Detection of Rare Antimicrobial Resistance Profiles by Active and Passive Surveillance Approaches.

Antimicrobial resistance (AMR) surveillance systems are generally not specifically designed to detect emerging resistances and usually focus primarily on resistance to individual drugs. Evaluating the diversity of resistance, using ecological metrics, allows the assessment of sampling protocols with regard to the detection of rare phenotypes, comprising combinations of resistances. Surveillance data of phenotypic AMR of Canadian poultry Salmonella Heidelberg and swine Salmonella Typhimurium var. 5- were used to contrast active (representative isolates derived from healthy animals) and passive (diagnostic isolates) surveillance and assess their suitability for detecting emerging resistance patterns. Although in both datasets the prevalences of resistance to individual antimicrobials were not significantly different between the two surveillance systems, analysis of the diversity of entire resistance phenotypes demonstrated that passive surveillance of diagnostic isolates detected more unique phenotypes. Whilst the most appropriate surveillance method will depend on the relevant objectives, under the conditions of this study, passive surveillance of diagnostic isolates was more effective for the detection of rare and therefore potentially emerging resistance phenotypes.AEM was supported by the William Stewart Fellowship whilst at the University of Glasgow, and is currently supported by Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/ M014088/1; RR is supported by BBSRC grant BB/ E010326/1 and BB/L004070/1; LM is supported by BB/K01126X/1, BB/L004070/1, BB/F015313/1, National Science Foundation DEB1216040 and an EU-funded Marie Curie Initial Training Network (MCITN) program (NEMATODE SYSTEM HEALTH project (FP7-PEOPLE-2010-ITN- ID:264639)).This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pone.015851

Serologic and Molecular Detection of Granulocytic Ethrlichiosis in Rhode Island

A new indirect fluorescent-antibody (IFA) assay with antigen produced in vitro in the human promyelocytic leukemia cell line HL60 was used to identify the first recognized case of human granulocytic ehrlichiosis in Rhode Island. This IFA assay was used to detect granulocytic ehrlichiae in white-footed mice and in a dog inhabiting the area surrounding the patient’s residence. Host-seeking Ixodes scapularis ticks found in the same habitat also were infected. I. scapularis ticks collected from other locations were fed on dogs and New Zealand White rabbits to assess the competency of these species as hosts of granulocytotropic Ehrlichia. Tick-induced infections of dogs were confirmed by serologic testing, tissue culture isolation, and PCR amplification, whereas several rabbits seroconverted but were PCR and culture negative. PCR amplification of the 16S rRNA gene and DNA sequencing of the PCR products or culture isolation was used to confirm granulocytic Ehrlichia infections in humans, dogs, white-footed mice, and ticks

Crowd-sourcing of structure-from-motion data for terrain modelling in a real-world disaster scenario:a proof of concept

Structure-from-motion (SfM) photogrammetry techniques are now widely available to generate digital terrain models (DTMs) from optical imagery, providing an alternative to costlier options such as LiDAR or satellite surveys. SfM could be a useful tool in hazard studies because its minimal cost makes it accessible even in developing regions and its speed of use can provide updated data rapidly in hazard-prone regions. Our study is designed to assess whether crowd-sourced SfM data is comparable to an industry standard LiDAR dataset, demonstrating potential real-world use of SfM if employed for disaster risk reduction purposes. Three groups with variable SfM knowledge utilized 16 different camera models, including four camera phones, to collect 1001 total photos in one hour of data collection. Datasets collected by each group were processed using VisualSFM, and the point densities, accuracies and distributions of points in the resultant point clouds (DTM skeletons) were compared. Our results show that the point clouds are resilient to inconsistency in users’ SfM knowledge: crowd-sourced data collected by a moderately informed general public yields topography results comparable in data density and accuracy to those produced with data collected by highly-informed SfM users or experts using LiDAR. This means that in a real-world scenario involving participants with a diverse range of expertise, topography models could be produced from crowd-sourced data quite rapidly and to a very high standard. This could be beneficial to disaster risk reduction as a relatively quick, simple and low-cost method to attain rapidly updated knowledge of terrain attributes, useful for the prediction and mitigation of many natural hazards

Economic evaluation of access to musculoskeletal care: The case of waiting for total knee arthroplasty

