Conditioning the logistic branching process on non-extinction

We consider a birth and death process in which death is due to both `natural death' and to competition between individuals, modelled as a quadratic function of population size. The resulting `logistic branching process' has been proposed as a model for numbers of individuals in populations competing for some resource, or for numbers of species. However, because of the quadratic death rate, even if the intrinsic growth rate is positive, the population will, with probability one, die out in finite time. There is considerable interest in understanding the process conditioned on non-extinction. In this paper, we exploit a connection with the ancestral selection graph of population genetics to find expressions for the transition rates in the logistic branching process conditioned on survival until some fixed time $T$, in terms of the distribution of a certain one-dimensional diffusion process at time $T$. We also find the probability generating function of the Yaglom distribution of the process and rather explicit expressions for the transition rates for the so-called Q-process, that is the logistic branching process conditioned to stay alive into the indefinite future. For this process, one can write down the joint generator of the (time-reversed) total population size and what in population genetics would be called the `genealogy' and in phylogenetics would be called the `reconstructed tree' of a sample from the population. We explore some ramifications of these calculations numerically

Assessment of selected soil parameters in a long-term Western Canadian organic field experiment

A long-term field study was used to compare soil nitrogen and phosphorous status, and soil aggregate stability in organic and conventional cropping systems. Two rotations were tested: a grain only and a grain-alfalfa hay rotation. The organic systems had a lower nitrate leaching potential than the same rotations under conventional management. After 13 years, one organic system (the grain-alfalfa; no manure return) is suffering serious soil P depletion. However, the grain only and the grain-alfalfa with manure return to land systems had soil P levels similar to the prairie grass control treatment and showed no signs of P deficiency. Despite having lower levels of organic carbon, the organic soils had higher levels of wet aggregate stability than conventionally managed soils

Design for Service Innovation & Development. Final Report

This is an AHRC research report exploring design's contribution to Service Innovation and New Service Development

Associations between maternal depressive symptoms and child feeding practices in a cross-sectional study of low-income mothers and their young children

Background: Maternal depression may influence feeding practices important in determining child eating behaviors and weight. However, the association between maternal depressive symptoms and feeding practices has been inconsistent, and most prior studies used self-report questionnaires alone to characterize feeding. The purpose of this study was to identify feeding practices associated with maternal depressive symptoms using multiple methodologies, and to test the hypothesis that maternal depressive symptoms are associated with less responsive feeding practices. Methods: In this cross-sectional, observational study, participants (n = 295) included low-income mothers and their 4- to 8-year-old children. Maternal feeding practices were assessed via interviewer-administered questionnaires, semi-structured narrative interviews, and videotaped observations in home and laboratory settings. Maternal depressive symptoms were measured using the Center for Epidemiologic Studies-Depression scale (CES-D). Regression analyses examined associations between elevated depressive symptoms (CES-D score ≥16) and measures of maternal feeding practices, adjusting for: child sex, food fussiness, number of older siblings; and maternal age, body mass index (BMI), education, race/ethnicity, single parent status, perceived child weight, and concern about child weight. Results: Thirty-one percent of mothers reported depressive symptoms above the screening cutoff. Mothers with elevated depressive symptoms reported more pressuring of children to eat (β = 0.29; 95% Confidence Interval (CI): 0.03, 0.54) and more overall demandingness (β = 0.16; 95% CI: 0.03, 0.29), and expressed lower authority in child feeding during semi-structured narrative interview (Odds Ratio (OR) for low authority: 2.82; 95% CI: 1.55, 5.12). In homes of mothers with elevated depressive symptoms, the television was more likely audible during meals (OR: 1.91; 95% CI: 1.05, 3.48) and mothers were less likely to eat with children (OR: 0.48; 95% CI: 0.27, 0.85). There were no associations between maternal depressive symptoms and encouragement or discouragement of food in laboratory eating interactions. Conclusions: Mothers with elevated depressive symptoms demonstrated less responsive feeding practices than mothers with lower levels of depressive symptoms. These results suggest that screening for maternal depressive symptoms may be useful when counseling on healthy child feeding practices. Given inconsistencies across methodologies, future research should include multiple methods of characterizing feeding practices and direct comparisons of different methodologies

