Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping.

Connectivity mapping is a recently developed technique for discovering the underlying connections between different biological states based on gene-expression similarities. The sscMap method has been shown to provide enhanced sensitivity in mapping meaningful connections leading to testable biological hypotheses and in identifying drug candidates with particular pharmacological and/or toxicological properties. Challenges remain, however, as to how to prioritise the large number of discovered connections in an unbiased manner such that the success rate of any following-up investigation can be maximised. We introduce a new concept, gene-signature perturbation, which aims to test whether an identified connection is stable enough against systematic minor changes (perturbation) to the gene-signature. We applied the perturbation method to three independent datasets obtained from the GEO database: acute myeloid leukemia (AML), cervical cancer, and breast cancer treated with letrozole. We demonstrate that the perturbation approach helps to identify meaningful biological connections which suggest the most relevant candidate drugs. In the case of AML, we found that the prevalent compounds were retinoic acids and PPAR activators. For cervical cancer, our results suggested that potential drugs are likely to involve the EGFR pathway; and with the breast cancer dataset, we identified candidates that are involved in prostaglandin inhibition. Thus the gene-signature perturbation approach added real values to the whole connectivity mapping process, allowing for increased specificity in the identification of possible therapeutic candidates.

A hypercyclic finite rank perturbation of a unitary operator

A unitary operator V and a rank 2 operator R acting on a Hilbert space H are constructed such that V + R is hypercyclic. This answers affirmatively a question of Salas whether a finite rank perturbation of a hyponormal operator can be supercyclic.

Stellar jitter from variable gravitational redshift: implications for radial velocity confirmation of habitable exoplanets

A variation of gravitational redshift, arising from stellar radius fluctuations, will introduce astrophysical noise into radial velocity measurements by shifting the centroid of the observed spectral lines. Shifting the centroid does not necessarily introduce line asymmetries. This is fundamentally different from other types of stellar jitter so far identified, which do result from line asymmetries. Furthermore, only a very small change in stellar radius, ˜0.01 per cent, is necessary to generate a gravitational redshift variation large enough to mask or mimic an Earth-twin. We explore possible mechanisms for stellar radius fluctuations in low-mass stars. Convective inhibition due to varying magnetic field strengths and the Wilson depression of starspots are both found to induce substantial gravitational redshift variations. Finally, we investigate a possible method for monitoring/correcting this newly identified potential source of jitter and comment on its impact for future exoplanet searches.

Proton radiography as an electromagnetic field and density perturbation diagnostic (invited)

Laser driven proton beams have been used to diagnose transient fields and density perturbations in laser produced plasmas. Grid deflectometry techniques have been applied to proton radiography to obtain precise measurements of proton beam angles caused by electromagnetic fields in laser produced plasmas. Application of proton radiography to laser driven implosions has demonstrated that density conditions in compressed media can be diagnosed with million electron volt protons. This data has shown that proton radiography can provide unique insight into transient electromagnetic fields in super critical density plasmas and provide a density perturbation diagnostics in compressed matter.

Electronic properties of interfaces and defects from many-body perturbation theory: Recent developments and applications

We review some recent developments in many body perturbation theory (MBPT) calculations that have enabled the study of interfaces and defects. Starting from the theoretical basis of MBPT, Hedin's equations are presented, leading to the CW and CWI' approximations. We introduce the perturbative approach, that is the one most commonly used for obtaining quasiparticle (QP) energies. The practical strategy presented for dealing with the frequency dependence of the self energy operator is based on either plasmon-pole models (PPM) or the contour deformation technique, with the latter being more accurate. We also discuss the extrapolar method for reducing the number of unoccupied states which need to be included explicity in the calculations. The use of the PAW method in the framework of MBPT is also described. Finally, results which have been obtained using, MBPT for band offsets a interfaces and for defects presented, with companies on the main difficulties and cancels.

Schematic representation of the QP corrections (marked with ) to the band edges (E and E-v) and a defect level (F) for a Si/SiO2 interface (Si and O atoms are represented in blue and red, respectively, in the ball and stick model) with an oxygen vacancy leading to a Si-Si bond (the Si atoms involved in this bond are colored light blue).

