Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential

In this article, we focus on the analysis of competitive gene set methods for detecting the statistical significance of pathways from gene expression data. Our main result is to demonstrate that some of the most frequently used gene set methods, GSEA, GSEArot and GAGE, are severely influenced by the filtering of the data in a way that such an analysis is no longer reconcilable with the principles of statistical inference, rendering the obtained results in the worst case inexpressive. A possible consequence of this is that these methods can increase their power by the addition of unrelated data and noise. Our results are obtained within a bootstrapping framework that allows a rigorous assessment of the robustness of results and enables power estimates. Our results indicate that when using competitive gene set methods, it is imperative to apply a stringent gene filtering criterion. However, even when genes are filtered appropriately, for gene expression data from chips that do not provide a genome-scale coverage of the expression values of all mRNAs, this is not enough for GSEA, GSEArot and GAGE to ensure the statistical soundness of the applied procedure. For this reason, for biomedical and clinical studies, we strongly advice not to use GSEA, GSEArot and GAGE for such data sets.

Variable temperature electrochemical strain microscopy of Sm-doped ceria

Variable temperature electrochemical strain microscopy has been used to study the electrochemical activity of Sm-doped ceria as a function of temperature and bias. The electrochemical strain microscopy hysteresis loops have been collected across the surface at different temperatures and the relative activity at different temperatures has been compared. The relaxation behavior of the signal at different temperatures has been also evaluated to relate kinetic process during bias induced electrochemical reactions with temperature and two different kinetic regimes have been identified. The strongly non-monotonic dependence of relaxation behavior on temperature is interpreted as evidence for water-mediated mechanisms.

Gapped Two-Body Hamiltonian for Continuous-Variable Quantum Computation

We introduce a family of Hamiltonian systems for measurement-based quantum computation with continuous variables. The Hamiltonians (i) are quadratic, and therefore two body, (ii) are of short range, (iii) are frustration-free, and (iv) possess a constant energy gap proportional to the squared inverse of the squeezing. Their ground states are the celebrated Gaussian graph states, which are universal resources for quantum computation in the limit of infinite squeezing. These Hamiltonians constitute the basic ingredient for the adiabatic preparation of graph states and thus open new venues for the physical realization of continuous-variable quantum computing beyond the standard optical approaches. We characterize the correlations in these systems at thermal equilibrium. In particular, we prove that the correlations across any multipartition are contained exactly in its boundary, automatically yielding a correlation area law. © 2011 American Physical Society.

Sliding window two-thermocouple sensor characterization for variable flow environments

A two-thermocouple sensor characterization method for use in variable flow applications is proposed. Previous offline methods for constant velocity flow are extended using sliding data windows and polynomials to accommodate variable velocity. Analysis of Monte-Carlo simulation studies confirms that the unbiased and consistent parameter estimator outperforms alternatives in the literature and has the added advantage of not requiring a priori knowledge of the time constant ratio of thermocouples. Experimental results from a test rig are also presented. © 2008 The Institute of Measurement and Control.

The C-Terminal Variable Region Specifies the Dynamic Properties of Arabidopsis Microtubule-Associated Protein MAP65 Isotypes

The microtubule-associated protein, MAP65, is a member of a family of divergent microtubule-associated proteins from different organisms generally involved in maintaining the integrity of the central spindle in mitosis. The dicotyledon Arabidopsis thaliana and the monocotyledon rice (Oryza sativa) genomes contain 9 and 11 MAP65 genes, respectively. In this work, we show that the majority of these proteins fall into five phylogenetic clades, with the greatest variation between clades being in the C-terminal random coil domain. At least one Arabidopsis and one rice isotype is within each clade, indicating a functional specification for the C terminus. In At MAP65-1, the C-terminal domain is a microtubule binding region (MTB2) harboring the phosphorylation sites that control its activity. The At MAP65 isotypes show differential localization to microtubule arrays and promote microtubule polymerization with variable efficiency in a MTB2-dependent manner. In vivo studies demonstrate that the dynamics of the association and dissociation of different MAP65 isotypes with microtubules can vary up to 10-fold and that this correlates with their ability to promote microtubule polymerization. Our data demonstrate that the C-terminal variable region, MTB2, determines the dynamic properties of individual isotypes and suggest that slower turnover is conditional for more efficient microtubule polymerization.

