Geometry and Topology of Escape II: Homotopic Lobe Dynamics

We continue our study of the fractal structure of escape-time plots for chaotic maps. In the preceding paper, we showed that the escape-time plot contains regular sequences of successive escape segments, called epistrophes, which converge geometrically upon each endpoint of every escape segment. In the present paper, we use topological techniques to: (1) show that there exists a minimal required set of escape segments within the escape-time plot; (2) develop an algorithm which computes this minimal set; (3) show that the minimal set eventually displays a recursive structure governed by an ``Epistrophe Start Rule'': a new epistrophe is spawned Delta = D+1 iterates after the segment to which it converges, where D is the minimum delay time of the complex.Comment: 13 pages, 8 figures, to appear in Chaos, second of two paper

Geometry and Topology of Escape I: Epistrophes

We consider a dynamical system given by an area-preserving map on a two-dimensional phase plane and consider a one-dimensional line of initial conditions within this plane. We record the number of iterates it takes a trajectory to escape from a bounded region of the plane as a function along the line of initial conditions, forming an ``escape-time plot''. For a chaotic system, this plot is in general not a smooth function, but rather has many singularities at which the escape time is infinite; these singularities form a complicated fractal set. In this article we prove the existence of regular repeated sequences, called ``epistrophes'', which occur at all levels of resolution within the escape-time plot. (The word ``epistrophe'' comes from rhetoric and means ``a repeated ending following a variable beginning''.) The epistrophes give the escape-time plot a certain self-similarity, called ``epistrophic'' self-similarity, which need not imply either strict or asymptotic self-similarity.Comment: 15 pages, 9 figures, to appear in Chaos, first of two paper

Depth profiling of the elemental surface composition of the oral microorganism S. salivarius HB and fibrillar mutants by X-ray photoelectron spectroscopy

X-ray photoelectron spectroscopy (XPS) on microbial cell surfaces requires freeze-drying of cells, and as a result, the cell surface appendages flatten out on the cell surface and form a collapsed fibrillar mass. At present, it is unclear how the density, length and composition of these fibrils influence the elemental surface composition as probed by XPS. The sampling depth of XPS can be varied by changing the electron take-off angle. In this article, we made a depth profiling of the collapsed fibrillar mass of Streptococcus salivarius HB and fibril-deficient mutants by angle-dependent XPS. Methylamine tungstate negative staining and ruthenium red staining followed by sectioning revealed distinct classes of fibrils with various lengths on each of the strains. Interpretation of the angle dependence of the oxygen/carbon (O/C) and phosphorus/carbon (P/C) surface concentration ratios of these strains was difficult. However, the angle dependence of the nitrogen/carbon (N/C) surface concentration ratio could be fully interpreted: N/C did not vary with sampling depth on a bald strain, S. salivarius HBC12 and on S. salivarius HB7, a strain with a dense array of fibrils of uniform length. N/C decreased with sampling depth in case of a sparsely fibrillated strain, S. salivarius HBV51 and eventually reached the value observed for the bald strain, HBC12. A high N/C at small sampling depth was observed for S. salivarius HB with protruding, protein rich fibrils. We conclude that elemental depth profiling of microbial cell surfaces by XPS can be interpreted to coincide with structural and biochemical information on the cell surface as obtained by electron microscopy and can therefore be considered as a useful technique to study structural features of cell surfaces in combination with electron microscopy.</p

White matter integrity as a predictor of response to treatment in first episode psychosis

The integrity of brain white matter connections is central to a patient's ability to respond to pharmacological interventions. This study tested this hypothesis using a specific measure of white matter integrity, and examining its relationship to treatment response using a prospective design in patients within their first episode of psychosis. Diffusion tensor imaging data were acquired in 63 patients with first episode psychosis and 52 healthy control subjects (baseline). Response was assessed after 12 weeks and patients were classified as responders or non-responders according to treatment outcome. At this second time-point, they also underwent a second diffusion tensor imaging scan. Tract-based spatial statistics were used to assess fractional anisotropy as a marker of white matter integrity. At baseline, non-responders showed lower fractional anisotropy than both responders and healthy control subjects (P < 0.05; family-wise error-corrected), mainly in the uncinate, cingulum and corpus callosum, whereas responders were indistinguishable from healthy control subjects. After 12 weeks, there was an increase in fractional anisotropy in both responders and non-responders, positively correlated with antipsychotic exposure. This represents one of the largest, controlled investigations of white matter integrity and response to antipsychotic treatment early in psychosis. These data, together with earlier findings on cortical grey matter, suggest that grey and white matter integrity at the start of treatment is an important moderator of response to antipsychotics. These findings can inform patient stratification to anticipate care needs, and raise the possibility that antipsychotics may restore white matter integrity as part of the therapeutic response

Association of a Novel High Molecular Weight, Serine-Rich Protein (SrpA) with Fibril-Mediated Adhesion of the Oral Biofilm Bacterium Streptococcus Cristatus

