Environmental inactivation and irrigation-mediated regrowth of Escherichia coli O157:H7 on romaine lettuce when inoculated in a fecal slurry matrix

Field trials were conducted in July–August and October 2012 to quantify the inactivation rate of Escherichia coli O157:H7 when mixed with fecal slurry and applied to romaine lettuce leaves. Lettuce was grown under commercial conditions in Salinas Valley, California. One-half milliliter of rabbit, chicken, or pig fecal slurry, containing an average of 4.05 × 107 CFU E. coli O157:H7 (C0), was inoculated onto the upper (adaxial) surface of a lower leaf on 288 heads of lettuce per trial immediately following a 2.5 h irrigation event. To estimate the bacterial inactivation rate as a function of time, fecal matrix, irrigation and seasonal climate effects, sets of lettuce heads (n = 28) were sampled each day over 10 days and the concentration of E. coli O157:H7 (Ct) determined. E. coli O157:H7 was detected on 100% of heads during the 10-day duration, with concentrations ranging from ≤340 MPN/head (∼5-log reduction) to >3.45 × 1012 MPN/head (∼5-log growth). Relative to C0, on day 10 (Ct = 12) we observed an overall 2.6-log and 3.2-log mean reduction of E. coli O157:H7 in July and October, respectively. However, we observed relative maximum concentrations due to bacterial growth on day 6 (maximum Ct = 8) apparently stimulated by foliar irrigation on day 5. From this maximum there was a mean 5.3-log and 5.1-log reduction by day 10 (Ct = 12) for the July and October trials, respectively. This study provides insight into the inactivation and growth kinetics of E. coli O157:H7 on romaine lettuce leaves under natural field conditions. This study provides evidence that harvesting within 24 h post irrigation has the potential to increase the concentration of E. coli O157:H7 contamination, if present on heads of romaine lettuce; foliar irrigation can temporarily stimulate substantial regrowth of E. coli O157:H7

WeBo 1: A Young Barium Star Surrounded by a Ring-Like Planetary Nebula

WeBo 1 (PN G135.6+01.0), a previously unrecognized planetary nebula with a remarkable thin-ring morphology, was discovered serendipitously on Digitized Sky Survey images. The central star is found to be a late-type giant with overabundances of carbon and s-process elements. The giant is chromospherically active and photometrically variable, with a probable period of 4.7 days; this suggests that the star is spotted, and that 4.7 days is its rotation period. We propose a scenario in which one component of a binary system became an AGB star with a dense stellar wind enriched in C and s-process elements; a portion of the wind was accreted by the companion, contaminating its atmosphere and spinning up its rotation. The AGB star has now become a hot subdwarf, leaving the optical companion as a freshly contaminated barium star inside an ionized planetary nebula.Comment: 4 pages, 3 figures; Accepted for January 2003 issue of Astronomical Journa

Regulatory objectivity in action: Mild cognitive impairment and the collective production of uncertainty

In this paper, we investigate recent changes in the definition and approach to Alzheimer’s disease brought about by growing clinical, therapeutic and regulatory interest in the prodromal or preclinical aspects of this condition. In the last decade, there has been an increased interest in the biomolecular and epidemiological characterization of pre-clinical dementia. It is argued that early diagnosis of dementia, and particularly of Alzheimer‘s disease, will facilitate the prevention of dementing processes and lower the prevalence of the condition in the general population. The search for a diagnostic category or biomarker that would serve this purpose is an ongoing but problematic endeavour for research and clinical communities in this area. In this paper, we explore how clinical and research actors, in collaboration with regulatory institutions and pharmaceutical companies, come to frame these domains as uncertainties and how they re-deploy uncertainty in the ‘collective production’ of new diagnostic conventions and bioclinical standards. While drawing as background on ethnographic, documentary and interview data, the paper proposes an in-depth, contextual analysis of the proceedings of an international meeting organized by the Peripheral and Central Nervous System Drug Advisory Committee of the US Food and Drug Administration to discuss whether or not a particular diagnostic convention — mild cognitive impairment — exists and how best it ought to be studied. Based on this analysis we argue that the deployment of uncertainty is reflexively implicated in bioclinical collectives’ search for rules and conventions, and furthermore that the collective production of uncertainty is central to the ‘knowledge machinery’ of regulatory objectivity

Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

<p>Abstract</p> <p>Background</p> <p>Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications.</p> <p>Results</p> <p>We propose a new method to assess taxon sampling developing Clarke and Warwick statistics. This method aims to measure the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, our method also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses we describe in this paper.</p> <p>Conclusions</p> <p>We show that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators' expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.</p

Nuclear Energy Research Initiative Project No. 02 103 Innovative Low Cost Approaches to Automating QA/QC of Fuel Particle Production Using On Line Nondestructive Methods for Higher Reliability Final Project Report

This Nuclear Energy Research Initiative (NERI) project was tasked with exploring, adapting, developing and demonstrating innovative nondestructive test methods to automate nuclear coated particle fuel inspection so as to provide the United States (US) with necessary improved and economical Quality Assurance and Control (QA/QC) that is needed for the fuels for several reactor concepts being proposed for both near term deployment [DOE NE & NERAC, 2001] and Generation IV nuclear systems. Replacing present day QA/QC methods, done manually and in many cases destructively, with higher speed automated nondestructive methods will make fuel production for advanced reactors economically feasible. For successful deployment of next generation reactors that employ particle fuels, or fuels in the form of pebbles based on particles, extremely large numbers of fuel particles will require inspection at throughput rates that do not significantly impact the proposed manufacturing processes. The focus of the project is nondestructive examination (NDE) technologies that can be automated for production speeds and make either: (I) On Process Measurements or (II) In Line Measurements. The inspection technologies selected will enable particle “quality” qualification as a particle or group of particles passes a sensor. A multiple attribute dependent signature will be measured and used for qualification or process control decisions. A primary task for achieving this objective is to establish standard signatures for both good/acceptable particles and the most problematic types of defects using several nondestructive methods

Variations in Stress Sensitivity and Genomic Expression in Diverse S. cerevisiae Isolates

Interactions between an organism and its environment can significantly influence phenotypic evolution. A first step toward understanding this process is to characterize phenotypic diversity within and between populations. We explored the phenotypic variation in stress sensitivity and genomic expression in a large panel of Saccharomyces strains collected from diverse environments. We measured the sensitivity of 52 strains to 14 environmental conditions, compared genomic expression in 18 strains, and identified gene copy-number variations in six of these isolates. Our results demonstrate a large degree of phenotypic variation in stress sensitivity and gene expression. Analysis of these datasets reveals relationships between strains from similar niches, suggests common and unique features of yeast habitats, and implicates genes whose variable expression is linked to stress resistance. Using a simple metric to suggest cases of selection, we found that strains collected from oak exudates are phenotypically more similar than expected based on their genetic diversity, while sake and vineyard isolates display more diverse phenotypes than expected under a neutral model. We also show that the laboratory strain S288c is phenotypically distinct from all of the other strains studied here, in terms of stress sensitivity, gene expression, Ty copy number, mitochondrial content, and gene-dosage control. These results highlight the value of understanding the genetic basis of phenotypic variation and raise caution about using laboratory strains for comparative genomics

Exploring the relationships between housing, neighbourhoods and mental wellbeing for residents of deprived areas

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; Housing-led regeneration has been shown to have limited effects on mental health. Considering housing and neighbourhoods as a psychosocial environment, regeneration may have greater impact on positive mental wellbeing than mental ill-health. This study examined the relationship between the positive mental wellbeing of residents living in deprived areas and their perceptions of their housing and neighbourhoods.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods:&lt;/b&gt; A cross-sectional study of 3,911 residents in 15 deprived areas in Glasgow, Scotland. Positive mental wellbeing was measured using the Warwick-Edinburgh Mental Wellbeing Scale.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Using multivariate mulit-nomial logistic regressions and controlling for socio-demographic characteristics and physical health status, we found that several aspects of people's residential psychosocial environments were strongly associated with higher mental wellbeing. Mental wellbeing was higher when respondents considered the following: their neighbourhood had very good aesthetic qualities (RRR 3.3, 95% CI 1.9, 5.8); their home and neighbourhood represented personal progress (RRR 3.2 95% CI 2.2, 4.8; RRR 2.6, 95% CI 1.8, 3.7, respectively); their home had a very good external appearance (RRR 2.6, 95% CI 1.3, 5.1) and a very good front door (both an aesthetic and a security/control item) (RRR 2.1, 95% CI 1.2, 3.8); and when satisfaction with their landlord was very high (RRR 2.3, 95% CI 2.2,4.8). Perception of poor neighbourhood aesthetic quality was associated with lower wellbeing (RRR 0.4, 95% CI 0.3, 0.5).&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study has shown that for people living in deprived areas, the quality and aesthetics of housing and neighbourhoods are associated with mental wellbeing, but so too are feelings of respect, status and progress that may be derived from how places are created, serviced and talked about by those who live there. The implication for regeneration activities undertaken to improve housing and neighbourhoods is that it is not just the delivery of improved housing that is important for mental wellbeing, but also the quality and manner of delivery.&lt;/p&gt

