Logic Integer Programming Models for Signaling Networks

We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as well as quantitative data has so far not been exploited in Molecular Biology, which is mostly driven by experimental research, relying on first-order or statistical models. The arising logic statements and integer programs are analyzed and can be solved with standard software. For a restricted class of problems the logic models reduce to a polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic model enables enumeration of possible time resolutions in poly-logarithmic time. Computational experiments are included

State of Mnemiopsis leidyi (Ctenophora: Lobata) and mesozooplankton in Iranian waters of the Caspian Sea during 2008 in comparison with previous surveys

Mnemiopsis leidyi which was accidentally introduced into the Caspian Sea in 1999 and since then has colonized extensively. The horizontal distribution of M. leidyi and dominant mesozooplankton species was investigated in the south western Caspian Sea during February, May, July and November 2008. The average number and biomass of M. leidyi were in the same range (ca 200 individuals m^-3 (2000 ind m^-2)) and 16 g wet weight m^-3 (180 g m^-2) in comparison with previous surveys. As in previous years the population consisted mainly of individuals <1 cm. The decline in mesozooplankton species observed since 1996 continued in 2008. Only two species of the previously recorded 24 Cladocera species were found in 2008. Of five Copepoda species recorded in 1996, only one, Acartia tonsa, was found in 2008 and even here adult individuals have reduced 3-fold since 1996. Bivalve larvae have declined by one order of magnitude since 1996. Among the dominant species, only the numbers of Cirripedia larvae and in part the numbers of Pleopis polyphemoides (Cladocera) were in the same range as in 1996

Trends in biomass, density and diversity of North Sea macrofauna

Total biomass and biomass of large taxonomic groups (polychaetes, molluscs, crustaceans, echinoderms) and species diversity of the macrofauna were determined for almost 200 North Sea stations sampled synoptically by seven vessels during Spring 1986 and for 120 additional stations sampled in earlier years by the Marine Laboratory in Aberdeen. There exists a clear and significant decreasing trend in biomass with latitude, both in total biomass and for the different taxonomic groups. Apart from latitude, sediment composition and chlorophyll a content of the sediment also infuence total biomass and biomass of most groups significantly. Biomass increases consistently in finer sediments and sediments with a higher chlorophyll a content. The same trends are found for the results within laboratories. Some interaction exists, indicating weak laboratory and zonal effects. Diversity, as measured by Hill's diversity index N1 = (exp H′) shows a clear and significant trend with latitude. Towards the north of the North Sea diversity increases considerably. The trend is also found for laboratories separately and is everywhere equally strong. Also longitude and depth show an effect on diversity. Sediment variables have no clear influence on diversity. Other diversity measures show the same trend but are more variable than N1,. Total density tends to increase towards the north, but sediment related variables have a larger influence. Mean individual weight becomes considerably smaller towards the northern part of the North Sea

Ocean current connectivity propelling the secondary spread of a marine invasive comb jelly across western Eurasia

Aim: Invasive species are of increasing global concern. Nevertheless, the mechanisms driving furtherdistribution after the initial establishment of non-native species remain largely unresolved, especiallyin marine systems. Ocean currents can be a major driver governing range occupancy, but this hasnot been accounted for in most invasion ecology studies so far. We investigate how well initialestablishment areas are interconnected to later occupancy regions to test for the potential role ofocean currents driving secondary spread dynamics in order to infer invasion corridors and thesource–sink dynamics of a non-native holoplanktonic biological probe species on a continental scale.Location: Western Eurasia.Time period: 1980s–2016.Major taxa studied: ‘Comb jelly’ Mnemiopsis leidyi.Methods: Based on 12,400 geo-referenced occurrence data, we reconstruct the invasion historyof M. leidyi in western Eurasia. We model ocean currents and calculate their stability to match thetemporal and spatial spread dynamics with large-scale connectivity patterns via ocean currents.Additionally, genetic markers are used to test the predicted connectivity between subpopulations.Results: Ocean currents can explain secondary spread dynamics, matching observed range expansionsand the timing of first occurrence of our holoplanktonic non-native biological probe species,leading to invasion corridors in western Eurasia. In northern Europe, regional extinctions after coldwinters were followed by rapid recolonizations at a speed of up to 2,000 km per season. SourceJASPERS ET AL. | 815areas hosting year-round populations in highly interconnected regions can re-seed genotypes overlarge distances after local extinctions.Main conclusions: Although the release of ballast water from container ships may contribute tothe dispersal of non-native species, our results highlight the importance of ocean currents drivingsecondary spread dynamics. Highly interconnected areas hosting invasive species are crucial forsecondary spread dynamics on a continental scale. Invasion risk assessments should considerlarge-scale connectivity patterns and the potential source regions of non-native marine species

