Optimal Kullback-Leibler Aggregation via Information Bottleneck

In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost; The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a sub-optimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.Comment: 13 pages, 4 figure

The Time Course of Gene Expression during Reactive Gliosis in the Optic Nerve

Reactive gliosis is a complex process that involves changes in gene expression and morphological remodeling. The mouse optic nerve, where astrocytes, microglia and oligodendrocytes interact with retinal ganglion cell axons and each other, is a particularly suitable model for studying the molecular mechanisms of reactive gliosis. We triggered gliosis at the mouse optic nerve head by retro orbital nerve crush. We followed the expression profiles of 14,000 genes from 1 day to 3 months, as the optic nerve formed a glial scar. The transcriptome showed profound changes. These were greatest shortly after injury; the numbers of differentially regulated genes then dropped, returning nearly to resting levels by 3 months. Different genes were modulated with very different time courses, and functionally distinct groups of genes responded in partially overlapping waves. These correspond roughly to two quick waves of inflammation and cell proliferation, a slow wave of tissue remodeling and debris removal, and a final stationary phase that primarily reflects permanent structural changes in the axons. Responses from astrocytes, microglia and oligodendrocytes were distinctively different, both molecularly and morphologically. Comparisons to other models of brain injury and to glaucoma indicated that the glial responses depended on both the tissue and the injury. Attempts to modulate glial function after axonal injuries should consider different mechanistic targets at different times following the insult

Source or decomposition of soil organic matter: what is more important with increasing forest age in a subalpine setting?

Afforestation has been the dominant land-use change in the Swiss Alps during the last decades which has not only the potential to increase soil organic carbon sequestration, but it has also the potential to alter soil organic matter (SOM) dynamics through the vegetation shift and change in organic matter (OM) input into soils. The effects of afforestation on SOM dynamics, however, are still not fully understood as specific sources of OM and modifications of soil processes influencing decomposition and preservation remain largely unknown on alpine to subalpine slopes. Within this study we aimed to identify the potential sources and the decomposition of OM in a subalpine afforestation chrono-sequence (0–130 years) with Norway spruce (Picea abies L.) on a former pasture by using a multi-proxy molecular marker approach. We observed that leaf-derived OM plays an essential role in the pasture areas, while root-derived OM only plays a minor role in pasture and forest areas. Needle-derived OM represents the dominant source of SOM with increasing forest age, while understory shrubs and moss also contribute to the OM input in younger forest stand ages. However, needle litter and buildup of organic layers and subsequently less input of fresh OM from organic horizons to mineral soil can result in increased OM decomposition in mineral soils rather than contributing to additional SOM stabilization in mineral soils. This was most pronounced in the oldest forest stand (130-year-old) in the investigated afforestation sequence, particularly in deeper soil horizons (10–45 cm). Thereby, our study provides new insights into SOM dynamics following afforestation, especially with respect to the long-term SOM sequestration potential of afforestation of subalpine pasture soils

Coherent collisional spin dynamics in optical lattices

We report on the observation of coherent, purely collisionally driven spin dynamics of neutral atoms in an optical lattice. For high lattice depths, atom pairs confined to the same lattice site show weakly damped Rabi-type oscillations between two-particle Zeeman states of equal magnetization, induced by spin changing collisions. This paves the way towards the efficient creation of robust entangled atom pairs in an optical lattice. Moreover, measurement of the oscillation frequency allows for precise determination of the spin-changing collisional coupling strengths, which are directly related to fundamental scattering lengths describing interatomic collisions at ultracold temperatures.Comment: revised version; 4 pages, 5 figure

Wake structure and kinematics in two insectivorous bats

We compare kinematics and wake structure over a range of flight speeds (4.0–8.2 m s(−1)) for two bats that pursue insect prey aerially, Tadarida brasiliensis and Myotis velifer. Body mass and wingspan are similar in these species, but M. velifer has broader wings and lower wing loading. By using high-speed videography and particle image velocimetry of steady flight in a wind tunnel, we show that three-dimensional kinematics and wake structure are similar in the two species at the higher speeds studied, but differ at lower speeds. At lower speeds, the two species show significant differences in mean angle of attack, body–wingtip distance and sweep angle. The distinct body vortex seen at low speed in T. brasiliensis and other bats studied to date is considerably weaker or absent in M. velifer. We suggest that this could be influenced by morphology: (i) the narrower thorax in this species probably reduces the body-induced discontinuity in circulation between the two wings and (ii) the wing loading is lower, hence the lift coefficient required for weight support is lower. As a result, in M. velifer, there may be a decreased disruption in the lift generation between the body and the wing, and the strength of the characteristic root vortex is greatly diminished, both suggesting increased flight efficiency. This article is part of the themed issue ‘Moving in a moving medium: new perspectives on flight’

Evaluation of competences at the community pharmacy settings

The General Level Framework (GLF) document provides a model to be used in evaluating and upgrading of pharmacists’ competences currently used in many countries. This study has several Objectives: To show the adaptation process of the GLF document to the Serbian pharmaceutical work practices and regulations; to illustrate the implementation of the GLF document; to evaluate and monitor the development of pharmacists’ competencies. Materials and Methods: The adaptation, analysis, validation and adjustment of the GLF document were conducted using the expert panel method. The implementation was conducted on a sample of pharmacists employed in Subotica Pharmacy chain. Later, the evaluation of the pharmacists’ competencies was performed at two observation points (at the beginning of the study and after 6 months) by the team of seven GLF members. Results and Discussion: The GLF document was reviewed by 14 members of the expert panel. During the content validation performed at the expert panel meeting, all competencies stated in the GLF document were rated according to their importance with an average grade of between 8.26 and 9.80 and thus reached a consensus regarding all 26 competencies. During the evaluation of the pharmacists’ competences, the greatest improvement after the second observation was noted in the “Patient consent” competency, followed by the “Drug history”, “The prescription is legal“, “Health needs”, “Provision of written information” and “Assessing outcomes of contributions” competencies. All the competencies in the GLF document were accepted for the implementation in the Subotica Pharmacy chain. Six of the competencies there was a significant improvement observed

Long lived transients in gene regulation

Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof

Hamiltonian and physical Hilbert space in polymer quantum mechanics

In this paper, a version of polymer quantum mechanics, which is inspired by loop quantum gravity, is considered and shown to be equivalent, in a precise sense, to the standard, experimentally tested, Schroedinger quantum mechanics. The kinematical cornerstone of our framework is the so called polymer representation of the Heisenberg-Weyl (H-W) algebra, which is the starting point of the construction. The dynamics is constructed as a continuum limit of effective theories characterized by a scale, and requires a renormalization of the inner product. The result is a physical Hilbert space in which the continuum Hamiltonian can be represented and that is unitarily equivalent to the Schroedinger representation of quantum mechanics. As a concrete implementation of our formalism, the simple harmonic oscillator is fully developed.Comment: 19 pages, 2 figures. Comments and references added. Version to be published in CQ