G-spots cause incorrect expression measurement in Affymetrix microarrays

Abstract Background High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's presence. However, probes that contain a G-spot (a sequence of four or more guanines) behave abnormally and it has been suggested that these probes are responding to some biochemical effect such as the formation of G-quadruplexes. Results We have tested this expectation by examining the correlation coefficients between pairs of probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. We confirm the finding that G-spot probes are poorly correlated with others in their probesets and reveal that, by contrast, they are highly correlated with one another. We demonstrate that the correlation is most marked when the G-spot is at the 5' end of the probe. Conclusion Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes. </jats:sec

Results of recent NASA research on low-speed aerodynamic characteristics of supersonic cruise aircraft

The relatively low values of lift-curve slope produced by highly swept arrow wings, coupled with the low scrape angle of the fuselage, resulted in relatively low values of take-off and approach lift coefficients. Through the use of more efficient high-lift systems and the application of propulsive-lift concepts, it is possible to optimize the engine-airframe design for maximum range potential and also to provide good low-speed performance. Nose strakes provide significant improvements in directional stability characteristics and the use of a propulsive lateral control system provides a solution to problems associated with inherently low levels of lateral control

Affymetrix probes containing runs of contiguous guanines are not gene-specific

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene&#x27;s presence. However, we demonstrate by data mining thousands of CEL files from NCBI&#x27;s GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

Freezing line of the Lennard-Jones fluid: a Phase Switch Monte Carlo study

We report a Phase Switch Monte Carlo (PSMC) method study of the freezing line of the Lennard-Jones (LJ) fluid. Our work generalizes to soft potentials the original application of the method to hard sphere freezing, and builds on a previous PSMC study of the LJ system by Errington (J. Chem. Phys. {\bf 120}, 3130 (2004)). The latter work is extended by tracing a large section of the Lennard-Jones freezing curve, the results for which we compare to a previous Gibbs-Duhem integration study. Additionally we provide new background regarding the statistical mechanical basis of the PSMC method and extensive implementation details.Comment: 18 pages, 6 figure

Summary of information on low-speed lateral-directional derivatives due to rate of change of sideslip beta prime

The results presented show that the magnitudes of the aerodynamic stability derivatives due to rate of change of sideslip become quite large at high angles of attack for swept- and delta-wing configurations, and that such derivatives have large effects on the calculated dynamic stability of these configurations at high angles of attack. The wind-tunnel test techniques used to measure the beta prime derivatives and various approaches used to predict them are discussed. Both the conventional oscillating-airfoil theory and the lag-of-the-sidewash theory are shown to be inadequate for predicting the vertical-tail contribution to the acceleration-in-sideslip derivative; a flow-field-lag theory, which is discussed, appears to give qualitative agreement with experimental data for a current twin-jet fighter configuration

Barbell back squat:How do resistance bands affect muscle activation and knee kinematics?

ObjectivesThis study aimed to determine whether looped resistance bands affect knee kinematics and lower body muscle activation during the barbell back squat.MethodsTwenty-six healthy participants (13 female, 13 male) calculated their one repetition maximum (RM) prior to data collection. Each participant performed three squats at both 80% and 40% 1RM wearing a light resistance band, an extra-heavy resistance band and no resistance band.Vicon 3D motion analysis cameras were used to collect the kinematic data, and Delsys Trigno Lab wireless electromyography (EMG) system was used to measure vastus medialis, vastus lateralis, gluteus maximus, gluteus medius and biceps femoris muscle activity. Peak knee flexion angle, peak knee valgus angle and maximum tibial rotation values were examined. Peak EMG values were also analysed after being normalised and expressed as a percentage of maximum voluntary contraction (MVC).ResultsGluteus maximus (GM) activity is significantly increased when a resistance band is used during squatting. However, squatting with a resistance band is detrimental to knee kinematics as it leads to an increase in knee valgus angle and maximum tibial rotation angle. A direct correlation is recorded between an increase in resistance and an increase in these two angles.ConclusionsSquatting with resistance bands is likely to increase the risk of knee injury. Coaches and clinicians who already implement this technique are advised to remove resistance band squats from training and rehabilitation programmes. Further research evaluating the long-term effects of using resistance bands during the barbell back squat should be considered

Slug flow

Introduction: When two phases flow concurrently in a pipe, they can distribute themselves in a number of different configurations. The gas could be uniformly dispersed throughout the liquid in the form of small bubbles. There could be large gas bubbles almost filling the tube. There could be an annulus of liquid and core of vapor with or without drops of liquid in it. The interface could be smooth or wavy. When one describes how the phases are distributed, one is specifying the flow regime. Such a description is necessary before any mathematical model can be constructed which will predict a quantity such as pressure drop It is naive to expect that a single mathematical model would adequately encompass all possible two-phase flow regimes, even for a single geometric configuration. Therefore, we shall begin by saying that for this work the results that have been obtained and the conclusions that have been drawn apply only to fully developed slug flow in a round vertical pipe. Slug flow is characterized by large bubblesalmost filling the tubewhich are separated by slugs of liquid. The nose of the bubble is rounded and the tail generally flat. One may or may not find small bubbles in the slug following the large bubble. A number of typical slug flow bubbles are pictured in Figures 4-10. Bubbles very similar to these have been studied by Dumistrescu (1), and Davis and Taylor (2). Both these references consider the same problem. How rapidly will a closed tube full of liquid empty when the bottom is suddenly opened to the atmosphere. The approach used by both authors is to assume that the asymptotic rise velocity (for large times) can be calculated from potential flow theory. The boundary condition at the pipe wall is that the velocity is axial. At the bubble boundary it is assumed that the pressure is constant, The problem is then to find the shape of the bobble that would satisfy the constant pressure boundary condition.(cont.) This was done approximately and in both cases the comparison with experiment was satisfactory though the deviations became large for small tubes. The work of Davis and Taylor, and Dumitrescu served as the starting point for this investigation. The boundary condition at the bubble wall for large bubbles, constant pressure, was still valid to an excellent approximation and the finiteness of the slug flow bubbles did not appear to make much difference in their rise velocity. In the next section, the fluctuation period, the mean density, and the pressure drop will be expressed in terms of the pipe area, the Taylor bubble rise velocity and the flow rates of the two phases. In subsequent sections the observations rade of bubble shape, length and velocity will be described and then a comparison of computed and measured pressure drops given.Office of Naval Research DSR Projec

Supersymmetric minisuperspace with non-vanishing fermion number

The Lagrangean of $N=1$ supergravity is dimensionally reduced to one (time-like) dimension assuming spatial homogeneity of any Bianchi type within class A of the classification of Ellis and McCallum. The algebra of the supersymmetry generators, the Lorentz generators, the diffeomorphism generators and the Hamiltonian generator is determined and found to close. In contrast to earlier work, infinitely many physical states with non-vanishing even fermion number are found to exist in these models, indicating that minisuperspace models in supergravity may be just as useful as in pure gravity.Comment: 4 page