Study of meta-analysis strategies for network inference using information-theoretic approaches

© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Reverse engineering of gene regulatory networks (GRNs) from gene expression data is a classical challenge in systems biology. Thanks to high-throughput technologies, a massive amount of gene-expression data has been accumulated in the public repositories. Modelling GRNs from multiple experiments (also called integrative analysis) has; therefore, naturally become a standard procedure in modern computational biology. Indeed, such analysis is usually more robust than the traditional approaches focused on individual datasets, which typically suffer from some experimental bias and a small number of samples. To date, there are mainly two strategies for the problem of interest: the first one (”data merging”) merges all datasets together and then infers a GRN whereas the other (”networks ensemble”) infers GRNs from every dataset separately and then aggregates them using some ensemble rules (such as ranksum or weightsum). Unfortunately, a thorough comparison of these two approaches is lacking. In this paper, we evaluate the performances of various metaanalysis approaches mentioned above with a systematic set of experiments based on in silico benchmarks. Furthermore, we present a new meta-analysis approach for inferring GRNs from multiple studies. Our proposed approach, adapted to methods based on pairwise measures such as correlation or mutual information, consists of two steps: aggregating matrices of the pairwise measures from every dataset followed by extracting the network from the meta-matrix.Peer ReviewedPostprint (author's final draft

Evershed clouds as precursors of moving magnetic features around sunspots

The relation between the Evershed flow and moving magnetic features (MMFs) is studied using high-cadence, simultaneous spectropolarimetric measurements of a sunspot in visible (630.2 nm) and near-infrared (1565 nm) lines. Doppler velocities, magnetograms, and total linear polarization maps are calculated from the observed Stokes profiles. We follow the temporal evolution of two Evershed clouds that move radially outward along the same penumbral filament. Eventually, the clouds cross the visible border of the spot and enter the moat region, where they become MMFs. The flux patch farther from the sunspot has the same polarity of the spot, while the MMF closer to it has opposite polarity and exhibits abnormal circular polarization profiles. Our results provide strong evidence that at least some MMFs are the continuation of the penumbral Evershed flow into the moat. This, in turn, suggests that MMFs are magnetically connected to sunspots.Comment: To appear in ApJ Letters, Vol 649, 2006 September 20 issu

Granular Scale Magnetic Flux Cancellations in the Photosphere

We investigate the evolution of 5 granular-scale magnetic flux cancellations just outside the moat region of a sunspot by using accurate spectropolarimetric measurements and G-band images with the Solar Optical Telescope aboard Hinode. The opposite polarity magnetic elements approach a junction of the intergranular lanes and then they collide with each other there. The intergranular junction has strong red shifts, darker intensities than the regular intergranular lanes, and surface converging flows. This clearly confirms that the converging and downward convective motions are essential for the approaching process of the opposite-polarity magnetic elements. However, motion of the approaching magnetic elements does not always match with their surrounding surface flow patterns in our observations. This suggests that, in addition to the surface flows, subsurface downward convective motions and subsurface magnetic connectivities are important for understanding the approach and collision of the opposite polarity elements observed in the photosphere. We find that the horizontal magnetic field appears between the canceling opposite polarity elements in only one event. The horizontal fields are observed along the intergranular lanes with Doppler red shifts. This cancellation is most probably a result of the submergence (retraction) of low-lying photospheric magnetic flux. In the other 4 events, the horizontal field is not observed between the opposite polarity elements at any time when they approach and cancel each other. These approaching magnetic elements are more concentrated rather than gradually diffused, and they have nearly vertical fields even while they are in contact each other. We thus infer that the actual flux cancellation is highly time dependent events at scales less than a pixel of Hinode SOT (about 200 km) near the solar surface.Comment: Accepted for publication in the Astrophysical Journa

Quiet Sun magnetic fields from space-borne observations: simulating Hinode's case

We examine whether or not it is possible to derive the field strength distribution of quiet Sun internetwork regions from very high spatial resolution polarimetric observations in the visible. In particular, we consider the case of the spectropolarimeter attached to the Solar Optical Telescope aboard Hinode. Radiative magneto-convection simulations are used to synthesize the four Stokes profiles of the \ion{Fe}{1} 630.2 nm lines. Once the profiles are degraded to a spatial resolution of 0\farcs32 and added noise, we infer the atmospheric parameters by means of Milne-Eddington inversions. The comparison of the derived values with the real ones indicates that the visible lines yield correct internetwork field strengths and magnetic fluxes, with uncertainties smaller than $\sim$150 G, when a stray light contamination factor is included in the inversion. Contrary to the results of ground-based observations at 1\arcsec, weak fields are retrieved wherever the field is weak in the simulation.Comment: Accepted for publication in ApJ Letter

The formation and disintegration of magnetic bright points observed by Sunrise/IMaX

