Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data

MOTIVATION: Microarray data are used in a range of application areas in biology, although often it contains considerable numbers of missing values. These missing values can significantly affect subsequent statistical analysis and machine learning algorithms so there is a strong motivation to estimate these values as accurately as possible before using these algorithms. While many imputation algorithms have been proposed, more robust techniques need to be developed so that further analysis of biological data can be accurately undertaken. In this paper, an innovative missing value imputation algorithm called collateral missing value estimation (CMVE) is presented which uses multiple covariance-based imputation matrices for the final prediction of missing values. The matrices are computed and optimized using least square regression and linear programming methods. RESULTS: The new CMVE algorithm has been compared with existing estimation techniques including Bayesian principal component analysis imputation (BPCA), least square impute (LSImpute) and K-nearest neighbour (KNN). All these methods were rigorously tested to estimate missing values in three separate non-time series (ovarian cancer based) and one time series (yeast sporulation) dataset. Each method was quantitatively analyzed using the normalized root mean square (NRMS) error measure, covering a wide range of randomly introduced missing value probabilities from 0.01 to 0.2. Experiments were also undertaken on the yeast dataset, which comprised 1.7% actual missing values, to test the hypothesis that CMVE performed better not only for randomly occurring but also for a real distribution of missing values. The results confirmed that CMVE consistently demonstrated superior and robust estimation capability of missing values compared with other methods for both series types of data, for the same order of computational complexity. A concise theoretical framework has also been formulated to validate the improved performance of the CMVE algorithm. AVAILABILITY: The CMVE software is available upon request from the authors.     

The molecular morphology of bovine heart mitochondrial NADH----ubiquinone reductase. Native disulfide-linked subunits and rotenone-induced conformational changes

Bovine heart mitochondrial NADH----ubiquinone reductase (complex I), contains two disulfide-linked subunits of 75 and 33 kDa as revealed by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis with beta-mercaptoethanol omitted from preparation of the sample for the first dimension. Two unidentified polypeptides (110-115 and 69 kDa) are also found in disulfide linkage with the two complex I subunits. The 110-115-kDa polypeptide appears to be pyridine dinucleotide transhydrogenase by several criteria including selective precipitation with an antibody raised to the purified transhydrogenase. The two disulfide-linked subunits were also found in a product cross-linked for 2 min with dithiobis (succinimidyl propionate) (DSP) along with five other complex I subunits of 53-57, 42, 24-27, 17-18, and 12.5-15.5 kDa (Gondal, J.A., and Anderson, W.M. (1985) J. Biol. Chem. 260, 5931-5935) indicating that these seven subunits lie within 11-12 A of each other at one or more points in space in the enzyme's interior. Cross-linking of complex I with DSP for 2 min in the presence of 1 microM rotenone yielded a cross-linked product consisting of the two natural disulfide-linked subunits and the 110-115- and 69-kDa polypeptides. This suggests that rotenone induces a conformational change in the enzyme that moves the seven DSP cross-linked subunits away from each other and outside the 11-12 A bridging distance of DSP. This alteration in conformation may be communicated to iron-sulfur center N-2 within the hydrophobic outer shell of the enzyme to prevent electron transfer to its natural electron acceptor, ubiquinone. A model of rotenone action based upon these observations is presented.     

An early Miocene deep‐water decapod crustacean faunule from the Vienna Basin (Western Carpathians,Slovakia)

Abstract: A decapod crustacean faunule from the lower Miocene (upper Burdigalian, ‘Karpatian’) of the Slovakian part of the Vienna Basin comprise five new species: Callianopsis marianae (Ctenochelidae), Crosniera schweitzerae (Thomassiniidae), Agononida cerovensis and Munidopsis lieskovensis (both Galatheidae) plus Mursia harnicari (Calappidae). The new species of Callianopsis is the first undoubted member of the genus to be recorded from Europe; it is based on sexually dimorphic major and minor chelae as well as on portions of carapace and abdomen. Crosniera schweitzerae sp. nov. and Agononida cerovensis sp. nov. constitute the first fossil members of these genera. Additional material of an enigmatic crab, Styrioplax exiguus, and a re‐examination of the type material, confirms assignment of that genus to the subfamily Rhizopinae (family Pilumnidae). Palaeoecological data suggest that deposition of the levels (Lak?árska Nová Ves Formation) from which these taxa were collected took place under generally low‐energy, deep‐water conditions that were conducive to the preservation of delicate structures. Palaeobiogeographical affinities of the described taxa suggest a trans‐Atlantic migration during the early Miocene.     

Population structure of the Japanese eel, Anguilla japonica

Mitochondrial DNA (mtDNA) sequences that include (a) a part of the cytochrome b gene, (b) two tRNA genes, and (c) a part of the noncoding D-loop region of 31 Anguilla japonica (Japanese eel) and 1 A. marmorata collected from Taiwan, Japan, and mainland China were determined to evaluate the population structure of Japanese eel. Among 30 genotypes identified from the 31 Japanese eel mtDNAs sequenced, there are 58 variable sites, predominantly clustered at the D-loop region. The phylogenetic tree constructed by the unweighted pair-group method with arithmetic mean shows neither significant genealogical branches nor geographic clusters. Furthermore, the sequence-statistics test reveals little, if any, significant genetic differentiation. These results indicate that the 31 Japanese eels might come from a single population. Analysis of sequence variation in mtDNA by using the relationship between the number of segregating sites and the average number of nucleotide differences under the neutral mutation hypothesis reveals that neutral mutation acts as a major factor influencing the evolutionary divergence of the Japanese eel mitochondrial genome sequenced, especially in the noncoding region.      