The Mediterranean Sea Regime Shift at the End of the 1980s, and Intriguing Parallelisms with Other European Basins

Background: Regime shifts are abrupt changes encompassing a multitude of physical properties and ecosystem variables, which lead to new regime conditions. Recent investigations focus on the changes in ecosystem diversity and functioning associated to such shifts. Of particular interest, because of the implication on climate drivers, are shifts that occur synchronously in separated basins. Principal Findings: In this work we analyze and review long-term records of Mediterranean ecological and hydro-climate variables and find that all point to a synchronous change in the late 1980s. A quantitative synthesis of the literature (including observed oceanic data, models and satellite analyses) shows that these years mark a major change in Mediterranean hydrographic properties, surface circulation, and deep water convection (the Eastern Mediterranean Transient). We provide novel analyses that link local, regional and basin scale hydrological properties with two major indicators of large scale climate, the North Atlantic Oscillation index and the Northern Hemisphere Temperature index, suggesting that the Mediterranean shift is part of a large scale change in the Northern Hemisphere. We provide a simplified scheme of the different effects of climate vs. temperature on pelagic ecosystems. Conclusions: Our results show that the Mediterranean Sea underwent a major change at the end of the 1980s that encompassed atmospheric, hydrological, and ecological systems, for which it can be considered a regime shift. We further provide evidence that the local hydrography is linked to the larger scale, northern hemisphere climate. These results suggest that the shifts that affected the North, Baltic, Black and Mediterranean (this work) Seas at the end of the 1980s, that have been so far only partly associated, are likely linked as part a northern hemisphere change. These findings bear wide implications for the development of climate change scenarios, as synchronous shifts may provide the key for distinguishing local (i.e., basin) anthropogenic drivers, such as eutrophication or fishing, from larger scale (hemispheric) climate drivers

Spawning of bluefin tuna in the black sea: historical evidence, environmental constraints and population plasticity

<div><p>The lucrative and highly migratory Atlantic bluefin tuna, <em>Thunnus thynnus</em> (Linnaeus 1758<em>;</em> Scombridae), used to be distributed widely throughout the north Atlantic Ocean, Mediterranean Sea and Black Sea. Its migrations have supported sustainable fisheries and impacted local cultures since antiquity, but its biogeographic range has contracted since the 1950s. Most recently, the species disappeared from the Black Sea in the late 1980s and has not yet recovered. Reasons for the Black Sea disappearance, and the species-wide range contraction, are unclear. However bluefin tuna formerly foraged and possibly spawned in the Black Sea. Loss of a locally-reproducing population would represent a decline in population richness, and an increase in species vulnerability to perturbations such as exploitation and environmental change. Here we identify the main genetic and phenotypic adaptations that the population must have (had) in order to reproduce successfully in the specific hydrographic (estuarine) conditions of the Black Sea. By comparing hydrographic conditions in spawning areas of the three species of bluefin tunas, and applying a mechanistic model of egg buoyancy and sinking rate, we show that reproduction in the Black Sea must have required specific adaptations of egg buoyancy, fertilisation and development for reproductive success. Such adaptations by local populations of marine fish species spawning in estuarine areas are common as is evident from a meta-analysis of egg buoyancy data from 16 species of fish. We conclude that these adaptations would have been necessary for successful local reproduction by bluefin tuna in the Black Sea, and that a locally-adapted reproducing population may have disappeared. Recovery of bluefin tuna in the Black Sea, either for spawning or foraging, will occur fastest if any remaining locally adapted individuals are allowed to survive, and by conservation and recovery of depleted Mediterranean populations which could through time re-establish local Black Sea spawning and foraging.</p> </div