BACKGROUND: The projected demand for total knee arthroplasty is staggering. At its root, the solution involves increasing supply or decreasing demand. Other developed nations have used rationing and wait times to distribute this service. However, economic impact and cost-effectiveness of waiting for TKA is unknown. METHODS: A Markov decision model was constructed for a cost-utility analysis of three treatment strategies for end-stage knee osteoarthritis: 1) TKA without delay, 2) a waiting period with no non-operative treatment and 3) a non-operative treatment bridge during that waiting period in a cohort of 60 year-old patients. Outcome probabilities and effectiveness were derived from the literature. Costs were estimated from the societal perspective with national average Medicare reimbursement. Effectiveness was expressed in quality-adjusted life years (QALYs) gained. Principal outcome measures were average incremental costs, effectiveness, and quality-adjusted life years; and net health benefits. RESULTS: In the base case, a 2-year wait-time both with and without a non-operative treatment bridge resulted in a lower number of average QALYs gained (11.57 (no bridge) and 11.95 (bridge) vs. 12.14 (no delay). The average cost was $1,660 higher for TKA without delay than wait-time with no bridge, but$1,810 less than wait-time with non-operative bridge. The incremental cost-effectiveness ratio comparing wait-time with no bridge to TKA without delay was $2,901/QALY. When comparing TKA without delay to waiting with non-operative bridge, TKA without delay produced greater utility at a lower cost to society. CONCLUSIONS: TKA without delay is the preferred cost-effective treatment strategy when compared to a waiting for TKA without non-operative bridge. TKA without delay is cost saving when a non-operative bridge is used during the waiting period. As it is unlikely that patients waiting for TKA would not receive non-operative treatment, TKA without delay may be an overall cost-saving health care delivery strategy. Policies aimed at increasing the supply of TKA should be considered as savings exist that could indirectly fund those strategies

Simulated 50 % radiation dose reduction in coronary CT angiography using adaptive iterative dose reduction in three-dimensions (AIDR3D)

To compare the image quality of coronary CT angiography (CTA) studies between standard filtered back projection (FBP) and adaptive iterative dose reduction in three-dimensions (AIDR3D) reconstruction using CT noise additional software to simulate reduced radiation exposure. Images from 93 consecutive clinical coronary CTA studies were processed utilizing standard FBP, FBP with 50 % simulated dose reduction (FBP50 %), and AIDR3D with simulated 50 % dose reduction (AIDR50 %). Signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were measured within 5 regions-of-interest, and image quality for each reconstruction strategy was assessed by two independent readers using a 4-point scale. Compared to FBP, the SNR measured from the AIDR50 % images was similar or higher (airway: 38.3 ± 12.7 vs. 38.5 ± 14.5, p = 0.81, fat: 5.5 ± 1.9 vs. 5.4 ± 2.0, p = 0.20, muscle: 3.2 ± 1.2 vs. 3.1 ± 1.3, p = 0.38, aorta: 22.6 ± 9.4 vs. 20.2 ± 9.7, p < 0.0001, liver: 2.7 ± 1.0 vs. 2.3 ± 1.1, p < 0.0001), while the SNR of the FBP50 % images were all lower (p values < 0.0001). The CNR measured from AIDR50 % images was also higher than that from the FBP images for the aorta relative to muscle (20.5 ± 9.0 vs. 18.3 ± 9.2, p < 0.0001). The interobserver agreement in the image quality score was excellent (κ = 0.82). The quality score was significantly higher for the AIDR50 % images compared to the FBP images (3.6 ± 0.6 vs. 3.3 ± 0.7, p = 0.004). Simulated radiation dose reduction applied to clinical coronary CTA images suggests that a 50 % reduction in radiation dose can be achieved with adaptive iterative dose reduction software with image quality that is at least comparable to images acquired at standard radiation exposure and reconstructed with filtered back projection

Molecular Characterization of Haemaphysalis Species and a Molecular Genetic Key for the Identification of Haemaphysalis of North America

Haemaphysalis longicornis (Acari: Ixodidae), the Asian longhorned tick, is native to East Asia, but has become established in Australia and New Zealand, and more recently in the United States. In North America, there are other native Haemaphysalis species that share similar morphological characteristics and can be difficult to identify if the specimen is damaged. The goal of this study was to develop a cost-effective and rapid molecular diagnostic assay to differentiate between exotic and native Haemaphysalis species to aid in ongoing surveillance of H. longicornis within the United States and help prevent misidentification. We demonstrated that restriction fragment length polymorphisms (RFLPs) targeting the 16S ribosomal RNA and the cytochrome c oxidase subunit I (COI) can be used to differentiate H. longicornis from the other Haemaphysalis species found in North America. Furthermore, we show that this RFLP assay can be applied to Haemaphysalis species endemic to other regions of the world for the rapid identification of damaged specimens. The work presented in this study can serve as the foundation for region specific PCR-RFLP keys for Haemaphysalis and other tick species and can be further applied to other morphometrically challenging taxa