Genomic and biologic comparisons of cyprinid herpesvirus 3 strains

Cyprinid herpesvirus 3 (CyHV-3) is the archetypal fish alloherpesvirus and the etiologic agent of a lethal disease in common and koi carp. To date, the genome sequences of only four CyHV-3 isolates have been published, but no comparisons of the biologic properties of these strains have been reported. We have sequenced the genomes of a further seven strains from various geographical sources, and have compared their growth in vitro and virulence in vivo. The major findings were: (i) the existence of the two genetic lineages previously described as European and Asian was confirmed, but inconsistencies between the geographic origin and genotype of some strains were revealed; (ii) potential inter-lineage recombination was detected in one strain, which also suggested the existence of a third, as yet unidentified lineage; (iii) analysis of genetic disruptions led to the identification of non-essential genes and their potential role in virulence; (iv) comparison of the in vitro and in vivo properties of strains belonging to the two lineages revealed that inter-lineage polymorphisms do not contribute to the differences in viral fitness observed; and (v) a negative correlation was observed among strains between viral growth in vitro and virulence in vivo. This study illustrates the importance of coupling genomic and biologic comparisons of viral strains in order to enhance understanding of viral evolution and pathogenesis

Effectiveness of Nanolime as a Stone Consolidant: A 4-Year Study of Six Common UK Limestones

Protecting stone buildings from weathering and decay is a major challenge in the conservation of built heritage. Most of the stone consolidants currently available are well suited to silicate stones, but are less compatible with limestone. In this paper we present for the first time the results over a 4-year period of various consolidation treatments carried out using nanolime on 6 of the most representative and significant stones used in historic buildings in the United Kingdom. Tests investigated the influence of stone type, environmental conditions and pre-treatments on the effectiveness of the consolidation treatment. A comprehensive and rigorous testing programme was carried out to evaluate the short (12 weeks) and longer-term (4 years) effects. Stone samples were characterised before and after treatment using light and electron microscopy, sorptivity tests and a novel methodology employing drilling resistance to interrogate the near surface effects. Results show that for some of the stones, such as Clunch and Bath Stone, the positive effect of the treatment with nanolime is noticeable after 4 years since application. However, results for other stones such as Portland and magnesian limestone showed that the initial beneficial effect of the treatment is reduced after 4 years. Nanolime treatment of Ham Stone produced an unnoticeable effect on the continuous natural reduction of the drilling resistance of the specimen over time. The results presented are of immense value to conservators as they provide essential guidance on the most appropriate repair approach. Impact to the conservation industry will be to avoid the use of nanolime on stones where there is no perceivable benefit, reducing the risk of adverse effects, including potential damage to buildings. In additional costs will be saved which might otherwise have been spent on ineffective treatments

Label-Free Analysis and Sorting of Microalgae and Cyanobacteria in Microdroplets by Intrinsic Chlorophyll Fluorescence for the Identification of Fast Growing Strains.

Microalgae and cyanobacteria are promising organisms for sustainable biofuel production, but several challenges remain to make this economically viable, including identification of optimized strains with high biomass productivity. Here we report on a novel methodology for the label-free screening and sorting of cyanobacteria and microalgae in a microdroplet platform. We show for the first time that chlorophyll fluorescence can be used to measure differences in biomass between populations of picoliter microdroplets containing different species of cyanobacteria, Synechocystis PCC 6803 and Synechococcus PCC 7002, which exhibit different growth dynamics in bulk culture. The potential and robustness of this label-free screening approach is further demonstrated by the screening and sorting of cells of the green alga Chlamydomonas reinhardtii encapsulated in droplets.Author R.J.B. was supported by a Doctoral Training Grant from the Engineering and Physical Sciences Research Council (EPSRC) of the UK (Reference EP/P505445/1), and author J.J.L. was in receipt of a studentship from the Biotechnology and Biological Sciences Research Council (BBSRC) of the U.K. as part of the Cambridge BBSRC-DTP Programme (Reference BB/J014540/1). Authors S.A.-C., C.A., and A.G.S. acknowledge funding from the EC within the FP7 DEMA project, Grant Agreement No. 309086, and authors Z.Y., C.A., and A.G.S. were in receipt of funding from BBSRC sLoLa Award Reference BB/L002957/1.This is the final version of the article. It first appeared from the American Chemical Society via https://doi.org/10.1021/acs.analchem.6b0236