Robustness of Transcriptional Regulation in Yeast-like Model Boolean Networks

We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a dynamically determinant subnetwork, we explore the robustness of transcriptional regulation as a function of the type of Boolean functions used in the model that mimic the influence of regulating agents on the transcription level of a gene. We compare the results obtained for the actual yeast network with those from two different model networks, one with similar in-degree distribution as the yeast and random otherwise, and another due to Balcan et al., where the global topology of the yeast network is reproduced faithfully. We, surprisingly, find that the first set of model networks better reproduce the results found with the actual yeast network, even though the Balcan et al. model networks are structurally more similar to that of yeast.Comment: 7 pages, 4 figures, To appear in Int. J. Bifurcation and Chaos, typos were corrected and 2 references were adde

Circulating Biologically Active Adrenomedullin Predicts Organ Failure and Mortality in Sepsis

BACKGROUND: Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Biologically active adrenomedullin (bio-ADM) is an emerging biomarker for sepsis. We explored whether bio-ADM concentration could predict severity, organ failure, and 30-day mortality in septic patients. METHODS: In 215 septic patients (109 patients with sepsis; 106 patients with septic shock), bio-ADM concentration was measured at diagnosis of sepsis, using sphingotest bio-ADM (Sphingotec GmbH, Hennigsdorf, Germany) and analyzed in terms of sepsis severity, vasopressor use, and 30-day mortality. The number of organ failures, sequential (sepsis-related) organ failure assessment (SOFA) score, and 30-day mortality were compared according to bio-ADM quartiles. RESULTS: Bio-ADM concentration was significantly higher in patients with septic shock, vasopressor use, and non-survivors than in patients with solitary sepsis, no vasopressor use, and survivors, respectively (all P<0.0001). Bio-ADM quartiles were associated with the number of organ failures (P<0.0001), as well as SOFA cardiovascular, renal, coagulation, and liver subscores (all P<0.05). The 30-day mortality rate showed a stepwise increase in each bio-ADM quartile (all P<0.0001). Bio-ADM concentration and SOFA score equally predicted the 30-day mortality (area under the curve: 0.827 vs 0.830). CONCLUSIONS: Bio-ADM could serve as a useful and objective biomarker to predict severity, organ failure, and 30-day mortality in septic patients

The Ionizing Source of the Nucleus of NGC1097

We present new observations in X-ray and optical/ultraviolet of the nucleus of NGC1097, known for the abrupt appearance of broad, double-peaked Balmer lines in its spectrum in 1991. These new observations are used to construct the spectral energy distribution (SED) of the central engine. From the SED we infer that this AGN is radio-loud and has a bolometric luminosity L_Bol ~ 10^42 erg/s, implying a low Eddington ratio of L_Bol/L_Edd ~ 10^{-4}. These results suggest that the central ionizing source is an advection-dominated accretion flow (ADAF) in the form of an ellevated structure which photoionizes an outer thin disk. We fit a simplified ADAF model to the SED and obtain limits on the values of the mass accretion rate Mdot and accretion efficiency \eta, namely Mdot/Mdot_Edd >= 10^{-3} and \eta <= 10^{-2}. We identify an energy budget problem: if the central photoionizing source is isotropic, the covering factor of the line-emitting portion of the thin accretion disk is ~ 6, i. e. the central source accounts for only 20% of the energy emitted in the double-peaked Balmer lines.Comment: 4 pages, 3 figures, to appear in the proceedings of "The Interplay among Black Holes, Stars and ISM in Galactic Nuclei", IAU 222, eds. Th. Storchi Bergmann, L.C. Ho, and H.R. Schmit