The surface of the oral plaque bacterium Streptococcus cristatus is decorated with a lateral tuft of fibrils. The fibrillar tuft functions in the adhesion of S. cristatus to heterologous bacterial species in the plaque biofilm. The tuft typically consists of a densely packed fringe of shorter fibrils 238 ± 19 nm long with longer, less abundant fibrils 403 ± 66 nm long projecting through the fringe of short fibrils. The two types of fibrils in the tufts of S. cristatus have been refractory to biochemical separation, complicating their characterization. A hexadecane partition assay was used to enrich for subpopulations of S. cristatus CR311 (type strain NCTC 12479) having distinct fibrillar morphotypes. Negative staining in the TEM revealed that cells of a hydrophobic subpopulation of S. cristatus (CR311var1) carried only the long fibrils (395 ± 32 nm). A hydrophilic subpopulation of S. cristatus (CR311var3) consisted of mixed morphotypes having no fibrils or remnant short fibrils (223 ± 49 nm). No long fibrils were observed on any cells in the CR311var3 subpopulation. The CR311var3 morphotype, unlike the wild-type strain and CR311var1, was not able to form corncobs with either Corynebacterium matruchotii or Fusobacterium nucleatum. Variant CR311var3 did not express the novel gene srpA, which encodes a high molecular weight (321,882 Da) serine-rich protein, SrpA. The SrpA protein contains two extensive repeat motifs of 17 and 71 amino acids and a gram-positive cell wall anchor consensus sequence (LPNTG). The unusual properties of SrpA most closely resemble those of Fap1, the fimbrial-associated adhesin protein of Streptococcus parasanguis. The association of long fibrils, high surface hydrophobicity, ability to form corncob formations, and expression of the srpA gene suggest that SrpA is a long fibril protein in S. cristatus

Design of the Spitzer Space Telescope Heritage Archive

It is predicted that Spitzer Space Telescope’s cryogen will run out in April 2009, and the final reprocessing for the cryogenic mission is scheduled to end in April 2011, at which time the Spitzer archive will be transferred to the NASA/IPAC Infrared Science Archive (IRSA) for long-term curation. The Spitzer Science Center (SSC) and IRSA are collaborating to design and deploy the Spitzer Heritage Archive (SHA), which will supersede the current Spitzer archive. It will initially contain the raw and final reprocessed cryogenic science products, and will eventually incorporate the final products from the Warm mission. The SHA will be accompanied by tools deemed necessary to extract the full science content of the archive and by comprehensive documentation

Mapping urban green infrastructure : a novel landscape-based approach to incorporating land-use and land-cover in the mapping of human-dominated systems

Common approaches to mapping green infrastructure in urbanized landscapes invariably focus on measures of land-use or land-cover and associated functional or physical traits. However, such one-dimensional perspectives do not accurately capture the character and complexity of the landscapes in which urban inhabitants live. The new approach presented in this paper demonstrates how open-source, high spatial and temporal resolution data with global coverage can be used to measure and represent the landscape qualities of urban environments. Through going beyond simple metrics of quantity, such as percentage green and blue cover it is now possible to explore the extent to which landscape quality helps to unpick the mixed evidence presented in the literature on the benefits of urban nature to human well-being. Here we present a landscape approach, employing remote sensing, GIS and data reduction techniques, to map urban green infrastructure elements in a large UK city-region. Comparison with existing urban datasets demonstrates considerable improvement in terms of coverage and thematic detail. The characterisation of landscapes, using census tracts as spatial units, and subsequent exploration of associations with social-ecological attributes highlights the further detail which can be uncovered with the approach. For example, eight urban landscape types identified for the case study city exhibited associations with distinct socio-economic conditions accountable not only to quantities but also qualities of green and blue space. The identification of individual landscape features through simultaneous measures of land-use and land cover demonstrated unique and significant associations between the former and indicators of human health and ecological condition. The approach may therefore provide a promising basis for developing further insight into the processes and characteristics which affect human health and wellbeing in urban areas, both in the UK and beyond

A Research-Based Curriculum for Teaching the Photoelectric Effect

Physics faculty consider the photoelectric effect important, but many erroneously believe it is easy for students to understand. We have developed curriculum on this topic including an interactive computer simulation, interactive lectures with peer instruction, and conceptual and mathematical homework problems. Our curriculum addresses established student difficulties and is designed to achieve two learning goals, for students to be able to (1) correctly predict the results of photoelectric effect experiments, and (2) describe how these results lead to the photon model of light. We designed two exam questions to test these learning goals. Our instruction leads to better student mastery of the first goal than either traditional instruction or previous reformed instruction, with approximately 85% of students correctly predicting the results of changes to the experimental conditions. On the question designed to test the second goal, most students are able to correctly state both the observations made in the photoelectric effect experiment and the inferences that can be made from these observations, but are less successful in drawing a clear logical connection between the observations and inferences. This is likely a symptom of a more general lack of the reasoning skills to logically draw inferences from observations.Comment: submitted to American Journal of Physic

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

Environmental DNA (eDNA ) analysis is a rapid, cost‐effective, non‐invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species‐specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and “metabarcoding” have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA . We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real‐time quantitative PCR (qPCR ) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using high‐throughput sequencing technology. With qPCR and a detection threshold of 1 of 12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4 of 12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species‐specific surveys