Electronic properties of zircon and hafnon from many-body perturbation theory

The electronic properties of zircon and hafnon, two wide-gap high-kappa materials, are investigated using many-body perturbation theory (MBPT) combined with the Wannier interpolation technique. For both materials, the calculated band structures differ from those obtained within density-functional theory and MBPT by (i) a slight displacement of the highest valence-band maximum from the Gamma point and (ii) an opening of the indirect band gap to 7.6 and 8.0 eV for zircon and hafnon, respectively. The introduction of vertex corrections in the many-body self-energy does not modify the results except for a global rigid shift of the many-body corrections.

Density functionals from many-body perturbation theory: The band gap for semiconductors and insulators

Theoretically the Kohn-Sham band gap differs from the exact quasiparticle energy gap by the derivative discontinuity of the exchange-correlation functional. In practice for semiconductors and insulators the band gap calculated within any local or semilocal density approximations underestimates severely the experimental energy gap. On the other hand, calculations with an "exact" exchange potential derived from many-body perturbation theory via the optimized effective potential suggest that improving the exchange-correlation potential approximation can yield a reasonable agreement between the Kohn-Sham band gap and the experimental gap. The results in this work show that this is not the case. In fact, we add to the exact exchange the correlation that corresponds to the dynamical (random phase approximation) screening in the GW approximation. This accurate exchange-correlation potential provides band structures similar to the local density approximation with the corresponding derivative discontinuity that contributes 30%-50% to the energy gap. Our self-consistent results confirm substantially the results for Si and other semiconductors obtained perturbatively [R. W. Godby , Phys. Rev. B 36, 6497 (1987)] and extend the conclusion to LiF and Ar, a wide-gap insulator and a noble-gas solid. (c) 2006 American Institute of Physics.

Coupled Effects of a Perturbation in a Complex Structure Observed with SDO/AIA, SDO/HMI and ROSA/HARDcam

We study properties of intensity fluctuations in NOAA Active Region 11250 observed on 13 July 2011 starting at UT 13:32. Included are data obtained in the EUV bands of the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory (SDO/AIA) as well as nearly simultaneous observations of the chromosphere made, at much higher spatial and temporal resolution, with the Rapid Oscillations in the Solar Atmosphere (ROSA) and Hydrogen-Alpha Rapid Dynamics camera (HARDcam) systems at the Dunn Solar Telescope. A complex structure seen in both the ROSA/HARDcam and SDO data sets comprises a system of loops extending outward from near the boundary of the leading sunspot umbra. It is visible in the ROSA Ca II K and HARDcam Hα images, as well as the SDO 304 Å, 171 Å and 193 Å channels, and it thus couples the chromosphere, transition region and corona. In the ground-based images the loop structure is 4.1 Mm long. Some 17.5 Mm, can be traced in the SDO/AIA data. The chromospheric emissions observed by ROSA and HARDcam appear to occupy the inner, and apparently cooler and lower, quarter of the loop. We compare the intensity fluctuations of two points within the structure. From alignment with SDO/HMI images we identify a point "A" near the loop structure, which sits directly above a bipolar magnetic feature in the photosphere. Point "B" is characteristic of locations within the loops that are visible in both the ROSA/HARDcam and the SDO/AIA data. The intensity traces for point A are quiet during the first part of the data string. At time ~ 19 min they suddenly begin a series of impulsive brightenings. In the 171 Å and 193 Å coronal lines the brightenings are localized impulses in time, but in the transition region line at 304 Å they are more extended in time. The intensity traces in the 304 Å line for point B shows a quasi-periodic signal that changes properties at about 19 min. The wavelet power spectra are characterized by two periodicities. A 6.7 min period extends from the beginning of the series until about 25 minutes, and another signal with period ~3 min starts at about 20 min. The 193 Å power spectrum has a characteristic period of 5 min, before the 20 min transition and a 2.5 min periodicity afterward. In the case of HARDcam Hα data a localized 4 min periodicity can be found until about 7 min, followed by a quiet regime. After ~20 min a 2.3 min periodicity appears. Interestingly a coronal loop visible in the 94 Å line that is centrally located in the AR, running from the leading umbra to the following polarity, at about time 20 min undergoes a strong brightening beginning at the same moment all along 15 Mm of its length. The fact that these different signals all experience a clear-cut change at time about 20 min suggests an underlying organizing mechanism. Given that point A has a direct connection to the photospheric magnetic bipole, we conjecture that the whole extended structure is connected in a complex manner to the underlying magnetic field. The periodicities in these features may favor the wave nature rather than upflows and interpretations will be discussed.

