Biostatistical design and analysis using R: A practical guide (book review)

Book revie

Approximate Self-Assembly of the Sierpinski Triangle

The Tile Assembly Model is a Turing universal model that Winfree introduced in order to study the nanoscale self-assembly of complex (typically aperiodic) DNA crystals. Winfree exhibited a self-assembly that tiles the first quadrant of the Cartesian plane with specially labeled tiles appearing at exactly the positions of points in the Sierpinski triangle. More recently, Lathrop, Lutz, and Summers proved that the Sierpinski triangle cannot self-assemble in the "strict" sense in which tiles are not allowed to appear at positions outside the target structure. Here we investigate the strict self-assembly of sets that approximate the Sierpinski triangle. We show that every set that does strictly self-assemble disagrees with the Sierpinski triangle on a set with fractal dimension at least that of the Sierpinski triangle (roughly 1.585), and that no subset of the Sierpinski triangle with fractal dimension greater than 1 strictly self-assembles. We show that our bounds are tight, even when restricted to supersets of the Sierpinski triangle, by presenting a strict self-assembly that adds communication fibers to the fractal structure without disturbing it. To verify this strict self-assembly we develop a generalization of the local determinism method of Soloveichik and Winfree

An optimal method of moments to measure the charge asymmetry at the Z0Z^0

Parity violation at LEP or SLC can be measured through the charge asymmetry. An optimal method of moments is developed here to measure this asymmetry, as well as similar asymmetries. This method is equivalent to the likelihood fit. It is simpler in use, as it gives analytical formulas for both the asymmetry and its statistical error. These formulas give the dependence of the accuracy on the experimental angular acceptance explicitly.Comment: 7 pages of uuencoded postscript, NIKHEF preprint NIKHEF-H/94-0

Scaled tree fractals do not strictly self-assemble

In this paper, we show that any scaled-up version of any discrete self-similar {\it tree} fractal does not strictly self-assemble, at any temperature, in Winfree's abstract Tile Assembly Model.Comment: 13 pages, 3 figures, Appeared in the Proceedings of UCNC-2014, pp 27-39; Unconventional Computation and Natural Computation - 13th International Conference, UCNC 2014, London, ON, Canada, July 14-18, 2014, Springer Lecture Notes in Computer Science ISBN 978-3-319-08122-

Engineering vascularised tissues in vitro

Tissue engineering aims at replacing or regenerating tissues lost due to diseases or traumas (Langer and Vacanti, 1993). However, mimicking in vitro the physiological complexity of vascularized tissue is a major obstacle, which possibly contributes to impaired healing in vivo. In higher organisms, native features including the vascular network, the lymphatic networks and interstitial flow promote both mass transport and organ development. Attempts to mimic those features in engineered tissues will lead to more clinically relevant cell-based therapies. Aside from current strategies promoting angiogenesis from the host, an alternative concept termed prevascularization is emerging. It aims at creating a biological vasculature inside an engineered tissue prior to implantation. This vasculature can rapidly anastamose with the host and enhances tissue survival and differentiation. Interestingly, growing evidence supports a role of the vasculature in regulating pattern formation and tissue differentiation. Thus, prevascularized tissues also benefit from an intrinsic contribution of their vascular system to their development. From those early attempts are emerging a body of principles and strategies to grow and maintain, in vitro, those self-assembled biological vascular networks. This could lead to the generation of engineered tissues of more physiologically relevant complexity and improved regenerative potential

Comparison of N. Atlantic heat storage estimates during the Argo period (1999–2010)

Ocean heat storage is an essential component of the climate system and there is considerable interest in its accurate evaluation. There are a number of heat storage products produced by many different groups. These products are derived from Argo as well as other platforms, for example XBT and CTD, in the last decade. Here we compare two heat storage estimates for the North Atlantic 0–2000 m from 10° to 70° N. One derived solely from Argo data whilst the other is derived from Argo and other platforms. It is found that there is a positive trend in heat storage over the period 1999–2010. This trend is influenced by a strong air–sea interaction event in 2009–2010, and this reduces the upward trend 1999–2008 identified previously. Both data sets are consistent with each other for the layer 0–1000 m on a timescale of beyond 1 yr. There are significant differences at sub-annual time scales and in the layer 1000–2000 m

Modelling the Choice of Car Parks in Urban Areas and Managing the Demand for Parking.

Car parks are an essential piece of infrastructure associated with the road networks, yet commonly available traffic assignment models do not to explicitly integrate them into the modelling process. This research attempts to integrate the choice of car parks in urban areas into the travellers’ route choice and incorporates both the route and car park choice in a joint modelling framework of traffic assignment based on equilibrium approach. This paper illustrates the implementation of the model in a commonly used standard suite of traffic assignment software. The proposed method considers multiple user classes - commuter and non-commuter flows, and involves modelling the demand for short stay and long stay car parks over multiple departure periods. A special search time delay function has been developed to represent the disutility in searching for a place in a car park, which is integrated further into the function of generalised cost of travel. This technique has been successfully applied to study the choice of car parks in the case of a simple hypothetical network. Another larger numerical example illustrates the case of managing the demand between two car parks in Leeds, England

How do microorganisms reach the stratosphere?

A number of studies have demonstrated that bacteria and fungi are present in the stratosphere. Since the tropopause is generally regarded as a barrier to the upward movement of particles it is difficult to see how such microorganisms can reach heights above 17 km. Volcanoes provide an obvious means by which this could be achieved, but these occur infrequently and any microorganisms entering the stratosphere from this source will rapidly fall out of the stratosphere. Here, we suggest mechanisms by which microorganisms might reach the stratosphere on a more regular basis; such mechanisms are, however, likely only to explain how micrometre to submicrometre particles could be elevated into the stratosphere. Intriguingly, clumps of bacteria of size in excess of 10 μm have been found in stratospheric samples. It is difficult to understand how such clumps could be ejected from the Earth to this height, suggesting that such bacterial masses may be incoming to Earth. We suggest that the stratospheric microflora is made up of two components: (a) a mixed population of bacteria and fungi derived from Earth, which can occasionally be cultured; and (b) a population made up of clumps of, viable but non-culturable, bacteria which are too large to have originated from Earth; these, we suggest, have arrived in the stratosphere from space. Finally, we speculate on the possibility that the transfer of bacteria from the Earth to the highly mutagenic stratosphere may have played a role in bacterial evolution