Numerical equilibrium analysis for structured consumer resource models

In this paper, we present methods for a numerical equilibrium and stability analysis for models of a size structured population competing for an unstructured resource. We concentrate on cases where two model parameters are free, and thus existence boundaries for equilibria and stability boundaries can be defined in the (two-parameter) plane. We numerically trace these implicitly defined curves using alternatingly tangent prediction and Newton correction. Evaluation of the maps defining the curves involves integration over individual size and individual survival probability (and their derivatives) as functions of individual age. Such ingredients are often defined as solutions of ODE, i.e., in general only implicitly. In our case, the right-hand sides of these ODE feature discontinuities that are caused by an abrupt change of behavior at the size where juveniles are assumed to turn adult. So, we combine the numerical solution of these ODE with curve tracing methods. We have implemented the algorithms for “Daphnia consuming algae” models in C-code. The results obtained by way of this implementation are shown in the form of graphs

Sleep dysfunction and EEG alterations in mice overexpressing alpha-synuclein.

BackgroundSleep disruptions occur early and frequently in Parkinson's disease (PD). PD patients also show a slowing of resting state activity. Alpha-synuclein is causally linked to PD and accumulates in sleep-related brain regions. While sleep problems occur in over 75% of PD patients and severely impact the quality of life of patients and caregivers, their study is limited by a paucity of adequate animal models.ObjectiveThe objective of this study was to determine whether overexpression of wildtype alpha-synuclein could lead to alterations in sleep patterns reminiscent of those observed in PD by measuring sleep/wake activity with rigorous quantitative methods in a well-characterized genetic mouse model.MethodsAt 10 months of age, mice expressing human wildtype alpha-synuclein under the Thy-1 promoter (Thy1-aSyn) and wildtype littermates underwent the subcutaneous implantation of a telemetry device (Data Sciences International) for the recording of electromyograms (EMG) and electroencephalograms (EEG) in freely moving animals. Surgeries and data collection were performed without knowledge of mouse genotype.ResultsThy1-aSyn mice showed increased non-rapid eye movement sleep during their quiescent phase, increased active wake during their active phase, and decreased rapid eye movement sleep over a 24-h period, as well as a shift in the density of their EEG power spectra toward lower frequencies with a significant decrease in gamma power during wakefulness.ConclusionsAlpha-synuclein overexpression in mice produces sleep disruptions and altered oscillatory EEG activity reminiscent of PD, and this model provides a novel platform to assess mechanisms and therapeutic strategies for sleep dysfunction in PD

Entanglement growth in quench dynamics with variable range interactions

Studying entanglement growth in quantum dynamics provides both insight into the underlying microscopic processes and information about the complexity of the quantum states, which is related to the efficiency of simulations on classical computers. Recently, experiments with trapped ions, polar molecules, and Rydberg excitations have provided new opportunities to observe dynamics with long-range interactions. We explore nonequilibrium coherent dynamics after a quantum quench in such systems, identifying qualitatively different behavior as the exponent of algebraically decaying spin-spin interactions in a transverse Ising chain is varied. Computing the build-up of bipartite entanglement as well as mutual information between distant spins, we identify linear growth of entanglement entropy corresponding to propagation of quasiparticles for shorter range interactions, with the maximum rate of growth occurring when the Hamiltonian parameters match those for the quantum phase transition. Counter-intuitively, the growth of bipartite entanglement for long-range interactions is only logarithmic for most regimes, i.e., substantially slower than for shorter range interactions. Experiments with trapped ions allow for the realization of this system with a tunable interaction range, and we show that the different phenomena are robust for finite system sizes and in the presence of noise. These results can act as a direct guide for the generation of large-scale entanglement in such experiments, towards a regime where the entanglement growth can render existing classical simulations inefficient.Comment: 17 pages, 7 figure

Revealing quantum statistics with a pair of distant atoms

Quantum statistics have a profound impact on the properties of systems composed of identical particles. In this Letter, we demonstrate that the quantum statistics of a pair of identical massive particles can be probed by a direct measurement of the exchange symmetry of their wave function even in conditions where the particles always remain spatially well separated and thus the exchange contribution to their interaction energy is negligible. We present two protocols revealing the bosonic or fermionic nature of a pair of particles and discuss possible implementations with a pair of trapped atoms or ions.Comment: 4+13 pages, v2 corresponds to the version published by PR