Stiffness Analysis and Experiment of a Novel 5-DoF Parallel Kinematic Machine Considering Gravitational Effects

In order to carry out high-precision machining of aerospace structural components with large size, thin wall and complex surface, this paper proposes a novel parallel kinematic machine (PKM) and formulates its semi-analytical theoretical stiffness model considering gravitational effects that is verified by stiffness experiments. From the viewpoint of topology structure, the novel PKM consists of two substructures in terms of the redundant and overconstrained parallel mechanisms that are connected by two interlinked revolute joints. The theoretical stiffness model of the novel PKM is established based upon the virtual work principle and deformation superposition principle after mapping the stiffness models of substructures from joint space to operated space by Jacobian matrices and considering the deformation contributions of interlinked revolute joints to two substructures. Meanwhile, the component gravities are treated as external payloads exerting on the end reference point of the novel PKM resorting to static equivalence principle. This approach is proved by comparing the theoretical stiffness values with experimental stiffness values in the same configurations, which also indicates equivalent gravity can be employed to describe the actual distributed gravities in an acceptable accuracy manner. Finally, on the basis of the verified theoretical stiffness model, the stiffness distributions of the novel PKM are illustrated and the contributions of component gravities to the stiffness of the novel PKM are discussed.

Proposed role for COUP-TFII in regulating fetal Leydig cell steroidogenesis, perturbation of which leads to masculinization disorders in rodents

Reproductive disorders that are common/increasing in prevalence in human males may arise because of deficient androgen production/action during a fetal 'masculinization programming window'. We identify a potentially important role for Chicken Ovalbumin Upstream Promoter-Transcription Factor II (COUP-TFII) in Leydig cell (LC) steroidogenesis that may partly explain this. In rats, fetal LC size and intratesticular testosterone (ITT) increased ~3-fold between e15.5-e21.5 which associated with a progressive decrease in the percentage of LC expressing COUP-TFII. Exposure of fetuses to dibutyl phthalate (DBP), which induces masculinization disorders, dose-dependently prevented the age-related decrease in LC COUP-TFII expression and the normal increases in LC size and ITT. We show that nuclear COUP-TFII expression in fetal rat LC relates inversely to LC expression of steroidogenic factor-1 (SF-1)-dependent genes (StAR, Cyp11a1, Cyp17a1) with overlapping binding sites for SF-1 and COUP-TFII in their promoter regions, but does not affect an SF-1 dependent LC gene (3β-HSD) without overlapping sites. We also show that once COUP-TFII expression in LC has switched off, it is re-induced by DBP exposure, coincident with suppression of ITT. Furthermore, other treatments that reduce fetal ITT in rats (dexamethasone, diethylstilbestrol (DES)) also maintain/induce LC nuclear expression of COUP-TFII. In contrast to rats, in mice DBP neither causes persistence of fetal LC COUP-TFII nor reduces ITT, whereas DES-exposure of mice maintains COUP-TFII expression in fetal LC and decreases ITT, as in rats. These findings suggest that lifting of repression by COUP-TFII may be an important mechanism that promotes increased testosterone production by fetal LC to drive masculinization. As we also show an age-related decline in expression of COUP-TFII in human fetal LC, this mechanism may also be functional in humans, and its susceptibility to disruption by environmental chemicals, stress and pregnancy hormones could explain the origin of some human male reproductive disorders.