Experimental and computational investigations of electron dynamics in micro atmospheric pressure radio-frequency plasma jets operated in He/N2 mixtures

The electron power absorption dynamics in radio frequency driven micro atmospheric pressure capacitive plasma jets are studied based on experimental phase resolved optical emission spectroscopy and the computational particle in cell simulations with Monte Carlo treatment of collisions. The jet is operated at 13.56 MHz in He with different admixture concentrations of N2 and at several driving voltage amplitudes. We find the spatio-temporal dynamics of the light emission of the plasma at various wavelengths to be markedly different. This is understood by revealing the population dynamics of the upper levels of selected emission lines/bands based on comparisons between experimental and simulation results. The populations of these excited states are sensitive to different parts of the electron energy distribution function and to contributions from other excited states. Mode transitions of the electron power absorption dynamics from the Ω- to the Penning-mode are found to be induced by changing the N2 admixture concentration and the driving voltage amplitude. Our numerical simulations reveal details of this mode transition and provide novel insights into the operation details of the Penning-mode. The characteristic excitation/emission maximum at the time of maximum sheath voltage at each electrode is found to be based on two mechanisms: (i) a direct channel, i.e. excitation/emission caused by electrons generated by Penning ionization inside the sheaths and (ii) an indirect channel, i.e. secondary electrons emitted from the electrode due to the impact of positive ions generated by Penning ionization at the electrodes

Studies of new Higgs boson interactions through nonresonant HH production in the b¯bγγ fnal state in pp collisions at √s = 13 TeV with the ATLAS detector

A search for nonresonant Higgs boson pair production in the b ¯bγγ fnal state is performed using 140 fb−1 of proton-proton collisions at a centre-of-mass energy of 13 TeV recorded by the ATLAS detector at the CERN Large Hadron Collider. This analysis supersedes and expands upon the previous nonresonant ATLAS results in this fnal state based on the same data sample. The analysis strategy is optimised to probe anomalous values not only of the Higgs (H) boson self-coupling modifer κλ but also of the quartic HHV V (V = W, Z) coupling modifer κ2V . No signifcant excess above the expected background from Standard Model processes is observed. An observed upper limit µHH &lt; 4.0 is set at 95% confdence level on the Higgs boson pair production cross-section normalised to its Standard Model prediction. The 95% confdence intervals for the coupling modifers are −1.4 &lt; κλ &lt; 6.9 and −0.5 &lt; κ2V &lt; 2.7, assuming all other Higgs boson couplings except the one under study are fxed to the Standard Model predictions. The results are interpreted in the Standard Model efective feld theory and Higgs efective feld theory frameworks in terms of constraints on the couplings of anomalous Higgs boson (self-)interactions

Comparison of inclusive and photon-tagged jet suppression in 5.02 TeV Pb+Pb collisions with ATLAS

Parton energy loss in the quark–gluon plasma (QGP) is studied with a measurement of photon-tagged jet production in 1.7 nb−1 of Pb+Pb data and 260 pb−1 of pp data, both at sNN=5.02 TeV, with the ATLAS detector. The process pp →γ+jet+X and its analogue in Pb+Pb collisions is measured in events containing an isolated photon with transverse momentum (pT) above 50 GeV and reported as a function of jet pT. This selection results in a sample of jets with a steeply falling pT distribution that are mostly initiated by the showering of quarks. The pp and Pb+Pb measurements are used to report the nuclear modification factor, RAA, and the fractional energy loss, Sloss, for photon-tagged jets. In addition, the results are compared with the analogous ones for inclusive jets, which have a significantly smaller quark-initiated fraction. The RAA and Sloss values are found to be significantly different between those for photon-tagged jets and inclusive jets, demonstrating that energy loss in the QGP is sensitive to the colour-charge of the initiating parton. The results are also compared with a variety of theoretical models of colour-charge-dependent energy loss