VEIDase is a principal caspase-like activity involved in plant programmed cell death and essential for embryonic pattern formation

Plant embryogenesis is intimately associated with programmed cell death. The mechanisms of initiation and control of programmed cell death during plant embryo development are not known. Proteolytic activity associated with caspase-like proteins is paramount for control of programmed cell death in animals and yeasts. Caspase family of proteases has unique strong preference for cleavage of the target proteins next to asparagine residue. In this work, we have used synthetic peptide substrates containing caspase recognition sites and corresponding specific inhibitors to analyse the role of caspase-like activity in the regulation of programmed cell death during plant embryogenesis. We demonstrate that VEIDase is a principal caspase-like activity implicated in plant embryogenesis. This activity increases at the early stages of embryo development that coincide with massive cell death during shape remodeling. The VEIDase activity exhibits high sensitivity to pH, ionic strength and Zn2+ concentration. Altogether, biochemical assays show that VEIDase plant caspase-like activity resembles that of both mammalian caspase-6 and yeast metacaspase, YCA1. In vivo, VEIDase activity is localised specifically in the embryonic cells during both the commitment and in the beginning of the execution phase of programmed cell death. Inhibition of VEIDase prevents normal embryo development via blocking the embryo-suspensor differentiation. Our data indicate that the VEIDase activity is an integral part in the control of plant developmental cell death programme, and that this activity is essential for the embryo pattern formation.

Ser6 in the maize actin-depolymerizing factor, ZmADF3, is phosphorylated by a calcium-stimulated protein kinase and is essential for the control of functional activity

Maize actin-depolymerizing factor, ZmADF, binds both G- and F-actin and enhances in vitro actin dynamics. Evidence from studies on vertebrate ADF/cofilin supports the view that this class of protein responds to intracellular and extracellular signals and causes actin reorganization. As a test to determine whether such signal-responsive pathways existed in plants, this study addressed the ability of maize ADF to be phosphorylated and the likely effects of such phosphorylation on its capacity to modulate actin dynamics. It is shown that maize ADF3 (ZmADF3) can be phosphorylated by a calcium-stimulated protein kinase present in a 40-70% ammonium sulphate fraction of a plant cell extract. Phosphorylation is shown to be on Ser6, which is only one of nine amino acids that are fully conserved among the ADF/cofilin proteins across distantly related species. In addition, an analogue of phosphorylated ZmADF3 created by mutating Ser6 to Asp6 (zmadf3-4) does not bind G- or F-actin and has little effect on the enhancement of actin dynamics. These results are discussed in context of the previously observed actin reorganization in root hair cells.

An allelic series reveals essential roles for FY in plant development in addition to flowering-time control.

The autonomous pathway functions to promote flowering in Arabidopsis by limiting the accumulation of the floral repressor FLOWERING LOCUS C (FLC). Within this pathway FCA is a plant-specific, nuclear RNA-binding protein, which interacts with FY, a highly conserved eukaryotic polyadenylation factor. FCA and FY function to control polyadenylation site choice during processing of the FCA transcript. Null mutations in the yeast FY homologue Pfs2p are lethal. This raises the question as to whether these essential RNA processing functions are conserved in plants. Characterisation of an allelic series of fy mutations reveals that null alleles are embryo lethal. Furthermore, silencing of FY, but not FCA, is deleterious to growth in Nicotiana. The late-flowering fy alleles are hypomorphic and indicate a requirement for both intact FY WD repeats and the C-terminal domain in repression of FLC. The FY C-terminal domain binds FCA and in vitro assays demonstrate a requirement for both C-terminal FY-PPLPP repeats during this interaction. The expression domain of FY supports its roles in essential and flowering-time functions. Hence, FY may mediate both regulated and constitutive RNA 3'-end processing.

COS1: an Arabidopsis coronatine insensitive1 suppressor essential for regulation of jasmonate-mediated plant defense and senescence.

The Arabidopsis thaliana CORONATINE INSENSITIVE1 (COI1) gene encodes an F-box protein to assemble SCF(COI1) complexes essential for response to jasmonates (JAs), which are a family of plant signaling molecules required for many essential functions, including plant defense and reproduction. To better understand the molecular basis of JA action, we screened for suppressors of coi1 and isolated a coi1 suppressor1 (cos1) mutant. The cos1 mutation restores the coi1-related phenotypes, including defects in JA sensitivity, senescence, and plant defense responses. The COS1 gene was cloned through a map-based approach and found to encode lumazine synthase, a key component in the riboflavin pathway that is essential for diverse yet critical cellular processes. We demonstrated a novel function for the riboflavin pathway that acts downstream of COI1 in the JA signaling pathway and is required for suppression of the COI1-mediated root growth, senescence, and plant defense.

The ASK1 and ASK2 genes are essential for Arabidopsis early development.