Accuracy and reproducibility of automated, standardized coronary transluminal attenuation gradient measurements

Purpose Coronary Computed Tomography Angiography (CCTA) contrast opacification gradients, or Transluminal Attenuation Gradients (TAG) offer incremental value to predict functionally significant lesions. This study introduces and evaluates an automated gradients software package that can potentially supplant current, labor-intensive manual TAG calculation methods. Methods All 60 major coronary arteries in 20 patients who underwent a clinically indicated single heart beat 320×0.5 mm detector row CCTA were retrospectively evaluated by two readers using a previously validated manual measurement approach and two additional readers who used the new automated gradient software. Accuracy of the automated method against the manual measurements, considered the reference standard, was assessed via linear regression and Bland-Altman analyses. Inter- and intra-observer reproducibility and factors that can affect accuracy or reproducibility of both manual and automated TAG measurements, including CAD severity and iterative reconstruction, were also assessed. Results Analysis time was reduced by 68% when compared to manual TAG measurement. There was excellent correlation between automated TAG and the reference standard manual TAG. Bland-Altman analyses indicated low mean differences (1 HU/cm) and narrower inter- and intra-observer limits of agreement for automated compared to manual measurements (25% and 36% reduction with automated software, respectively). Among patient and technical factors assessed, none affected agreement of manual and automated TAG measurement. Conclusion Automated 320×0.5 mm detector row gradient software reduces computation time by 68% with high accuracy and reproducibility

Can the Universe Create Itself?

The question of first-cause has troubled philosophers and cosmologists alike. Now that it is apparent that our universe began in a Big Bang explosion, the question of what happened before the Big Bang arises. Inflation seems like a very promising answer, but as Borde and Vilenkin have shown, the inflationary state preceding the Big Bang must have had a beginning also. Ultimately, the difficult question seems to be how to make something out of nothing. This paper explores the idea that this is the wrong question --- that that is not how the Universe got here. Instead, we explore the idea of whether there is anything in the laws of physics that would prevent the Universe from creating itself. Because spacetimes can be curved and multiply connected, general relativity allows for the possibility of closed timelike curves (CTCs). Thus, tracing backwards in time through the original inflationary state we may eventually encounter a region of CTCs giving no first-cause. This region of CTCs, may well be over by now (being bounded toward the future by a Cauchy horizon). We illustrate that such models --- with CTCs --- are not necessarily inconsistent by demonstrating self-consistent vacuums for Misner space and a multiply connected de Sitter space in which the renormalized energy-momentum tensor does not diverge as one approaches the Cauchy horizon and solves Einstein's equations. We show such a Universe can be classically stable and self-consistent if and only if the potentials are retarded, giving a natural explanation of the arrow of time. Some specific scenarios (out of many possible ones) for this type of model are described. For example: an inflationary universe gives rise to baby universes, one of which turns out to be itself. Interestingly, the laws of physics may allow the Universe to be its own mother.Comment: 48 pages, 8 figure

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been “rediscovered” by this approach. In summary, we identified 13 additional candidate genes of domestication

Carbon sequestration in the deep Atlantic enhanced by Saharan dust

Enhanced atmospheric input of dust-borne nutrients and minerals to the remote surface ocean can potentially increase carbon uptake and sequestration at depth. Nutrients can enhance primary productivity, and mineral particles act as ballast, increasing sinking rates of particulate organic matter. Here we present a two-year time series of sediment trap observations of particulate organic carbon flux to 3,000 m depth, measured directly in two locations: the dust-rich central North Atlantic gyre and the dust-poor South Atlantic gyre. We find that carbon fluxes are twice as high and a higher proportion of primary production is exported to depth in the dust-rich North Atlantic gyre. Low stable nitrogen isotope ratios suggest that high fluxes result from the stimulation of nitrogen fixation and productivity following the deposition of dust-borne nutrients. Sediment traps in the northern gyre also collected intact colonies of nitrogen-fixing Trichodesmium species. Whereas ballast in the southern gyre is predominantly biogenic, dust-derived mineral particles constitute the dominant ballast element during the enhanced carbon fluxes in the northern gyre. We conclude that dust deposition increases carbon sequestration in the North Atlantic gyre through the fertilization of the nitrogen-fixing community in surface waters and mineral ballasting of sinking particles