Loading of a cold atomic beam into a magnetic guide

We demonstrate experimentally the continuous and pulsed loading of a slow and cold atomic beam into a magnetic guide. The slow beam is produced using a vapor loaded laser trap, which ensures two-dimensional magneto-optical trapping, as well as cooling by a moving molasses along the third direction. It provides a continuous flux larger than $10^9$ atoms/s with an adjustable mean velocity ranging from 0.3 to 3 m/s, and with longitudinal and transverse temperatures smaller than $100 \mu$K. Up to $3 10^8$ atoms/s are injected into the magnetic guide and subsequently guided over a distance of 40 cm.Comment: 10 pages, 10 figures, accepted for publication to EPJ

Deterministic entanglement of ions in thermal states of motion

We give a detailed description of the implementation of a Molmer-Sorensen gate entangling two Ca+ ions using a bichromatic laser beam near-resonant with a quadrupole transition. By amplitude pulse shaping and compensation of AC-Stark shifts we achieve a fast gate operation without compromising the error rate. Subjecting different input states to concatenations of up to 21 individual gate operations reveals Bell state fidelities above 0.80. In principle, the entangling gate does not require ground state cooling of the ions as long as the Lamb-Dicke criterion is fulfilled. We present the first experimental evidence for this claim and create Bell states with a fidelity of 0.974(1) for ions in a thermal state of motion with a mean phonon number of =20(2) in the mode coupling to the ions' internal states.Comment: 18 pages, 9 figures (author name spelling corrected

Integrative DNA methylome analysis of pan-cancer biomarkers in cancer discordant monozygotic twin-pairs

BACKGROUND: A key focus in cancer research is the discovery of biomarkers that accurately diagnose early lesions in non-invasive tissues. Several studies have identified malignancy-associated DNA methylation changes in blood, yet no general cancer biomarker has been identified to date. Here, we explore the potential of blood DNA methylation as a biomarker of pan-cancer (cancer of multiple different origins) in 41 female cancer discordant monozygotic (MZ) twin-pairs sampled before or after diagnosis using the Illumina HumanMethylation450 BeadChip. RESULTS: We analysed epigenome-wide DNA methylation profiles in 41 cancer discordant MZ twin-pairs with affected individuals diagnosed with tumours at different single primary sites: the breast, cervix, colon, endometrium, thyroid gland, skin (melanoma), ovary, and pancreas. No significant global differences in whole blood DNA methylation profiles were observed. Epigenome-wide analyses identified one novel pan-cancer differentially methylated position at false discovery rate (FDR) threshold of 10 % (cg02444695, P = 1.8 × 10(-7)) in an intergenic region 70 kb upstream of the SASH1 tumour suppressor gene, and three suggestive signals in COL11A2, AXL, and LINC00340. Replication of the four top-ranked signals in an independent sample of nine cancer-discordant MZ twin-pairs showed a similar direction of association at COL11A2, AXL, and LINC00340, and significantly greater methylation discordance at AXL compared to 480 healthy concordant MZ twin-pairs. The effects at cg02444695 (near SASH1), COL11A2, and LINC00340 were the most promising in biomarker potential because the DNA methylation differences were found to pre-exist in samples obtained prior to diagnosis and were limited to a 5-year period before diagnosis. Gene expression follow-up at the top-ranked signals in 283 healthy individuals showed correlation between blood methylation and gene expression in lymphoblastoid cell lines at PRL, and in the skin tissue at AXL. A significant enrichment of differential DNA methylation was observed in enhancer regions (P = 0.03). CONCLUSIONS: We identified DNA methylation signatures in blood associated with pan-cancer, at or near SASH1, COL11A2, AXL, and LINC00340. Three of these signals were present up to 5 years prior to cancer diagnosis, highlighting the potential clinical utility of whole blood DNA methylation analysis in cancer surveillance