The requirement of CUL1 for Arabidopsis embryogenesis suggests that Skp1-CUL1-F-box protein (SCF) complexes play important roles during embryo development. Among the 21 Arabidopsis Skp1-like genes (ASKs), it is unknown which ASK gene(s) is essential for embryo development. In this study, we demonstrate a vital role for ASK1 and ASK2 in Arabidopsis embryogenesis and postembryonic development through analysis of the ask1 ask2 double mutant. Our detailed analysis indicates that the double mutations in both ASK1 and ASK2 affect cell division and cell expansion/elongation and cause a developmental delay during embryogenesis and lethality in seedling growth. The expression patterns of ASK1 and ASK2 were examined further and found to be consistent with their roles in embryogenesis and seedling development. We propose that mutations in ASK1 and ASK2 abolish all of the ASK1- and ASK2-based SCF and non-SCF complexes, resulting in alteration of gene expression and leading to defects in growth and development.

Voltage and power quality improvement strategy for a DFIG wind turbine during variable wind conditions

This paper presents a voltage and power quality enhancement scheme for a doubly-fed induction generator (DFIG) wind farm during variable wind conditions. The wind profiles were derived considering the measured data at a DFIG wind farm located in Northern Ireland (NI). The aggregated DFIG wind farm model was validated using measured data at a wind farm during variable generation. The voltage control strategy was developed considering the X/R ratio of the wind farm feeder which connects the wind farm and the grid. The performance of the proposed strategy was evaluated for different X/R ratios, and wind profiles with different characteristics. The impact of flicker propagation along the wind farm feeder and effectiveness of the proposed strategy is also evaluated with consumer loads connected to the wind farm feeder. It is shown that voltage variability and short-term flicker severity is significantly reduced following implementation of the novel strategy described.

Modelling and Control of a Variable-Speed Switched Reluctance Generator based Wind Turbine

This paper studies the system modelling and control aspects of switched reluctance generator (SRG) based variable speed wind turbines. A control system is implemented to provide proper operation of the SRG as well as power tracking capabilities for varying wind speeds. The control system for the grid side inverter that will allow the SRG to properly generate power to the system is also presented. Studies are presented of both the SRG and inverter control systems capabilities during a balanced three-phase fault. The paper will demonstrate that the SRG based wind turbine presents a feasible variable wind speed solution with good fault response capabilities.

A phase II study of vorinostat (MK-0683) in patients with polycythaemia vera and essential thrombocythaemia

Inhibition of histone deacetylases may be an important target in patients with myeloproliferative neoplasms. This investigator-initiated, non-randomized, open-label phase II multi-centre study included 63 patients (19 essential thrombocythaemia, 44 polycythaemia vera) from 15 centres. The primary objective was to evaluate if vorinostat was followed by a decline in clonal myeloproliferation as defined by European Leukaemia Net. Thirty patients (48%) completed the intervention period (24 weeks of therapy). An intention-to-treat response rate of 35% was identified. Pruritus was resolved [19% to 0% (P = 0·06)] and the prevalence of splenomegaly was lowered from 50% to 27% (P = 0·03). Sixty-five per cent of the patients experienced a decrease in JAK2 V617F allele burden (P = 0·006). Thirty-three patients (52% of patients) discontinued study drug before end of intervention due to adverse events (28 patients) or lack of response (5 patients). In conclusion, vorinostat showed effectiveness by normalizing elevated leucocyte and platelet counts, resolving pruritus and significantly reducing splenomegaly. However, vorinostat was associated with significant side effects resulting in a high discontinuation rate. A lower dose of vorinostat in combination with conventional and/or novel targeted therapies may be warranted in future studies.

Revised response criteria for polycythemia vera and essential thrombocythemia:an ELN and IWG-MRT consensus project

Standardized response criteria to interpret and compare clinical trials are needed for approval of new therapeutic agents by regulatory agencies. The European LeukemiaNet (ELN) response criteria for essential thrombocythemia (ET) and polycythemia vera (PV) issued in 2009 have been widely adopted as end points in a number of recent clinical trials. However, evidence exists that they do not predict response or provide clinically relevant measures of benefit for the patients. This article presents revised recommendations for assessing response in ET and PV provided by a working group established by ELN and International Working Group-Myeloproliferative Neoplasms Research and Treatment. New definitions of complete and partial remission incorporate clinical, hematological, and histological response assessments that include a standardized symptom assessment form and consider absence of disease progression and vascular events. We anticipate that these criteria will be adopted widely to facilitate the development of new and more effective therapies for ET and PV.