A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo

The current gene regulatory network (GRN) for the sea urchin embryo pertains to pregastrular specification functions in the endomesodermal territories. Here we extend gene regulatory network analysis to the adjacent oral and aboral ectoderm territories over the same period. A large fraction of the regulatory genes predicted by the sea urchin genome project and shown in ancillary studies to be expressed in either oral or aboral ectoderm by 24 h are included, though universally expressed and pan-ectodermal regulatory genes are in general not. The loci of expression of these genes have been determined by whole mount in situ hybridization. We have carried out a global perturbation analysis in which expression of each gene was interrupted by introduction of morpholino antisense oligonucleotide, and the effects on all other genes were measured quantitatively, both by QPCR and by a new instrumental technology (NanoString Technologies nCounter Analysis System). At its current stage the network model, built in BioTapestry, includes 22 genes encoding transcription factors, 4 genes encoding known signaling ligands, and 3 genes that are yet unknown but are predicted to perform specific roles. Evidence emerged from the analysis pointing to distinctive subcircuit features observed earlier in other parts of the GRN, including a double negative transcriptional regulatory gate, and dynamic state lockdowns by feedback interactions. While much of the regulatory apparatus is downstream of Nodal signaling, as expected from previous observations, there are also cohorts of independently activated oral and aboral ectoderm regulatory genes, and we predict yet unidentified signaling interactions between oral and aboral territories

Quenching of High pT Hadron Spectra by Hadronic Interactions in Heavy Ion Collisions at RHIC

Typically the materialization of high energetic transverse partons to hadronic jets is assumed to occur outside the reaction zone in a relativistic heavy ion collision. In contrast, a quantum mechanical estimate yields a time on the order of only a few fm/c for building up the hadronic wavefunction for jets with typical transverse momenta of pT < 10 GeV as accessible at RHIC facilities. The role of possible elastic or inelastic collisions of these high pT particles with the bulk of hadrons inside the fireball is addressed by means of an opacity expansion in the number of collisions. This analysis shows that the hadronic final state interactions can in principle account for the modification of the (moderate) high pT spectrum observed for central collisions at RHIC.Comment: 9 pages, 9 figures, standard revtex, final published versio

What is the benefit of ceilometers for aerosol remote sensing? An answer from EARLINET

With the establishment of ceilometer networks by national weather services, a discussion commenced to which extent these simple backscatter lidars can be used for aerosol research. Though primarily designed for the detection of clouds it was shown that at least observations of the vertical structure of the boundary layer might be possible. However, an assessment of the potential of ceilometers for the quantitative retrieval of aerosol properties is still missing. In this paper we discuss different retrieval methods to derive the aerosol backscatter coefficient beta(p),with special focus on the calibration of the ceilometers. Different options based on forward and backward integration methods are compared with respect to their accuracy and applicability. It is shown that advanced lidar systems such as those being operated in the framework of the European Aerosol Research Lidar Network (EARLINET) are excellent tools for the calibration, and thus beta(p) retrievals based on forward integration can readily be implemented and used for real-time applications. Furthermore, we discuss uncertainties introduced by incomplete overlap, the unknown lidar ratio, and water vapor absorption. The latter is relevant for the very large number of ceilometers operating in the spectral range around lambda = 905-910 nm. The accuracy of the retrieved beta(p) mainly depends on the accuracy of the calibration and the long-term stability of the ceilometer. Under favorable conditions, a relative error of beta(p) on the order of 10% seems feasible. In the case of water vapor absorption, corrections assuming a realistic water vapor distribution and laser spectrum are indispensable;otherwise errors on the order of 20% could occur. From case studies it is shown that ceilometers can be used for the reliable detection of elevated aerosol layers below 5 km, and can contribute to the validation of chemistry transport models, e. g.,the height of the boundary layer. However, the exploitation of ceilometer measurements is still in its infancy, so more studies are urgently needed to consolidate the present state of knowledge, which is based on a limited number of case studies

Observation of discrete, vortex light bullets

We report the first experimental observation of vortex light bullets that are discrete, spatiotemporal, solitary waves with orbital angular momentum. We analyze conditions for their existence and investigate their rich properties and dynamics. Vortex light bullets are excited in fiber arrays with spatially shaped femtosecond pulses and analyzed with a spatiotemporal cross correlator. Most importantly, we find that they have entirely new stability properties, being robust against considerable degrees of perturbation in a limited range of energies. All experimental findings are backed up by rigorous simulations, giving further insight into the rich dynamics of vortex light bullets

Origin and evolution of the light nuclides

After a short historical (and highly subjective) introduction to the field, I discuss our current understanding of the origin and evolution of the light nuclides D, He-3, He-4, Li-6, Li-7, Be-9, B-10 and B-11. Despite considerable observational and theoretical progress, important uncertainties still persist for each and every one of those nuclides. The present-day abundance of D in the local interstellar medium is currently uncertain, making it difficult to infer the recent chemical evolution of the solar neighborhood. To account for the observed quasi-constancy of He-3 abundance from the Big Bang to our days, the stellar production of that nuclide must be negligible; however, the scarce observations of its abundance in planetary nebulae seem to contradict this idea. The observed Be and B evolution as primaries suggests that the source composition of cosmic rays has remained quasi-constant since the early days of the Galaxy, a suggestion with far reaching implications for the origin of cosmic rays; however, the main idea proposed to account for that constancy, namely that superbubbles are at the source of cosmic rays, encounters some serious difficulties. The best explanation for the mismatch between primordial Li and the observed "Spite-plateau" in halo stars appears to be depletion of Li in stellar envelopes, by some yet poorly understood mechanism. But this explanation impacts on the level of the recently discovered early ``Li-6 plateau'', which (if confirmed), seriously challenges current ideas of cosmic ray nucleosynthesis.Comment: 18 pages, 9 figs. Invited Review in "Symposium on the Composition of Matter", honoring Johannes Geiss on the occasion of his 80th birthday (Grindelwald, Switzerland, Sept. 2006), to be published in Space Science Series of ISS

