Achieving the Shot-noise Limit Using Experimental Multi-shot Digital Holography Data

In this paper, we achieve the shot-noise limit using straightforward image-post-processing techniques with experimental multi-shot digital holography data (i.e., off-axis data composed of multiple noise and speckle realizations). First, we quantify the effects of frame subtraction (of the mean reference-only frame and the mean signal-only frame from the digital-hologram frames), which boosts the signal-to-noise ratio (SNR) of the baseline dataset with a gain of 2.4 dB. Next, we quantify the effects of frame averaging, both with and without the frame subtraction. We show that even though the frame averaging boosts the SNR by itself, the frame subtraction and the stability of the digital-hologram fringes are necessary to achieve the shot-noise limit. Overall, we boost the SNR of the baseline dataset with a gain of 8.1 dB, which is the gain needed to achieve the shot-noise limit

Inferring source attribution from a multi-year multi-source dataset of Salmonella in Minnesota

Salmonella enterica is a global health concern because of its widespread association with foodborne illness. Bayesian models have been developed to attribute the burden of human salmonellosis to specific sources with the ultimate objective of prioritizing intervention strategies. Important considerations of source attribution models include the evaluation of the quality of input data, assessment of whether attribution results logically reflect the data trends and identification of patterns within the data that might explain the detailed contribution of different sources to the disease burden. Here, more than 12,000 non-typhoidal Salmonella isolates from human, bovine, porcine, chicken and turkey sources that originated in Minnesota were analysed. A modified Bayesian source attribution model (available in a dedicated R package), accounting for non-sampled sources of infection, attributed 4,672 human cases to sources assessed here. Most (60%) cases were attributed to chicken, although there was a spike in cases attributed to a non-sampled source in the second half of the study period. Molecular epidemiological analysis methods were used to supplement risk modelling, and a visual attribution application was developed to facilitate data exploration and comprehension of the large multiyear data set assessed here. A large amount of within-source diversity and low similarity between sources was observed, and visual exploration of data provided clues into variations driving the attribution modelling results. Results from this pillared approach provided first attribution estimates for Salmonella in Minnesota and offer an understanding of current data gaps as well as key pathogen population features, such as serotype frequency, similarity and diversity across the sources. Results here will be used to inform policy and management strategies ultimately intended to prevent and control Salmonella infection in the state

Influence of intensive melt shearing on the microstructure and mechanical properties of an Al-Mg alloy with high added impurity content

The official published version can be accessed from the link below - Copyright @ The Minerals, Metals & Materials Society and ASM International 2011We have investigated the influence of melt conditioning by intensive shearing on the mechanical behavior and microstructure of Al-Mg-Mn-Fe-Cu-Si alloy sheet produced from a small book mold ingot with high added impurity content. The melt conditioned ingot has fine grains throughout its cross section, whereas a conventionally cast ingot, without melt shearing, has coarser grains and shows a wider variation of grain size. Both needle-shaped and coarse Chinese script iron bearing intermetallic particles are found in the microstructure at the center of the conventionally processed ingot, but for the melt conditioned ingot, only fine Chinese script intermetallic particles are observed. In addition to the iron bearing intermetallics, Mg2Si particles are also observed. The ingots were rolled to thin sheet and solution heat treated (SHT). During rolling, the iron-based intermetallics and Mg2Si particles are broken and aligned along the rolling direction. Yield strength (YS), ultimate tensile strength (UTS), and elongation of the intensively melt sheared and processed sheet are all improved compared to the conventionally cast and processed sheet. Fractographic analysis of the tensile fracture surfaces shows that the clustered and coarse iron bearing intermetallic particles are responsible for the observed reduction in mechanical properties of the conventionally cast sheet. We have shown that by refining the initial microstructure of the ingot by intensive shear melt conditioning, it is possible to achieve improved mechanical properties at the final sheet gage of an AlMgMn alloy with a high content of impurities.This study is under the Technology Strategy Board funded REALCAR projec

Fly-derived DNA and camera traps are complementary tools for assessing mammalian biodiversity

Background Metabarcoding of vertebrate DNA found in invertebrates (iDNA) represents a potentially powerful tool for monitoring biodiversity. Preliminary evidence suggests fly iDNA biodiversity assessments compare favorably with established approaches such as camera trapping or line transects. Aims and Methods To assess whether fly-derived iDNA is consistently useful for biodiversity monitoring across a diversity of ecosystems, we compared metabarcoding of the mitochondrial 16S gene of fly pool-derived iDNA (range = 49–105 flies/site, N = 784 flies) with camera traps (range = 198–1,654 videos of mammals identified to the species level/site) at eight sites, representing different habitat types in five countries across tropical Africa. Results We detected a similar number of mammal species using fly-derived iDNA (range = 8–15 species/site) and camera traps (range = 8–27 species/site). However, the two approaches detected mostly different species (range = 6%–43% of species detected/site were detected with both methods), with fly-derived iDNA detecting on average smaller-bodied species than camera traps. Despite addressing different phylogenetic components of local mammalian communities, both methods resulted in similar beta-diversity estimates across sites and habitats. Conclusion These results support a growing body of evidence that fly-derived iDNA is a cost- and time-efficient tool that complements camera trapping in assessing mammalian biodiversity. Fly-derived iDNA may facilitate biomonitoring in terrestrial ecosystems at broad spatial and temporal scales, in much the same way as water eDNA has improved biomonitoring across aquatic ecosystems.Peer Reviewe

Comparison of stochastic and deterministic models for gambiense sleeping sickness at different spatial scales : a health area analysis in the DRC