Smear morphology of cryptococcosis presenting as a subcutaneous swelling in healthy adults: a report of three cases

OBJECTIVE: To highlight the various morphological smear pattern in cases of subcutaneous Cryptococcus infection in healthy adults. METHOD: Cryptococcus is an opportunist fungus and primary infection is acquired through respiratory tract. Dissemination by blood stream results in systemic infection. Ten to 15% of systemic infection present as cutaneous lesions. Between December 2002 and April 2004 three healthy adults presented to us consecutively with subcutaneous swelling. RESULTS: We diagnosed these cases on FNAC as Cryptococcus. In all the three patients there was no history of local penetrating injury and any signs or symptoms of systemic disease. They were two male and one female, immuno competent and were negative for HIV 1 & 2 tested by ELISA. The sites were right abdominal flank, occipital and left anterior upper thigh. Aspirated materials were oily fibro fatty tissue and necrotic purulent materials. Cryptococcus numbers varied in all the smears so also their size and capsule thickness. Background smear morphology and tissue reaction were also different. It could be gelatinous, granulomatous, and cellulitic response or mixed responses and this can be picked up on cytological smears. Cultures were confirmatory in all the three cases. These lesions were resolved with antifungal treatment. CONCLUSION: Our brief article highlights the morphological spectrum on FNAC smears and diagnostic problems faced in these uncommon circumstances where the aspirates were purulent and the yeasts were small, few and thin walled. In the acute inflammatory smear with occasional giant cells and/or granulomas special stains like PAS or Mucicarmine are necessary to look for budding yeast of Cryptococcus with thin neck.     

Nutritional and toxic elemental analysis of dry fruits using laser induced breakdown spectroscopy (LIBS) and inductively coupled plasma atomic emission spectrometry (ICP-AES)

Quantitative investigation of essential and trace heavy elements present in health-beneficial dry fruits (Pistachio, Almonds, Black walnut, White walnut, and Cashew) was investigated using Laser Induced Breakdown Spectroscopy. For an accurate elemental exposure using LIBS technique, the local thermo-dynamical equilibrium of the laser induced plasma was established and verified using McWhirter criterion based on the electron number density in the plasma. Earlier to engage, our LIBS detector was optimized. For quantification of elements, standard calibration curves (CC)-LIBS method was applied. Using our LIBS system, the nutritional elements such as Al, Mg, Ca, Fe, K, Zn, and Na and toxins like Pb, Cr, and Cu were detected in dry fruits. The elemental quantification of dry fruit contents were validated using standard (ICP-AES) method and the relative accuracy of our experimental setup in comparison to ICP approach was in the ranging from 0.1 to 0.3 at 2.5-% error confidence.     

ACPA-positive and ACPA-negative rheumatoid arthritis differ in their requirements for combination DMARDs and corticosteroids: secondary analysis of a randomized controlled trial

Introduction

UK guidelines recommend that all early active rheumatoid arthritis (RA) patients are offered combination disease-modifying antirheumatic drugs (DMARDs) and short-term corticosteroids. Anti-citrullinated protein antibody (ACPA)-positive and ACPA-negative RA may differ in their treatment responses. We used data from a randomized controlled trial - the Combination Anti-Rheumatic Drugs in Early RA (CARDERA) trial - to examine whether responses to intensive combination treatments in early RA differ by ACPA status.

Methods

The CARDERA trial randomized 467 early active RA patients to receive: (1) methotrexate, (2) methotrexate/ciclosporin, (3) methotrexate/prednisolone or (4) methotrexate/ciclosporin/prednisolone in a factorial-design. Patients were assessed every six months for two years. In this analysis we evaluated 431 patients with available ACPA status. To minimize multiple testing we used a mixed-effects repeated measures ANOVA model to test for an interaction between ACPA and treatment on mean changes from baseline for each outcome (Larsen, disease activity scores on a 28-joint count (DAS28), Health Assessment Questionnaire (HAQ), EuroQol, SF-36 physical component summary (PCS) and mental component summary (MCS) scores). When a significant interaction was present, mean changes in outcomes were compared by treatment group at each time point using t-tests stratified by ACPA status. Odds ratios (ORs) for the onset of new erosions with treatment were calculated stratified by ACPA.

Results

ACPA status influenced the need for combination treatments to reduce radiological progression. ACPA-positive patients had significant reductions in Larsen score progression with all treatments. ACPA-positive patients receiving triple therapy had the greatest benefits: two-year mean Larsen score increases comprised 3.66 (95% confidence interval (CI) 2.27 to 5.05) with triple therapy and 9.58 (95% CI 6.76 to 12.39) with monotherapy; OR for new erosions with triple therapy versus monotherapy was 0.32 (95% CI 0.14 to 0.72; P = 0.003). ACPA-negative patients had minimal radiological progression irrespective of treatment. Corticosteroid’s impact on improving DAS28/PCS scores was confined to ACPA-positive RA.

Conclusions

ACPA status influences the need for combination DMARDs and high-dose tapering corticosteroids in early RA. In CARDERA, combination therapy was only required to prevent radiological progression in ACPA-positive patients; corticosteroids only provided significant disease activity and physical health improvements in ACPA-positive disease. This suggests ACPA is an important biomarker for guiding treatment decisions in early RA.

Trial registration

Current Controlled Trials ISRCTN32484878