The Intrinsic Fundamental Group of a Linear Category

We provide an intrinsic definition of the fundamental group of a linear category over a ring as the automorphism group of the fibre functor on Galois coverings. If the universal covering exists, we prove that this group is isomorphic to the Galois group of the universal covering. The grading deduced from a Galois covering enables us to describe the canonical monomorphism from its automorphism group to the first Hochschild-Mitchell cohomology vector space.Comment: Final version, to appear in Algebras and Representation Theor

Intermittent release of transients in the slow solar wind: 2. In situ evidence

In paper 1, we showed that the Heliospheric Imager (HI) instruments on the pair of NASA STEREO spacecraft can be used to image the streamer belt and, in particular, the variability of the slow solar wind which originates near helmet streamers. The observation of intense intermittent transient outflow by HI implies that the corresponding in situ observations of the slow solar wind and corotating interaction regions (CIRs) should contain many signatures of transients. In the present paper, we compare the HI observations with in situ measurements from the STEREO and ACE spacecraft. Analysis of the solar wind ion, magnetic field, and suprathermal electron flux measurements from the STEREO spacecraft reveals the presence of both closed and partially disconnected interplanetary magnetic field lines permeating the slow solar wind. We predict that one of the transients embedded within the second CIR (CIR‐D in paper 1) should impact the near‐Earth ACE spacecraft. ACE measurements confirm the presence of a transient at the time of CIR passage; the transient signature includes helical magnetic fields and bidirectional suprathermal electrons. On the same day, a strahl electron dropout is observed at STEREO‐B, correlated with the passage of a high plasma beta structure. Unlike ACE, STEREO‐B observes the transient a few hours ahead of the CIR. STEREO‐A, STEREO‐B, and ACE spacecraft observe very different slow solar wind properties ahead of and during the CIR analyzed in this paper, which we associate with the intermittent release of transients

Cosmic ray neon, Wolf-Rayet stars, and the superbubble origin of galactic cosmic rays

The abundances of neon isotopes in the galactic cosmic rays (GCRs) are reported using data from the Cosmic Ray Isotope Spectrometer (CRIS) aboard the Advanced Composition Explorer (ACE). We compare our ACE-CRIS data for neon and refractory isotope ratios, and data from other experiments, with recent results from two-component Wolf-Rayet (WR) models. The three largest deviations of GCR isotope ratios from solar-system ratios predicted by these models are indeed present in the GCRs. Since WR stars are evolutionary products of OB stars, and most OB stars exist in OB associations that form superbubbles, the good agreement of these data with WR models suggests that superbubbles are the likely source of at least a substantial fraction of GCRs.Comment: 22 pages, 6 figures Accepted for publication by Ap

Radiative decay of a massive particle and the non-thermal process in primordial nucleosynthesis

We consider the effects on big bang nucleosynthesis (BBN) of the radiative decay of a long-lived massive particle. If high-energy photons are emitted after the BBN epoch ($t \sim 1 - 10^3$ sec), they may change the abundances of the light elements through photodissociation processes, which may result in a significant discrepancy between standard BBN and observation. Taking into account recent observational and theoretical developments in this field, we revise our previous study constraining the abundance of the radiatively-decaying particles. In particular, on the theoretical side, it was recently claimed that the non-thermal production of $^6$Li, which is caused by the photodissociation of \hefour, most severely constrains the abundance of the radiatively-decaying particle. We will see, however, it is premature to emphasize the importance of the non-thermal production of $^6$Li because (i) the theoretical computation of the $^6$Li abundance has large uncertainty due to the lack of the precise understanding of the $^6$Li production cross section, and (ii) the observational data of $^6$Li abundance has large errors.Comment: 15 pages, using REVTeX and 3 postscript figure

Open charm and charmonium production at relativistic energies

We calculate open charm and charmonium production in $Au+Au$ reactions at $\sqrt{s}$ = 200 GeV within the hadron-string dynamics (HSD) transport approach employing open charm cross sections from $pN$ and $\pi N$ reactions that are fitted to results from PYTHIA and scaled in magnitude to the available experimental data. Charmonium dissociation with nucleons and formed mesons to open charm ($D+\bar{D}$ pairs) is included dynamically. The 'comover' dissociation cross sections are described by a simple phase-space model including a single free parameter, i.e. an interaction strength $M_0^2$, that is fitted to the $J/\Psi$ suppression data for $Pb+Pb$ collisions at SPS energies. As a novel feature we implement the backward channels for charmonium reproduction by $D \bar{D}$ channels employing detailed balance. From our dynamical calculations we find that the charmonium recreation is comparable to the dissociation by 'comoving' mesons. This leads to the final result that the total $J/\Psi$ suppression at $\sqrt{s}$ = 200 GeV as a function of centrality is slightly less than the suppression seen at SPS energies by the NA50 Collaboration, where the 'comover' dissociation is substantial and the backward channels play no role. Furthermore, even in case that all directly produced $J/\Psi$ mesons dissociate immediately (or are not formed as a mesonic state), a sizeable amount of charmonia is found asymptotically due to the $D+\bar{D} \to J/\Psi$ + meson channels in central collisions of $Au+Au$ at $\sqrt{s}$ = 200 GeV which, however, is lower than the $J/\Psi$ yield expected from binary scaling of $pp$ collisions.Comment: 42 pages, including 14 eps figures, discussions extended and references added, to be published in Phys. Rev.