The Ultraviolet Spectra of Active Galaxies With Double-Peaked Emission Lines

We present the results of UV spectroscopy of AGNs with double-peaked Balmer emission lines. In 2/3 of the objects, the far-UV resonance lines are strong, with single-peaked profiles resembling those of Seyfert galaxies. The Mg II line is the only UV line with a double-peaked profile. In the remaining objects, the far-UV resonance lines are relatively weak but still single-peaked. The latter group also displays prominent UV absorption lines, indicative of a low-ionization absorber. We interpret the difference in the profiles of the emission lines as resulting from two different regions: a dense, low-ionization accretion disk (the predominant source of the Balmer and Mg II lines), and a lower density, higher-ionization wind (the predominant source of the far-UV resonance lines). These results suggest a way of connecting the double-peaked emitters with the greater AGN population: in double-peaked emitters the accretion rate onto the black hole is low, making the wind feeble and allowing the lines from the underlying disk to shine through. This scenario also implies that in the majority of AGNs, the wind is the source of the broad emission lines.Comment: To appear in "The Interplay among Black Holes, Stars and ISM in Galactic Nuclei," IAU Coll. 222, eds. Storchi Bergmann, Ho, and Schmit

Lepton number violating interactions and their effects on neutrino oscillation experiments

Mixing between bosons that transform differently under the standard model gauge group, but identically under its unbroken subgroup, can induce interactions that violate the total lepton number. We discuss four-fermion operators that mediate lepton number violating neutrino interactions both in a model-independent framework and within supersymmetry (SUSY) without R-parity. The effective couplings of such operators are constrained by: i) the upper bounds on the relevant elementary couplings between the bosons and the fermions, ii) by the limit on universality violation in pion decays, iii) by the data on neutrinoless double beta decay and, iv) by loop-induced neutrino masses. We find that the present bounds imply that lepton number violating neutrino interactions are not relevant for the solar and atmospheric neutrino problems. Within SUSY without R-parity also the LSND anomaly cannot be explained by such interactions, but one cannot rule out an effect model-independently. Possible consequences for future terrestrial neutrino oscillation experiments and for neutrinos from a supernova are discussed.Comment: 28 pages, 2 figures, Late

Precision and scaling in morphogen gradient read-out

Morphogen gradients infer cell fate as a function of cellular position. Experiments in Drosophila embryos have shown that the Bicoid (Bcd) gradient is precise and exhibits some degree of scaling. We present experimental results on the precision of Bcd target genes for embryos with a single, double or quadruple dose of bicoid demonstrating that precision is highest at mid-embryo and position dependent, rather than gene dependent. This confirms that the major contribution to precision is achieved already at the Bcd gradient formation. Modeling this dynamic process, we investigate precision for inter-embryo fluctuations in different parameters affecting gradient formation. Within our modeling framework, the observed precision can only be achieved by a transient Bcd profile. Studying different extensions of our modeling framework reveals that scaling is generally position dependent and decreases toward the posterior pole. Our measurements confirm this trend, indicating almost perfect scaling except for anterior most expression domains, which overcompensate fluctuations in embryo length

Information Extraction From Chemical Patents

The development of new chemicals or pharmaceuticals is preceded by an indepth analysis of published patents in this field. This information retrieval is a costly and time inefficient step when done by a human reader, yet it is mandatory for potential success of an investment. The goal of the research project UIMA-HPC is to automate and hence speed-up the process of knowledge mining about patents. Multi-threaded analysis engines, developed according to UIMA (Unstructured Information Management Architecture) standards, process texts and images in thousands of documents in parallel. UNICORE (UNiform Interface to COmputing Resources) workflow control structures make it possible to dynamically allocate resources for every given task to gain best cpu-time/realtime ratios in an HPC environment

Interpreting experimental bounds on D^0 - \bar{D^0} mixing in the presence of CP violation

We analyse the most recent experimental data regarding D^0 - \bar{D^0} mixing, allowing for CP violation. We focus on the dispersive part of the mixing amplitude, M^D_{12}, which is sensitive to new physics contributions. We obtain a constraint on the mixing amplitude: |M^D_{12}| < 6.2\times 10^{-11} MeV at 95% C.L. . This constraint is weaker by a factor of about three than the one which is obtained when no CP violation is assumed.Comment: 9 pages, revtex4; One reference updated, one reference added, footnote 3 correcte