and CD8 T cells in arthritis, we generated transgenic mice deficient in CD4 and CD8 molecules expressing RA-susceptible gene HLA-DQ8. DQ8.CD4(-/-) mice were resistant to developing collagen-induced arthritis (CIA). However, DQ8.CD8(-/-) mice developed CIA with increased incidence and more severity than DQ8 mice. Both DQ8.CD8(-/-) and DQ8 mice produced rheumatoid factor. In addition, DQ8.CD8(-/-) mice produced antinuclear Abs. The B cell compartment and expression of DQ8 were normal in all the strains, although frequency of cells expressing DQ8 was less in CD4(-/-) mice. An increased frequency of CD3(+) double-negative (DN) T cells was found in DQ8.CD8(-/-) compared with DQ8.CD4(-/-) and DQ8 mice. These CD3(+) DN T cells produced high amounts of IL-10 in CD8-deficient mice. Analysis of cell division using a cell cycle tracking dye showed a higher rate of division of CD3(+) and CD3(+) DN T cells in DQ8.CD8(-/-) mice compared with DQ8.CD4(-/-) and DQ8 mice. Decreased apoptosis was seen in CIA-susceptible DQ8 and CD8-deficient mice, indicating a defect in activation-induced cell death. These observations suggest that CD4 cells are necessary for initiation of CIA in DQ8 mice. We hypothesize that CD8(+) T cells are not capable of initiating CIA in DQ8-transgenic mice but may have a regulatory/protective effect.     

Binding to faeces and influence on human anaerobes of antimicrobial agents used for selective decontamination

The degree of binding of ampicillin, cephradine, co-trimoxazole, gentamicin, nalidixic acid, neomycin, polymyxin B and tobramycin by faecal substance as well as the influence of these antibiotics on human intestinal obligate anaerobes was investigated. In contrast to ampicillin, cephradine, co-trimoxazole and nalidixic acid, the nonabsorbable antibiotics polymyxin B and neomycin were bound to a considerable degree by human faeces. The binding of tobramycin and gentamicin to the solid part of faeces was less effective. The inhibitory effect of co-trimoxazole, gentamicin, nalidixic acid, neomycin, polymyxin B and tobramycin on the human obligate anaerobes was weak as compared with ampicillin and cephradine. Drugs which effectively eliminate Enterobacteriaceae from the gastrointestinal tract and which have a moderate effect on obligate anaerobes, like polymyxin B, are particularly suitable for selective decontamination of the gastrointestinal tract. The strong inactivating binding of aminoglycosides and polymyxin B to faeces accounts for the relatively high oral dose needed for a suitable faecal concentration.     

Effect of prednisone on type I interferon signature in rheumatoid arthritis: consequences for response prediction to rituximab

IntroductionElevated type I interferon (IFN) response gene (IRG) expression has proven clinical relevance in predicting rituximab non-response in rheumatoid arthritis (RA). Interference between glucocorticoids (GCs) and type I IFN signaling has been demonstrated in vitro. Since GC use and dose are highly variable among patients before rituximab treatment, the aim of this study was to determine the effect of GC use on IRG expression in relation to rituximab response prediction in RA.MethodsIn two independent cohorts of 32 and 182 biologic-free RA patients and a third cohort of 40 rituximab-starting RA patients, peripheral blood expression of selected IRGs was determined by microarray or quantitative real-time polymerase chain reaction (qPCR), and an IFN-score was calculated. The baseline IFN-score was tested for its predictive value towards rituximab response in relation to GC use using receiver operating characteristics (ROC) analysis in the rituximab cohort. Patients with a decrease in disease activity score (∆DAS28) >1.2 after 6 months of rituximab were considered responders.ResultsWe consistently observed suppression of IFN-score in prednisone users (PREDN⁺) compared to non-users (PREDN⁻). In the rituximab cohort, analysis on PREDN⁻ patients (n = 13) alone revealed improved prediction of rituximab non-response based on baseline IFN-score, with an area under the curve (AUC) of 0.975 compared to 0.848 in all patients (n = 40). Using a group-specific IFN-score cut-off for all patients and PREDN⁻ patients alone, sensitivity increased from 41% to 88%, respectively, combined with 100% specificity.ConclusionsBecause of prednisone-related suppression of IFN-score, higher accuracy of rituximab response prediction was achieved in PREDN⁻ patients. These results suggest that the IFN-score-based rituximab response prediction model could be improved upon implementation of prednisone use.     

Human placental 17 beta-estradiol dehydrogenase: enzymatic activity in the last weeks of pregnancy and electrophoretic data.

A specific electrophoretic method for human placental 17 beta-estradiol dehydrogenase (17-HSD; EC 1.1.1.62) has been performed and a sample of about 180 placentae from Italian women has been examined. A common phenotype and only one electrophoretic variant have been observed. Also 17-HSD activity has been tested. A statistically significant negative correlation has been found between 17-HSD activity and both gestational age and birth weight in the last weeks of gestation in a group of at term newborns with weight appropriate for date. This reduction in enzymatic activity is in good agreement with the data on estrone and estradiol which both show a declining rate of increase in the last weeks of pregnancy.     

Lack of replication of genetic predictors for the rheumatoid arthritis response to anti-TNF treatments: a prospective case-only study

Introduction  

We aimed to replicate the strong associations that a recent genome wide association study (GWAS) has found between 16 single nucleotide polymorphisms (SNPs) and response to anti-tumour necrosis factor (TNF) treatment in 89 patients with rheumatoid arthritis (RA). This study is very important because, according to published simulations, associations as strong as the reported ones will mean that these SNPs could be used as predictors of response at the individual level.