Predicting the diversity of early epidemic spread on networks

The course of an epidemic exhibits average growth dynamics determined by features of the pathogen and the population, yet also features significant variability reflecting the stochastic nature of disease spread. The interplay of biological, social, structural and random factors makes disease forecasting extraordinarily complex. In this work, we reframe a stochastic branching process analysis in terms of probability generating functions and compare it to continuous time epidemic simulations on networks. In doing so, we predict the diversity of emerging epidemic courses on both homogeneous and heterogeneous networks. We show how the challenge of inferring the early course of an epidemic falls on the randomness of disease spread more so than on the heterogeneity of contact patterns. We provide an analysis which helps quantify, in real time, the probability that an epidemic goes supercritical or conversely, dies stochastically. These probabilities are often assumed to be one and zero, respectively, if the basic reproduction number, or R0, is greater than 1, ignoring the heterogeneity and randomness inherent to disease spread. This framework can give more insight into early epidemic spread by weighting standard deterministic models with likelihood to inform pandemic preparedness with probabilistic forecasts

Temporal and probabilistic comparisons of epidemic interventions

Forecasting disease spread is a critical tool to help public health officials design and plan public health interventions.However, the expected future state of an epidemic is not necessarily well defined as disease spread is inherently stochastic, contact patterns within a population are heterogeneous, and behaviors change. In this work, we use time-dependent probability generating functions (PGFs) to capture these characteristics by modeling a stochastic branching process of the spread of a disease over a network of contacts in which public health interventions are introduced over time. To achieve this, we define a general transmissibility equation to account for varying transmission rates (e.g. masking), recovery rates (e.g. treatment), contact patterns (e.g. social distancing) and percentage of the population immunized (e.g. vaccination). The resulting framework allows for a temporal and probabilistic analysis of an intervention's impact on disease spread, which match continuous-time stochastic simulations that are much more computationally expensive.To aid policy making, we then define several metrics over which temporal and probabilistic intervention forecasts can be compared: Looking at the expected number of cases and the worst-case scenario over time, as well as the probability of reaching a critical level of cases and of not seeing any improvement following an intervention.Given that epidemics do not always follow their average expected trajectories and that the underlying dynamics can change over time, our work paves the way for more detailed short-term forecasts of disease spread and more informed comparison of intervention strategies.Comment: 20 pages, 5 figure

Troubling identities: teacher education students` constructions of class and ethnicity

Working with diverse student populations productively depends on teachers and teacher educators recognizing and valuing difference. Too often, in teacher education programs, when markers of identity such as gender, ethnicity, \u27race\u27, or social class are examined, the focus is on developing student teachers\u27 understandings of how these discourses shape learner identities and rarely on how these also shape teachers\u27 identities. This article reports on a research project that explored how student teachers understand ethnicity and socio-economic status. In a preliminary stage of the research, we asked eight Year 3 teacher education students who had attended mainly Anglo-Australian, middle class schools as students and as student teachers, to explore their own ethnic and classed identities. The complexities of identity are foregrounded in both the assumptions we made in selecting particular students for the project and in the ways they constructed their own identities around ethnicity and social class. In this article we draw on these findings to interrogate how categories of identity are fluid, shifting and ongoing processes of negotiation, troubling and complex. We also consider the implications for teacher education.<br /

Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes

Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies

Existence of Integral mm-Varifolds minimizing ∫∣A∣p\int |A|^p and ∫∣H∣p\int |H|^p, p>mp>m, in Riemannian Manifolds

We prove existence and partial regularity of integral rectifiable $m$-dimensional varifolds minimizing functionals of the type $\int |H|^p$ and $\int |A|^p$ in a given Riemannian $n$-dimensional manifold $(N,g)$, $2\leq mm$, under suitable assumptions on $N$ (in the end of the paper we give many examples of such ambient manifolds). To this aim we introduce the following new tools: some monotonicity formulas for varifolds in $\mathbb{R}^S$ involving $\int |H|^p$, to avoid degeneracy of the minimizer, and a sort of isoperimetric inequality to bound the mass in terms of the mentioned functionals.Comment: 33 pages; this second submission corresponds to the published version of the paper, minor typos are fixe

Digitization workflows for flat sheets and packets of plants, algae, and fungi

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141708/1/aps31500065.pd

Checklist and distribution of the liverworts of the Andasibe (Périnet) region (Madagascar)

This updated checklist of Marchantiophyta (liverworts) of Andasibé (Périnet) region, Madagascar was compiled from the literature, from herbarium specimens and recent collections. A total of 222 species including 9 infraspecific taxa, from 62 genera are recorded. Five species: Cheilolejeunea ngongensis Malombe et Pócs, Cheilolejeunea unciloba (Lindenb.) Malombe, Heteroscyphus grandistipus (Steph.) Schiffn., Lejeunea angulifolia Mitt. and Kymatocalyx africanus Vána et Wigginton are newly reported for Madagascar. Detailed informations on species occurrences are provided as a basis for subsequent research on species distributions and conservation