A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Rotating molecular outflows: the young T Tauri star in CB26

The disk-outflow connection is thought to play a key role in extracting excess angular momentum from a forming proto-star. Though jet rotation has been observed in a few objects, no rotation of molecular outflows has been unambiguously reported so far. We report new millimeter-interferometric observations of the edge-on T Tauri star - disk system in the isolated Bok globule CB26. The aim of these observations was to study the disk-outflow relation in this 1Myr old low-mass young stellar object. The IRAM PdBI array was used to observe 12CO(2-1) at 1.3mm in two configurations, resulting in spectral line maps with 1.5 arcsec resolution. We use an empirical parameterized steady-state outflow model combined with 2-D line radiative transfer calculations and chi^2-minimization in parameter space to derive a best-fit model and constrain parameters of the outflow. The data reveal a previously undiscovered collimated bipolar molecular outflow of total length ~2000 AU, escaping perpendicular to the plane of the disk. We find peculiar kinematic signatures that suggest the outflow is rotating with the same orientation as the disk. However, we could not ultimately exclude jet precession or two misaligned flows as possible origin of the observed peculiar velocity field. There is indirect indication that the embedded driving source is a binary system, which, together with the youth of the source, could provide the clue to the observed kinematic features of the outflow. CB26 is so far the most promising source to study the rotation of a molecular outflow. Assuming that the outflow is rotating, we compute and compare masses, mass flux, angular momenta, and angular momentum flux of disk and outflow and derive disk dispersal timescales of 0.5...1 Myr, comparable to the age of the system.Comment: 14 pages, 6 figures, to appear in Astronomy & Astrophysic

Velocity asymmetries in YSO jets: Intrinsic and extrinsic mechanisms

It is a well established fact that some YSO jets (e.g. RW Aur) display different propagation speeds between their blue and red shifted parts, a feature possibly associated with the central engine or the environment in which the jet propagates. In order to understand the origin of asymmetric YSO jet velocities, we investigate the efficiency of two candidate mechanisms, one based on the intrinsic properties of the system and one based on the role of the external medium. In particular, a parallel or anti-parallel configuration between the protostellar magnetosphere and the disk magnetic field is considered and the resulting dynamics are examined both in an ideal and a resistive magneto-hydrodynamical (MHD) regime. Moreover, we explore the effects of a potential difference in the pressure of the environment, as a consequence of the non-uniform density distribution of molecular clouds. Ideal and resistive axisymmetric numerical simulations are carried out for a variety of models, all of which are based on a combination of two analytical solutions, a disk wind and a stellar outflow. We find that jet velocity asymmetries can indeed occur both when multipolar magnetic moments are present in the star-disk system as well as when non-uniform environments are considered. The latter case is an external mechanism that can easily explain the large time scale of the phenomenon, whereas the former one naturally relates it to the YSO intrinsic properties. [abridged]Comment: accepted for publication in A&

Accretion-ejection connection in the young brown dwarf candidate ISO-Cha1 217

As the number of observed brown dwarf outflows is growing it is important to investigate how these outflows compare to the well studied jets from young stellar objects. A key point of comparison is the relationship between outflow and accretion activity and in particular the ratio between the mass outflow and accretion rates ($\dot{M}_{out}$/$\dot{M}_{acc}$). The brown dwarf candidate ISO-ChaI 217 was discovered by our group, as part of a spectro-astrometric study of brown dwarfs, to be driving an asymmetric outflow with the blue-shifted lobe having a position angle of $\sim$ 20$^{\circ}$. The aim here is to further investigate the properties of ISO-ChaI 217, the morphology and kinematics of its outflow, and to better constrain ($\dot{M}_{out}$/$\dot{M}_{acc}$). The outflow is spatially resolved in the $[SII]\lambda \lambda 6716,6731$ lines and is detected out to $\sim$ 1\farcs6 in the blue-shifted lobe and ~ 1" in the red-shifted lobe. The asymmetry between the two lobes is confirmed although the velocity asymmetry is less pronounced with respect to our previous study. Using thirteen different accretion tracers we measure log($\dot{M}_{acc}$) [M$_{sun}$/yr]= -10.6 $\pm$ 0.4. As it was not possible to measure the effect of extinction on the ISO-ChaI 217 outflow $\dot{M}_{out}$ was derived for a range of values of A$_{v}$, up to a value of A$_{v}$ = 2.5 mag estimated for the source extinction. The logarithm of the mass outflow ($\dot{M}_{out}$) was estimated in the range -11.7 to -11.1 for both jets combined. Thus $\dot{M}_{out}$/$\dot{M}_{acc}$ [\Msun/yr] lies below the maximum value predicted by magneto-centrifugal jet launching models. Finally, both model fitting of the Balmer decrements and spectro-astrometric analysis of the H$\alpha$ line show that the bulk of the H I emission comes from the accretion flow.Comment: accepted by Astronomy & Astrophysic

Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks

The idea of 'date' and 'party' hubs has been influential in the study of protein-protein interaction networks. Date hubs display low co-expression with their partners, whilst party hubs have high co-expression. It was proposed that party hubs are local coordinators whereas date hubs are global connectors. Here we show that the reported importance of date hubs to network connectivity can in fact be attributed to a tiny subset of them. Crucially, these few, extremely central, hubs do not display particularly low expression correlation, undermining the idea of a link between this quantity and hub function. The date/party distinction was originally motivated by an approximately bimodal distribution of hub co-expression; we show that this feature is not always robust to methodological changes. Additionally, topological properties of hubs do not in general correlate with co-expression. Thus, we suggest that a date/party dichotomy is not meaningful and it might be more useful to conceive of roles for protein-protein interactions rather than individual proteins. We find significant correlations between interaction centrality and the functional similarity of the interacting proteins.Comment: 27 pages, 5 main figures, 4 supplementary figure

Launching of Conical Winds and Axial Jets from the Disk-Magnetosphere Boundary: Axisymmetric and 3D Simulations

We investigate the launching of outflows from the disk-magnetosphere boundary of slowly and rapidly rotating magnetized stars using axisymmetric and exploratory 3D magnetohydrodynamic (MHD) simulations. We find long-lasting outflows in both cases. (1) In the case of slowly rotating stars, a new type of outflow, a conical wind, is found and studied in simulations. The conical winds appear in cases where the magnetic flux of the star is bunched up by the disk into an X-type configuration. The winds have the shape of a thin conical shell with a half-opening angle 30-40 degrees. The conical winds may be responsible for episodic as well as long-lasting outflows in different types of stars. (2) In the case of rapidly rotating stars (the "propeller regime"), a two-component outflow is observed. One component is similar to the conical winds. A significant fraction of the disk matter may be ejected into the winds. A second component is a high-velocity, low-density magnetically dominated axial jet where matter flows along the opened polar field lines of the star. The jet has a mass flux about 10% that of the conical wind, but its energy flux (dominantly magnetic) can be larger than the energy flux of the conical wind. The jet's angular momentum flux (also dominantly magnetic) causes the star to spin-down rapidly. Propeller-driven outflows may be responsible for the jets in protostars and for their rapid spin-down. The jet is collimated by the magnetic force while the conical winds are only weakly collimated in the simulation region.Comment: 29 pages and 29 figures. This version has a major expansion after comments by a referee. The 1-st version is correct but mainly describes the conical wind. This version describes in greater detail both the conical winds and the propeller regime. Accepted to the MNRA

Nonradial and nonpolytropic astrophysical outflows IX. Modeling T Tauri jets with a low mass-accretion rate

Context: A large sample of T Tauri stars exhibits optical jets, approximately half of which rotate slowly, only at ten per cent of their breakup velocity. The disk-locking mechanism has been shown to be inefficient to explain this observational fact. Aims: We show that low mass accreting T Tauri stars may have a strong stellar jet component that can effectively brake the star to the observed rotation speed. Methods: By means of a nonlinear separation of the variables in the full set of the MHD equations we construct semi- analytical solutions describing the dynamics and topology of the stellar component of the jet that emerges from the corona of the star. Results: We analyze two typical solutions with the same mass loss rate but different magnetic lever arms and jet radii. The first solution with a long lever arm and a wide jet radius effectively brakes the star and can be applied to the visible jets of T Tauri stars, such as RY Tau. The second solution with a shorter lever arm and a very narrow jet radius may explain why similar stars, either Weak line T Tauri Stars (WTTS) or Classical T Tauri Stars (CTTS) do not all have visible jets. For instance, RY Tau itself seems to have different phases that probably depend on the activity of the star. Conclusions: First, stellar jets seem to be able to brake pre-main sequence stars with a low mass accreting rate. Second, jets may be visible only part time owing to changes in their boundary conditions. We also suggest a possible scenario for explaining the dichotomy between CTTS and WTTS, which rotate faster and do not have visible jets

The Disk Wind in the Young Binaries and the Origin of the Cyclic Activity of Young Stars

We present results of numerical modeling of the cyclic brightness modulation in the young binary systems with the eccentric orbits and low-mass secondary components. Brightness variations of the primary is due to the periodical extinction variations on the line-of-sight caused by the disk wind of the secondary and a common envelope it produces. A matter distribution in the envelope has been calculated in the ballistic approach. Calculations showed that for the young binaries with the elliptic orbits parameters of the photometric minima (their depth, duration and the shape of light curves) depend not only on the disk wind parameters and an inclination of the binary orbit to the line-of-sight but also on the longitude of the periastron. A modulation of the scattered radiation of the common envelope with a phase of the orbital period has been investigated in the single scattering approach. It is shown that an amplitude of the modulation is maximal when the system is seen edge-on and has also a non-zero value in the binaries observed pole-on. Possible applications of the theory to the young stellar objects are discussed. In particular, an attention is payed to a resemblance of the light curves in some models with light curves of the objects suspected as candidates to FUORs.Comment: 18 pages, 9 figures, accepted by Astronomy Letter

An Ancient Relation between Units of Length and Volume Based on a Sphere

The modern metric system defines units of volume based on the cube. We propose that the ancient Egyptian system of measuring capacity employed a similar concept, but used the sphere instead. When considered in ancient Egyptian units, the volume of a sphere, whose circumference is one royal cubit, equals half a hekat. Using the measurements of large sets of ancient containers as a database, the article demonstrates that this formula was characteristic of Egyptian and Egyptian-related pottery vessels but not of the ceramics of Mesopotamia, which had a different system of measuring length and volume units