Influence of cell cycle phase on calcification in the coccolithophore Emiliania huxleyi

Calcification of the cosmopolitan coccolithophore species Emiliania huxleyi was investigated in relation to the cell division cycle with the use of batch cultures. With a 12 : 12 h light : dark cycle, the population was synchronised to undergo division as a cohort, simultaneously passing through the G1 (assimilation), S (DNA replication), and G2+M (cell division and mitosis) phases. Cell division was followed with the use of quantitative DNA staining and flow cytometry. Simultaneously, carbon-14 (14C) assimilation in organic and inorganic carbon as well as cell abundance, size, and organic nitrogen content were measured at 2-h intervals. In additional experiments, changes in calcification and cell cycle stages were investigated in nitrogen-, phosphorus-, and light-limited cultures. Calcification occurred only during the G1 cell cycle phase, as seen by the very tight correlation between the percentage of cells in G1 and calcification during the dark period. When growth was limited by nitrogen, cells decreased in size, remained in the G1 phase, and showed a moderate increase in the cell-specific calcite content. Limitation of growth by phosphorus, however, caused a significant increase in cell size and a dramatic increase in cellular calcite. Light limitation, by slowing the growth rate, prolonged the time cells spent in the G1 phase with a corresponding increase in the cellular calcite content. These results help explain the differing responses of coccolithophorid growth to nitrogen, phosphorus, and light limitation

Gerbil: A Fast and Memory-Efficient kk-mer Counter with GPU-Support

A basic task in bioinformatics is the counting of $k$-mers in genome strings. The $k$-mer counting problem is to build a histogram of all substrings of length $k$ in a given genome sequence. We present the open source $k$-mer counting software Gerbil that has been designed for the efficient counting of $k$-mers for $k\geq32$. Given the technology trend towards long reads of next-generation sequencers, support for large $k$ becomes increasingly important. While existing $k$-mer counting tools suffer from excessive memory resource consumption or degrading performance for large $k$, Gerbil is able to efficiently support large $k$ without much loss of performance. Our software implements a two-disk approach. In the first step, DNA reads are loaded from disk and distributed to temporary files that are stored at a working disk. In a second step, the temporary files are read again, split into $k$-mers and counted via a hash table approach. In addition, Gerbil can optionally use GPUs to accelerate the counting step. For large $k$, we outperform state-of-the-art open source $k$-mer counting tools for large genome data sets.Comment: A short version of this paper will appear in the proceedings of WABI 201

On Elliptic equations involving surface measures

We show optimal Lipschitz regularity for very weak solutions of the (measure-valued) elliptic PDE $-\mathrm{div}(A(x) \nabla u) = Q \; \mathcal{H}^{n-1} \llcorner \Gamma$ in a smooth domain $\Omega \subset \mathbb{R}^n$. Here $\Gamma$ is a $C^{1,\alpha}$-regular hypersurface, $Q\in C^{0,\alpha}$ is a density on $\Gamma$, and $A$ is symmetric, uniformly elliptic and $W^{1,q}$-regular $(q > n)$. We also discuss optimality of these assumptions on the data. The equation can be understood as a special coupling of two $A$-harmonic functions with an interface $\Gamma$. As such it plays an important role in several free boundary problems, as we shall discuss.Comment: 59 pages, comments are welcome

Entropy, majorization and thermodynamics in general probabilistic theories

In this note we lay some groundwork for the resource theory of thermodynamics in general probabilistic theories (GPTs). We consider theories satisfying a purely convex abstraction of the spectral decomposition of density matrices: that every state has a decomposition, with unique probabilities, into perfectly distinguishable pure states. The spectral entropy, and analogues using other Schur-concave functions, can be defined as the entropy of these probabilities. We describe additional conditions under which the outcome probabilities of a fine-grained measurement are majorized by those for a spectral measurement, and therefore the "spectral entropy" is the measurement entropy (and therefore concave). These conditions are (1) projectivity, which abstracts aspects of the Lueders-von Neumann projection postulate in quantum theory, in particular that every face of the state space is the positive part of the image of a certain kind of projection operator called a filter; and (2) symmetry of transition probabilities. The conjunction of these, as shown earlier by Araki, is equivalent to a strong geometric property of the unnormalized state cone known as perfection: that there is an inner product according to which every face of the cone, including the cone itself, is self-dual. Using some assumptions about the thermodynamic cost of certain processes that are partially motivated by our postulates, especially projectivity, we extend von Neumann's argument that the thermodynamic entropy of a quantum system is its spectral entropy to generalized probabilistic systems satisfying spectrality.Comment: In Proceedings QPL 2015, arXiv:1511.0118

Calcification in coccolithophores : effects of environmental conditions and paleoproxy calibrations

Oceanic production of organic carbon and calcium carbonate by marine flora and fauna 'play' a major role in the Earth's cycling of carbon and calcium. Coccolithophores, as a major phytoplankton group, are involved in both cycles and are relevant in the regulation of the seewater calcium carbonate saturation state since the Mesozoic (251 million years ago). The present thesis investigates the influence of various environmental parameters on the physiology of coccolithophores, focusing on the process of biogenic calcification in regard to variations in the ocean's calcium and magnesium concentrations, as well as to changes in the macronutrient concentrations and in the seawater carbonate chemistry (ocean acidification)

Understanding and Supporting Decision-Making in Electronic Auctions: A NeuroIS Approach

Making use of the potential of NeuroIS, I apply a NeuroIS approach in this thesis to further the understanding of decision-making and to analyze the opportunities for NeuroIS in decision-support, both in electronic auctions