Network Models of Phage-Bacteria Coevolution

Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might affect the diversity of these groups, we developed a novel stochastic network model for examining the co-evolution of these ecologies. In our approach, nodes represent whole species or strains of bacteria or phages, rather than individuals, with "speciation" and extinction modelled by duplication and removal of nodes. Phage-bacteria links represent host-parasite relationships and temperate-virulent phage links denote prophage-encoded resistance. The effect of horizontal transfer of genetic information between strains was also included in the dynamical rules. The observed networks evolved in a highly dynamic fashion but the ecosystems were prone to collapse (one or more entire groups going extinct). Diversity could be stably maintained in the model only if the probability of speciation was independent of the diversity. Such an effect could be achieved in real ecosystems if the speciation rate is primarily set by the availability of ecological niches.Comment: 8 pages, 6 figure

CD4 count and tuberculosis risk in HIV-positive adults not on ART: a systematic review and meta-analysis

Background: CD4 cell count in adults with human immunodeficiency virus (HIV) infection (PLHIV) not receiving antiretroviral therapy (ART) influences tuberculosis (TB) risk. Despite widespread use in models informing resource allocation, this relationship has not been systematically reviewed. Methods: We systematically searched MEDLINE, Aidsinfo, Cochrane review database and Google Scholar for reports in English describing TB incidence stratified by updated CD4 cell count in cohorts of HIV-positive adults (age ≥15 years) not on ART (PROSPERO protocol no: CRD42016048888). Among inclusion criteria were: reporting precision for TB incidence, repeated CD4 measurements, and TB incidence reported for those not on ART or monotherapy. Study quality was assessed via the Newcastle-Ottawa tool for cohort studies. A Bayesian hierarchical model was fitted to estimate the pooled factor increase in TB incidence with respect to CD4 cell count decrement. Results: A total of 1,555 distinct records were identified from which 164 full text articles were obtained. Common reasons for exclusion of full texts were: no valid TB incidence, no repeat CD4 measurements, and not reporting TB incidence by ART status. The seven studies included reported on 1,206 TB cases among 41,271 individuals, with a typical median follow-up of four years. Studies were generally rated as moderate or high quality. Our meta-analysis estimated a 1.43 (95% credible interval: 1.16-1.88)-fold increase in TB incidence per 100 cells per mm3 decrease in CD4 cell count. Discussion: Our analysis confirms previous estimates of exponential increase in TB incidence with declining CD4 cell count in adults, emphasizing the importance of early ART initiation to reduce TB risk in PLHIV

Daily irrigation attenuates xylem abscisic acid concentration and increases leaf water potential of Pelargonium×hortorum compared with infrequent irrigation

The physiological response of plants to different irrigation frequencies may affect plant growth and water use efficiency (WUE; defined as shoot biomass/cumulative irrigation). Glasshouse-grown, containerized Pelargonium × hortorum BullsEye plants were irrigated either daily at 100% of plant evapotranspiration (ET) (well-watered; WW), or at 50% ET applied either daily [frequent deficit irrigation (FDI)] or cumulatively every 4 days [infrequent deficit irrigation (IDI)], for 24 days. Both FDI and IDI applied the same irrigation volume. Xylem sap was collected from the leaves, and stomatal conductance (gs) and leaf water potential (Ψleaf) measured every 2 days. As soil moisture decreased, gs decreased similarly under both FDI and IDI throughout the experiment. Ψleaf was maintained under IDI and increased under FDI. Leaf xylem abscisic acid (ABA) concentrations ([X-ABA]leaf) increased as soil moisture decreased under both IDI and FDI, and was strongly correlated with decreased gs, but [X-ABA]leaf was attenuated under FDI throughout the experiment (at the same level of soil moisture as IDI plants). These physiological changes corresponded with differences in plant production. Both FDI and IDI decreased growth compared with WW plants, and by the end of the experiment, FDI plants also had a greater shoot fresh weight (18%) than IDI plants. Although both IDI and FDI had higher WUE than WW plants during the first 10 days of the experiment (when biomass did not differ between treatments), the deficit irrigation treatments had lower WUE than WW plants in the latter stages when growth was limited. Thus, ABA-induced stomatal closure may not always translate to increased WUE (at the whole plant level) if vegetative growth shows a similar sensitivity to soil drying, and growers must adapt their irrigation scheduling according to crop requirements

Synthesis and photocatalytic activity of doped zinc oxide nanoparticles

In this study, we have investigated the effect of doping with cobalt and manganese oxide on the photocatalytic activity of nanoparticulate zinc oxide. Zinc oxide powders with controlled particle size, minimal agglomeration, and controlled chemical composition were manufactured by mechanochemical processing. The photocatalytic activity of the powders was measured using the spin trapping technique with electron paramagnetic resonance spectroscopy. It was found that the addition of cobalt oxide decreased the yield of photogenerated hydroxyl radicals. In contrast, doping with manganese oxide was found to substantially increase the rate of radical production.<br /