The evolution of the physical parameters of magnetic bright points (MBPs) located in the quiet Sun (mainly in the interwork) during their lifetime is studied. First we concentrate on the detailed description of the magnetic field evolution of three MBPs. This reveals that individual features follow different, generally complex, and rather dynamic scenarios of evolution. Next we apply statistical methods on roughly 200 observed MBP evolutionary tracks. MBPs are found to be formed by the strengthening of an equipartition field patch, which initially exhibits a moderate downflow. During the evolution, strong downdrafts with an average velocity of 2.4 km/s set in. These flows, taken together with the concurrent strengthening of the field, suggest that we are witnessing the occurrence of convective collapses in these features, although only 30% of them reach kG field strengths. This fraction might turn out to be larger when the new 4 m class solar telescopes are operational as observations of MBPs with current state of the art instrumentation could still be suffering from resolution limitations. Finally, when the bright point disappears (although the magnetic field often continues to exist) the magnetic field strength has dropped to the equipartition level and is generally somewhat weaker than at the beginning of the MBP's evolution. Noteworthy is that in about 10% of the cases we observe in the vicinity of the downflows small-scale strong (exceeding 2 km/s) intergranular upflows related spatially and temporally to these downflows.Comment: 19 pages, 13 figures; final version published in "The Astrophysical Journal

Temporal evolution of the Evershed flow in sunspots. I. Observational characterization of Evershed clouds

[Abridged] The magnetic and kinematic properties of the photospheric Evershed flow are relatively well known, but we are still far from a complete understanding of its nature. The evolution of the flow with time, which is mainly due to appearance of velocity packets called Evershed clouds (ECs), may provide information to further constrain its origin. Here we undertake a detailed analysis of the evolution of the Evershed flow by studying the properties of ECs. In this first paper we determine the sizes, proper motions, location in the penumbra, and frequency of appearance of ECs, as well as their typical Doppler velocities, linear and circular polarization signals, Stokes V area asymmetries, and continuum intensities. High-cadence, high-resolution, full vector spectropolarimetric measurements in visible and infrared lines are used to derive these parameters. We find that ECs appear in the mid penumbra and propage outward along filaments with large linear polarization signals and enhanced Evershed flows. The frequency of appearance of ECs varies between 15 and 40 minutes in different filaments. ECs exhibit the largest Doppler velocities and linear-to-circular polarization ratios of the whole penumbra. In addition, lines formed deeper in the atmosphere show larger Doppler velocities, much in the same way as the ''quiescent'' Evershed flow. According to our observations, ECs can be classified in two groups: type I ECs, which vanish in the outer penumbra, and type II ECs, which cross the outer penumbral boundary and enter the sunspot moat. Most of the observed ECs belong to type I. On average, type II ECs can be detected as velocity structures outside of the spot for only about 14 min. Their proper motions in the moat are significantly reduced with respect to the ones they had in the penumbra.Comment: Accepted for publication in A&

Two opposing hippocampus to prefrontal cortex pathways for the control of approach and avoidance behaviour

The decision to either approach or avoid a potentially threatening environment is thought to rely upon the coordinated activity of heterogeneous neural populations in the hippocampus and prefrontal cortex (PFC). However, how this circuitry is organized to flexibly promote both approach or avoidance at different times has remained elusive. Here, we show that the hippocampal projection to PFC is composed of two parallel circuits located in the superficial or deep pyramidal layers of the CA1/subiculum border. These circuits have unique upstream and downstream connectivity, and are differentially active during approach and avoidance behaviour. The superficial population is preferentially connected to widespread PFC inhibitory interneurons, and its activation promotes exploration; while the deep circuit is connected to PFC pyramidal neurons and fast spiking interneurons, and its activation promotes avoidance. Together this provides a mechanism for regulation of behaviour during approach avoidance conflict: through two specialized, parallel circuits that allow bidirectional hippocampal control of PFC

Two-dimensional solar spectropolarimetry with the KIS/IAA Visible Imaging Polarimeter

Spectropolarimetry at high spatial and spectral resolution is a basic tool to characterize the magnetic properties of the solar atmosphere. We introduce the KIS/IAA Visible Imaging Polarimeter (VIP), a new post-focus instrument that upgrades the TESOS spectrometer at the German VTT into a full vector polarimeter. VIP is a collaboration between the KIS and the IAA. We describe the optical setup of VIP, the data acquisition procedure, and the calibration of the spectropolarimetric measurements. We show examples of data taken between 2005 and 2008 to illustrate the potential of the instrument. VIP is capable of measuring the four Stokes profiles of spectral lines in the range from 420 to 700 nm with a spatial resolution better than 0.5". Lines can be sampled at 40 wavelength positions in 60 s, achieving a noise level of about 2 x 10E-3 with exposure times of 300 ms and pixel sizes of 0.17" x 0.17" (2 x 2 binning). The polarization modulation is stable over periods of a few days, ensuring high polarimetric accuracy. The excellent spectral resolution of TESOS allows the use of sophisticated data analysis techniques such as Stokes inversions. One of the first scientific results of VIP presented here is that the ribbon-like magnetic structures of the network are associated with a distinct pattern of net circular polarization away from disk center. VIP performs spectropolarimetric measurements of solar magnetic fields at a spatial resolution that is only slightly worse than that of the Hinode spectropolarimeter, while providing a 2D field field of view and the possibility to observe up to four spectral regions sequentially with high cadence. VIP can be used as a stand-alone instrument or in combination with other spectropolarimeters and imaging systems of the VTT for extended wavelength coverage.Comment: 10 pages, 8 figures, accepted by Astronomy and Astrophysics v2: figures updated with improved qualit