MiRNA Control of Vegetative Phase Change in Trees

After germination, plants enter juvenile vegetative phase and then transition to an adult vegetative phase before producing reproductive structures. The character and timing of the juvenile-to-adult transition vary widely between species. In annual plants, this transition occurs soon after germination and usually involves relatively minor morphological changes, whereas in trees and other perennial woody plants it occurs after months or years and can involve major changes in shoot architecture. Whether this transition is controlled by the same mechanism in annual and perennial plants is unknown. In the annual forb Arabidopsis thaliana and in maize (Zea mays), vegetative phase change is controlled by the sequential activity of microRNAs miR156 and miR172. miR156 is highly abundant in seedlings and decreases during the juvenile-to-adult transition, while miR172 has an opposite expression pattern. We observed similar changes in the expression of these genes in woody species with highly differentiated, well-characterized juvenile and adult phases (Acacia confusa, Acacia colei, Eucalyptus globulus, Hedera helix, Quercus acutissima), as well as in the tree Populus x canadensis, where vegetative phase change is marked by relatively minor changes in leaf morphology and internode length. Overexpression of miR156 in transgenic P. x canadensis reduced the expression of miR156-targeted SPL genes and miR172, and it drastically prolonged the juvenile phase. Our results indicate that miR156 is an evolutionarily conserved regulator of vegetative phase change in both annual herbaceous plants and perennial trees

Prognostic value of total tumor volume in patients with colorectal liver metastases:A secondary analysis of the randomized CAIRO5 trial with external cohort validation

Background:This study aimed to assess the prognostic value of total tumor volume (TTV) for early recurrence (within 6 months) and overall survival (OS) in patients with colorectal liver metastases (CRLM), treated with induction systemic therapy followed by complete local treatment.Methods: Patients with initially unresectable CRLM from the multicenter randomized phase 3 CAIRO5 trial (NCT02162563) who received induction systemic therapy followed by local treatment were included. Baseline TTV and change in TTV as response to systemic therapy were calculated using the CT scan before and the first after systemic treatment, and were assessed for their added prognostic value. The findings were validated in an external cohort of patients treated at a tertiary center. Results:In total, 215 CAIRO5 patients were included. Baseline TTV and absolute change in TTV were significantly associated with early recurrence (P = 0.005 and P = 0.040, respectively) and OS in multivariable analyses (P = 0.024 and P = 0.006, respectively), whereas RECIST1.1 was not prognostic for early recurrence (P = 0.88) and OS (P = 0.35). In the validation cohort (n = 85), baseline TTV and absolute change in TTV remained prognostic for early recurrence (P = 0.041 and P = 0.021, respectively) and OS in multivariable analyses (P &lt; 0.0001 and P = 0.012, respectively), and showed added prognostic value over conventional clinicopathological variables (increase C-statistic, 0.06; 95 % CI, 0.02 to 0.14; P = 0.008). Conclusion: Total tumor volume is strongly prognostic for early recurrence and OS in patients who underwent complete local treatment of initially unresectable CRLM, both in the CAIRO5 trial and the validation cohort. In contrast, RECIST1.1 did not show prognostic value for neither early recurrence nor OS.</p

Multiscale Coarse-Graining of the Protein Energy Landscape

A variety of coarse-grained (CG) models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states