Determinacy of refinements to the difference hierarchy of co-analytic sets

In this paper we develop a technique for proving determinacy of classes of the form ω²-Π¹₁+Γ (a refinement of the difference hierarchy on Π¹₁ lying between ω²-Π¹₁ and (ω²+1)-Π¹₁) from weak principles, establishing upper bounds for the determinacy- strength of the classes ω²-Π¹₁+Σ^0_α for all computable α and of ω²-Π¹₁+Δ¹₁. This bridges the gap between previously known hypotheses implying determinacy in this region

Low friction droplet transportation on a substrate with a selective Leidenfrost effect

An energy saving Leidenfrost levitation method is introduced to transport micro-droplets with virtually frictionless contact between the liquid and solid substrate. By micro-engineering the heating units, selective areas of the whole substrate can be electro-thermally activated. A droplet can be levitated as a result of the Leidenfrost effect, and further transported when the substrate is tilted slightly. The selective electro-heating produces a uniform temperature distribution on the heating units within 1 s, in response to a triggering voltage. Alongside these experimental observations, finite element simulations are conducted to understand the temperature profile of the selective heated substrate, and also generate phase diagrams to verify the Leidenfrost regime for different substrate materials. Finally, we demonstrate the possibility of controlling low friction high speed droplet transportation (~ 65 mm/s) when the substrate is tilted (~ 7 °) by structurally designing the substrate. This work establishes the basis for an entirely new approach to droplet microfluidics

Computational aspects of N-mixture models

The N-mixture model is widely used to estimate the abundance of a population in the presence of unknown detection probability from only a set of counts subject to spatial and temporal replication (Royle, 2004, Biometrics 60,105–115). We explain and exploit the equivalence of N-mixture and multivariate Poisson and negative-binomial models, which provides powerful new approaches for fitting these models. We show that particularly when detection probability and the number of sampling occasions are small, infinite estimates of abundance can arise. We propose a sample covariance as a diagnostic for this event, and demonstrate its good performance in the Poisson case. Infinite estimates may be missed in practice, due to numerical optimization procedures terminating at arbitrarily large values. It is shown that the use of a bound, K, for an infinite summation in the N-mixture likelihood can result in underestimation of abundance, so that default values of K in computer packages should be avoided. Instead we propose a simple automatic way to choose K. The methods are illustrated by analysis of data on Hermann’s tortoise Testudo hermanni

Caesarean section for non-medical reasons at term

Background: Caesarean section rates are progressively rising in many parts of the world. One suggested reason is increasing requests by women for caesarean section in the absence of clear medical indications, such as placenta praevia, HIV infection, contracted pelvis and, arguably, breech presentation or previous caesarean section. The reported benefits of planned caesarean section include greater safety for the baby, less pelvic floor trauma for the mother, avoidance of labour pain and convenience. The potential disadvantages, from observational studies, include increased risk of major morbidity or mortality for the mother, adverse psychological sequelae, and problems in subsequent pregnancies, including uterine scar rupture and greater risk of stillbirth and neonatal morbidity. An unbiased assessment of advantages and disadvantages would assist discussion of what has become a contentious issue in modern obstetrics. Objectives: To assess, from randomised trials, the effects on perinatal and maternal morbidity and mortality, and on maternal psychological morbidity, of planned caesarean delivery versus planned vaginal birth in women with no clear clinical indication for caesarean section. Search methods: We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (April 2009). Selection criteria: All comparisons of intention to perform caesarean section and intention for women to give birth vaginally; random allocation to treatment and control groups; adequate allocation concealment; women at term with single fetuses with cephalic presentations and no clear medical indication for caesarean section. Data collection and analysis: We identified no studies that met the inclusion criteria. Main results: There were no included trials. Authors' conclusions: There is no evidence from randomised controlled trials, upon which to base any practice recommendations regarding planned caesarean section for non-medical reasons at term. In the absence of trial data, there is an urgent need for a systematic review of observational studies and a synthesis of qualitative data to better assess the short- and long-term effects of caesarean section and vaginal birth

Modal Platonism and the problem of negativity.

The Platonic account of modality says, roughly, that truths about alien possibilities are grounded in uninstantiated universals. Recently, Ingram has raised a problem for this kind of view, which is that it apparently requires negative facts to play a truthmaking role. Ingram offers an alternative Platonic account which makes use of modal instantiation relations. In this paper, I highlight some of the costs of Ingram’s new account and argue that a more appealing version of Platonism—and modal theory in general—is one that is supplemented with an ontology of totality facts