Can Zipf's law be adapted to normalize microarrays?

BACKGROUND: Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented. RESULTS: Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques. CONCLUSION: Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays)

A semantic Grid for molecular science

Proceedings of the 2003 UK e-Science All Hands Meeting, 31st August - 3rd September, Nottingham UKThe properties of molecules have very well defined semantics and allow the creation of a semantic GRID. Markup languages (CML - Chemical Markup Language) and dictionary-based ontologies have been designed to support a wide range of applications, including chemical supply, publication and the safety of compounds. Many properties can be computed by Quantum Mechanical (QM) programs and we have developed a "black-box" system based on XML wrappers for all components. This is installed on a Condor system on which we have computed properties for 250, 000 compounds. The results of this will be available in an OpenData/OpenSource peer-to-peer (P2P) system (WorldWide Molecular Matrix - WWMM)

Generalized geometry, calibrations and supersymmetry in diverse dimensions

We consider type II backgrounds of the form R^{1,d-1} x M^{10-d} for even d, preserving 2^{d/2} real supercharges; for d = 4, 6, 8 this is minimal supersymmetry in d dimensions, while for d = 2 it is N = (2,0) supersymmetry in two dimensions. For d = 6 we prove, by explicitly solving the Killing-spinor equations, that there is a one-to-one correspondence between background supersymmetry equations in pure-spinor form and D-brane generalized calibrations; this correspondence had been known to hold in the d = 4 case. Assuming the correspondence to hold for all d, we list the calibration forms for all admissible D-branes, as well as the background supersymmetry equations in pure-spinor form. We find a number of general features, including the following: The pattern of codimensions at which each calibration form appears exhibits a (mod 4) periodicity. In all cases one of the pure-spinor equations implies that the internal manifold is generalized Calabi-Yau. Our results are manifestly invariant under generalized mirror symmetry.Comment: 28 pages, 1 tabl

Plant communities affect arbuscular mycorrhizal fungal diversity and community composition in grassland microcosms

The diversity of arbuscular mycorrhizal (AM) fungi was investigated in an unfertilized limestone grassland soil supporting different synthesized vascular plant assemblages that had developed for 3 yr. The experimental treatments comprised: bare soil; monocultures of the nonmycotrophic sedge Carex flacca; monocultures of the mycotrophic grass Festuca ovina; and a species-rich mixture of four forbs, four grasses and four sedges. The diversity of AM fungi was analysed in roots of Plantago lanceolata bioassay seedlings using terminal-restriction fragment length polymorphism (T-RFLP). The extent of AM colonization, shoot biomass and nitrogen and phosphorus concentrations were also measured. The AM diversity was affected significantly by the floristic composition of the microcosms and shoot phosphorus concentration was positively correlated with AM diversity. The diversity of AM fungi in P. lanceolata decreased in the order: bare soil > C. flacca > 12 species > F. ovina. The unexpectedly high diversity in the bare soil and sedge monoculture likely reflects differences in the modes of colonization and sources of inoculum in these treatments compared with the assemblages containing established AM-compatible plants

How fast is your detector? The effect of temporal response on image quality

With increasing interest in high-speed imaging, there should be an increased interest in the response times of our scanning transmission electron microscope detectors. Previous works have highlighted and contrasted the performance of various detectors for quantitative compositional or structural studies, but here, we shift the focus to detector temporal response, and the effect this has on captured images. The rise and decay times of eight detectors' single-electron response are reported, as well as measurements of their flatness, roundness, smoothness, and ellipticity. We develop and apply a methodology for incorporating the temporal detector response into simulations, showing that a loss of resolution is apparent in both the images and their Fourier transforms. We conclude that the solid-state detector outperforms the photomultiplier tube-based detectors in all areas bar a slightly less elliptical central hole and is likely the best detector to use for the majority of applications. However, using the tools introduced here, we encourage users to effectively evaluate which detector is most suitable for their experimental needs

An exploration of familial associations of two movement pattern-derived subgroups of chronic disabling low back pain; a cross-sectional cohort study

© 2016 Elsevier Ltd. Background: Altered movement patterns with pain have been demonstrated in children, adolescents and adults with chronic disabling low back pain (CDLBP). A previously developed classification system has identified different subgroups including active extension and multidirectional patterns in patients with CDLBP. While familial associations have been identified for certain spinal postures in standing, it is unknown whether a familial relationship might exist between movement pattern-derived subgroups in families with CDLBP. Objectives: This study explored whether familial associations in movement pattern-derived subgroups within and between members of families with CDLBP existed. Design: Cross-sectional cohort study. Method: 33 parents and 28 children with CDLBP were classified into two subgroups based on clinical analysis of video footage of postures and functional movements, combined with aggravating factors obtained from Oswestry Disability Questionnaire. Prevalence of subgroups within family members was determined, associations between parent and child's subgroup membership was evaluated using Fisher's exact test, and spearman's correlation coefficient was used to determine the strength of association between familial dyads. Results: The majority of parents were classified as active extenders, sons predominately multidirectional and daughters were evenly distributed between the two subgroups. No significant association was found when comparing subgroups in nine parent-child relationships. Conclusions: The exploration of a small cohort of family dyads in this study demonstrated that children's movement pattern-derived subgroups could not be explained by their parents' subgroup membership. These results cannot be generalised to the CLBP population due to this study's small sample. Larger sample studies are needed to further elucidate this issue

Quality of life before intensive care unit admission is a predictor of survival

Introduction: Predicting whether a critically ill patient will survive intensive care treatment remains difficult. The advantages of a validated strategy to identify those patients who will not benefit from intensive care unit (ICU) treatment are evident. Providing critical care treatment to patients who will ultimately die in the ICU is accompanied by an enormous emotional and physical burden for both patients and their relatives. The purpose of the present study was to examine whether health-related quality of life (HRQOL) before admission to the ICU can be used as a predictor of mortality. Methods: We conducted a prospective cohort study in a university-affiliated teaching hospital. Patients admitted to the ICU for longer than 48 hours were included. Close relatives completed the Short-form 36 (SF-36) within the first 48 hours o