The intensification of intervention activities against the fatal vector-borne disease gambiense human African trypanosomiasis (gHAT, sleeping sickness) in the last two decades has led to a large decline in the number of annually reported cases. However, while we move closer to achieving the ambitious target of elimination of transmission (EoT) to humans, pockets of infection remain, and it becomes increasingly important to quantitatively assess if different regions are on track for elimination, and where intervention efforts should be focused. We present a previously developed stochastic mathematical model for gHAT in the Democratic Republic of Congo (DRC) and show that this same formulation is able to capture the dynamics of gHAT observed at the health area level (approximately 10,000 people). This analysis was the first time any stochastic gHAT model has been fitted directly to case data and allows us to better quantify the uncertainty in our results. The analysis focuses on utilising a particle filter Markov chain Monte Carlo (MCMC) methodology to fit the model to the data from 16 health areas of Mosango health zone in Kwilu province as a case study. The spatial heterogeneity in cases is reflected in modelling results, where we predict that under the current intervention strategies, the health area of Kinzamba II, which has approximately one third of the health zone’s cases, will have the latest expected year for EoT. We find that fitting the analogous deterministic version of the gHAT model using MCMC has substantially faster computation times than fitting the stochastic model using pMCMC, but produces virtually indistinguishable posterior parameterisation. This suggests that expanding health area fitting, to cover more of the DRC, should be done with deterministic fits for efficiency, but with stochastic projections used to capture both the parameter and stochastic variation in case reporting and elimination year estimations

Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients.

Naturally acquired blood-stage infections of the malaria parasite Plasmodium falciparum typically harbour multiple haploid clones. The apparent number of clones observed in any single infection depends on the diversity of the polymorphic markers used for the analysis, and the relative abundance of rare clones, which frequently fail to be detected among PCR products derived from numerically dominant clones. However, minority clones are of clinical interest as they may harbour genes conferring drug resistance, leading to enhanced survival after treatment and the possibility of subsequent therapeutic failure. We deployed new generation sequencing to derive genome data for five non-propagated parasite isolates taken directly from 4 different patients treated for clinical malaria in a UK hospital. Analysis of depth of coverage and length of sequence intervals between paired reads identified both previously described and novel gene deletions and amplifications. Full-length sequence data was extracted for 6 loci considered to be under selection by antimalarial drugs, and both known and previously unknown amino acid substitutions were identified. Full mitochondrial genomes were extracted from the sequencing data for each isolate, and these are compared against a panel of polymorphic sites derived from published or unpublished but publicly available data. Finally, genome-wide analysis of clone multiplicity was performed, and the number of infecting parasite clones estimated for each isolate. Each patient harboured at least 3 clones of P. falciparum by this analysis, consistent with results obtained with conventional PCR analysis of polymorphic merozoite antigen loci. We conclude that genome sequencing of peripheral blood P. falciparum taken directly from malaria patients provides high quality data useful for drug resistance studies, genomic structural analyses and population genetics, and also robustly represents clonal multiplicity

Persistent anthrax as a major driver of wildlife mortality in a tropical rainforest

Anthrax is a globally important animal disease and zoonosis. Despite this, our current knowledge of anthrax ecology is largely limited to arid ecosystems, where outbreaks are most commonly reported. Here we show that the dynamics of an anthrax-causing agent, Bacillus cereus biovar anthracis, in a tropical rainforest have severe consequences for local wildlife communities. Using data and samples collected over three decades, we show that rainforest anthrax is a persistent and widespread cause of death for a broad range of mammalian hosts. We predict that this pathogen will accelerate the decline and possibly result in the extirpation of local chimpanzee (Pan troglodytes verus) populations. We present the epidemiology of a cryptic pathogen and show that its presence has important implications for conservation

Cytomegalovirus distribution and evolution in hominines

Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of CMV diversity in the hominine (African great ape and human) lineage, we hypothesized that chimpanzees and gorillas might have mutually exchanged CMVs in the past. Here, we performed a comprehensive molecular screening of all 9 African great ape species/subspecies, using 675 fecal samples collected from wild animals. We identified CMVs in eight species/subspecies, notably generating the first CMV sequences from bonobos. We used this extended dataset to test competing hypotheses with various degrees of co-divergence/number of host switches while simultaneously estimating the dates of these events in a Bayesian framework. The model best supported by the data involved the transmission of a gorilla CMV to the panine (chimpanzee and bonobo) lineage and the transmission of a panine CMV to the gorilla lineage prior to the divergence of chimpanzees and bonobos, more than 800,000 years ago. Panine CMVs then co-diverged with their hosts. These results add to a growing body of evidence suggesting that viruses with a double-stranded DNA genome (including other herpesviruses, adenoviruses, and papillomaviruses) often jumped between hominine lineages over the last few million years.Peer Reviewe

Intergenerational Communication – an interdisciplinary mapping review of research between 1996 and 2017

Concerns have been raised regarding the limited opportunities for intergenerational communication both outside and within the family. This “mapping review” draws together empirical literature in the topic published since 1996. Three hundred and twenty-four published studies met inclusion criteria, based on abstract review. The contents of each study were subjected to thematic analysis and nine broad themes emerged. These were (1) Dynamics of relationships, (2) Health & Well-being, (3) Learning & Literacy, (4) Attitudes, (5) Culture, (6) Digital, (7) Space, (8) Professional Development, and (9) Gender & Sexual Orientation. Studies commonly intersected disciplinary research areas. There was a marked rise across three key academic journals since 2007. An emergent finding was that a third of the studies relate to programs addressing intergenerational interventions, but many of these were primarily descriptive and failed to specify a primary outcome. Review implications and future research directions are discussed