Large-scale genomic correlations in Arabidopsis thaliana relate to chromosomal structure

BACKGROUND: The chromosomes of the plant Arabidopsis thaliana contain various genomic elements, distributed with appreciable spatial heterogeneity. Clustering of and/or correlations between these elements presumably should reflect underlying functional or structural factors. We studied the positional density fluctuations and correlations between genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, 180 bp tandem repeats, and conserved centromeric sequences (CCSs) in Arabidopsis in order to elucidate any patterns and possible responsible factors for their genomic distributions. RESULTS: The spatial distributions of all these elements obeyed a common pattern: the density profiles of each element within chromosomes exhibited low-frequency fluctuations indicative of regional clustering, and the individual density profiles tended to correlate with each other at large measurement scales. This pattern could be attributed to the influence of major chromosomal structures, such as centromeres. At smaller scales the correlations tended to weaken – evidence that localized cis-interactions between the different elements had a comparatively minor, if any, influence on their placement. CONCLUSION: The conventional notion that retrotransposon insertion sites are strongly influenced by cis-interactions was not supported by these observations. Moreover, we would propose that large-scale chromosomal structure has a dominant influence on the intrachromosomal distributions of genomic elements, and provides for an additional shared hierarchy of genomic organization within Arabidopsis

Fluctuations of work in nearly adiabatically driven open quantum systems

We extend the quantum jump method to nearly adiabatically driven open quantum systems in a way that allows for an accurate account of the external driving in the system-environment interaction. Using this framework, we construct the corresponding trajectory-dependent work performed on the system and derive the integral fluctuation theorem and the Jarzynski equality for nearly adiabatic driving. We show that such identities hold as long as the stochastic dynamics and work variable are consistently defined. We numerically study the emerging work statistics for a two-level quantum system and find that the conventional diabatic approximation is unable to capture some prominent features arising from driving such as the continuity of the probability density of work. Our results reveal the necessity of using accurate expressions for the drive-dressed heat exchange in future experiments probing jump time distributions.Comment: 15 pages, 5 figure

Moments of work in the two-point measurement protocol for a driven open quantum system

We study the distribution of work induced by the two-point measurement protocol for a driven open quantum system. We first derive a general form for the generating function of work for the total system, bearing in mind that the Hamiltonian does not necessarily commute with its time derivative. Using this result, we then study the first few moments of work by using the master equation of the reduced system, invoking approximations similar to the ones made in the microscopic derivation of the reduced density matrix. Our results show that already in the third moment of work, correction terms appear that involve commutators between the Hamiltonian and its time derivative. To demonstrate the importance of these terms, we consider a sinusoidally, weakly driven and weakly coupled open two-level quantum system, and indeed find that already in the third moment of work, the correction terms are significant. We also compare our results to those obtained with the quantum jump method and find a good agreement.Peer reviewe

Synchronous Counting and Computational Algorithm Design

Consider a complete communication network on $n$ nodes, each of which is a state machine. In synchronous 2-counting, the nodes receive a common clock pulse and they have to agree on which pulses are "odd" and which are "even". We require that the solution is self-stabilising (reaching the correct operation from any initial state) and it tolerates $f$ Byzantine failures (nodes that send arbitrary misinformation). Prior algorithms are expensive to implement in hardware: they require a source of random bits or a large number of states. This work consists of two parts. In the first part, we use computational techniques (often known as synthesis) to construct very compact deterministic algorithms for the first non-trivial case of $f = 1$. While no algorithm exists for $n < 4$, we show that as few as 3 states per node are sufficient for all values $n \ge 4$. Moreover, the problem cannot be solved with only 2 states per node for $n = 4$, but there is a 2-state solution for all values $n \ge 6$. In the second part, we develop and compare two different approaches for synthesising synchronous counting algorithms. Both approaches are based on casting the synthesis problem as a propositional satisfiability (SAT) problem and employing modern SAT-solvers. The difference lies in how to solve the SAT problem: either in a direct fashion, or incrementally within a counter-example guided abstraction refinement loop. Empirical results suggest that the former technique is more efficient if we want to synthesise time-optimal algorithms, while the latter technique discovers non-optimal algorithms more quickly

Quantifying non-Markovianity due to driving and a finite-size environment in an open quantum system

We study non-Markovian effects present in a driven qubit coupled to a finite environment using a recently proposed model developed in the context of calorimetric measurements of open quantum systems. To quantify the degree of non-Markovianity we use the Breuer-Laine-Piilo (BLP) measure [H.-P. Breuer, Phys. Rev. Lett. 103, 210401 (2009)]. We show that information backflow only occurs in the case of driving, in which case we investigate the dependence of memory effects on the environment size, driving amplitude, and coupling to the environment. We show that the degree of non-Markovianity strongly depends on the ratio between the driving amplitude and the coupling strength. We also show that the degree of non-Markovianity does not decrease monotonically as a function of the environment size

Current knowledge on biomarkers for contact sensitization and allergic contact dermatitis.

Contact sensitization is common and affects up to 20% of the general population. The clinical manifestation of contact sensitization is allergic contact dermatitis. This is a clinical expression that is sometimes difficult to distinguish from other types of dermatitis, for example irritant and atopic dermatitis. Several studies have examined the pathogenesis and severity of allergic contact dermatitis by measuring the absence or presence of various biomarkers. In this review, we provide a non-systematic overview of biomarkers that have been studied in allergic contact dermatitis. These include genetic variations and mutations, inflammatory mediators, alarmins, proteases, immunoproteomics, lipids, natural moisturizing factors, tight junctions, and antimicrobial peptides. We conclude that, despite the enormous amount of data, convincing specific biomarkers for allergic contact dermatitis are yet to be described