Sustainable Soesterkwartier

The municipality of Amersfoort wants to construct an endurable and sustainable eco-town in the Soesterkwartier neighbourhood, by taking future climate change into account. The impact of climate change at the location of the proposed eco-town was studied by a literature review

Thermal behavior of Quantum Cellular Automaton wires

We investigate the effect of a finite temperature on the behavior of logic circuits based on the principle of Quantum Cellular Automata (QCA) and of ground state computation. In particular, we focus on the error probability for a wire of QCA cells that propagates a logic state. A numerical model and an analytical, more approximate, model are presented for the evaluation of the partition function of such a system and, consequently, of the desired probabilities. We compare the results of the two models, assessing the limits of validity of the analytical approach, and provide estimates for the maximum operating temperature.Comment: 15 pages, 7 figures, uses revte

Contrasting timing of parturition of chital Axis axis and gaur Bos gaurus in tropical South India - the role of body mass and seasonal forage quality

Seasonal variation in forage availability and quality is understood to affect the annual timing of parturition in large herbivores. In India-where seasonal monsoonal rains define variation in forage availability and quality-chital Axis axis exhibit stronger seasonality in parturition than the larger gaur Bos gaurus. We hypothesized that this difference can be explained by forage requirements determined by body mass. We developed a model to simulate changes in leaf biomass and nitrogen content based on plant available moisture and nutrients, and calibrated our model with field data. Our results show that the minimum forage nitrogen content required by lactating gaur was available throughout the year, but that required by lactating chital was available for less than 40% of the year, i.e. during the early wet season, which coincides with the annual peak period of chital births. The three to four month spread of chital births, which begins in the dry season, implies that the period of highest quality is also important for females to replenish maternal reserves for future reproduction and help maximize the growth rate of neonates. This spread also indicates low synchrony of chital births and suggests that predator swamping was less important in influencing their timing of parturition. As monsoonal rain exhibits annual temporal variation, we analyzed our model under different rainfall patterns while keeping the total annual rainfall constant. We found that the difference between the durations of how long forage quality is available to satisfy the minimum requirements of lactating gaur and lactating chital is similar for all simulated patterns. This insensitivity to variable rainfall patterns lends support to our hypothesis that forage requirements determined by body mass is one plausible explanation for the variation in parturition strategies among large herbivores species

Oligotrophy and pelagic marine bacteria:Facts and fiction

Oligotrophy, or the inability of bacterial cells to propagate at elevated nutrient concentrations, is a controversial phenomenon in microbiology. The exact cause of the unculturability of many indigenous marine bacteria on standard laboratory media has still not been resolved. Unfortunately the physiology of such cells is difficult to investigate as long as high cell density cultures cannot be obtained. An extensive evaluation of experiments relating to oligotrophy and the cultivation of marine bacteria is presented in this review. When incorporating the findings of studies performed with molecular biological methods, the picture emerges that indigenous marine bacteria can be cultivated under certain conditions and that the 'oligotrophic way of life' is a transient characteristic. Although strong generalisations should not be made with respect to a biological system as diverse as the world's oceans, it should be anticipated that cells with unique physiological characteristics appear to exist in the oceanic system. When combining conventional physiological approaches with molecular biological techniques it is feasible to unveil the phenotypes that go with the encountered genotypes. In view of the enormous complexity of the oceanic system this will prove an ambitious, yet resourceful undertaking

Robust detection of alternative splicing in a population of single cells

Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3′ bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis of transcriptome variation to the gene level. To address these limitations, we developed SingleSplice, which uses a statistical model to detect genes whose isoform usage shows biological variation significantly exceeding technical noise in a population of single cells. Importantly, SingleSplice is tailored to the unique demands of single cell analysis, detecting isoform usage differences without attempting to infer expression levels for full-length transcripts. Using data from spike-in transcripts, we found that our approach detects variation in isoform usage among single cells with high sensitivity and specificity. We also applied SingleSplice to data from mouse embryonic stem cells and discovered a set of genes that show significant biological variation in isoform usage across the set of cells. A subset of these isoform differences are linked to cell cycle stage, suggesting a novel connection between alternative splicing and the cell cycle

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data

Accuracy of trajectory reconstruction using a subset of cells. (a) Graph showing how similar the SLICER trajectory is when computed using a random subset of lung cells. The blue bars show the similarity in cell ordering (units are percent sorted with respect to the trajectory constructed from all cells). The orange bars show the similarity in branch assignments (percentage of cells assigned to the same branch as the trajectory constructed from all cells). The values shown were obtained by averaging the results from five subsampled datasets for each percentage (80 %, 60 %, 40 %, and 20 %). (b) Order preservation and branch identity values computed as in panel (a), but for datasets sampled from the neural stem cell dataset. (PDF 106 kb

Reorganization of self-assembled DNA-based polymers using orthogonally addressable building blocks

Nature uses non-covalent interactions to achieve structural dynamic reconfiguration of biopolymers. Taking advantage of the programmability of DNA/DNA interactions we report here the rational design of orthogonal DNA-based addressable tiles that self-assemble into polymer-like structures that can be reconfigured by external inputs. The different tiles share the same sticky ends responsible for self-assembly but are rationally designed to contain a specific regulator-binding domain that can be orthogonally targeted by different DNA regulator strands. We show that by sequentially adding specific inputs it is possible to re-organize the formed structures to display well-defined distributions: homopolymers, random and block structures. The versatility of the systems presented in this study shows the ease with which DNA-based addressable monomers can be designed to create reconfigurable micron-scale DNA structures offering a new approach to the growing field of supramolecular polymers