Genomic comparisons among Escherichia coli strains B, K-12, and O157:H7 using IS elements as molecular markers

BACKGROUND: Insertion Sequence (IS) elements are mobile genetic elements widely distributed among bacteria. Their activities cause mutations, promoting genetic diversity and sometimes adaptation. Previous studies have examined their copy number and distribution in Escherichia coli K-12 and natural isolates. Here, we map most of the IS elements in E. coli B and compare their locations with the published genomes of K-12 and O157:H7. RESULTS: The genomic locations of IS elements reveal numerous differences between B, K-12, and O157:H7. IS elements occur in hok-sok loci (homologous to plasmid stabilization systems) in both B and K-12, whereas these same loci lack IS elements in O157:H7. IS elements in B and K-12 are often found in locations corresponding to O157:H7-specific sequences, which suggests IS involvement in chromosomal rearrangements including the incorporation of foreign DNA. Some sequences specific to B are identified, as reported previously for O157:H7. The extent of nucleotide sequence divergence between B and K-12 is <2% for most sequences adjacent to IS elements. By contrast, B and K-12 share only a few IS locations besides those in hok-sok loci. Several phenotypic features of B are explained by IS elements, including differential porin expression from K-12. CONCLUSIONS: These data reveal a high level of IS activity since E. coli B, K-12, and O157:H7 diverged from a common ancestor, including IS association with deletions and incorporation of horizontally acquired genes as well as transpositions. These findings indicate the important role of IS elements in genome plasticity and divergence

A survey of assistive technology (AT) knowledge and experiences of healthcare professionals in the UK and France: challenges and opportunities for workforce development

Background: Assistive Technologies (AT) in healthcare can increase independence and quality of life for users. Concurrently, new AT devices offer opportunities for individualised care solutions. Nonetheless, AT remains under-utilised and is poorly integrated in practice by healthcare professionals (HCPs). Although occupational therapists (OTs), physiotherapists and speech and language therapists (SLTs) consider that AT solutions can offer problem-solving approaches to personalised care, they have a lesser understanding of application of AT in their practice. In this paper, we report findings of a survey on AT knowledge and experiences of HCPs in UK and France. Training needs also explored in the survey are presented in a separate paper on development of online training for the ADAPT project. Method: A survey of 37 closed/open questions was developed in English and French by a team of healthcare researchers. Content was informed by published surveys and studies. Email invitations were circulated to contacts in Health Trusts in UK and France ADAPT regions and the survey was hosted on an online platform. Knowledge questions addressed AT understanding and views of impact on user’s lives. Experience questions focussed on current practices, prescription, follow-up, abandonment and practice standards. 429 HCPs completed the survey (UK=167; FR=262) between June and November 2018. Key results: Participants were mainly female (UK 89.2%; FR 82.8%) and qualified 10+ years (UK 66.5%; FR 62.2%). A key group in both countries were OTs (UK 34.1%; FR 46.6%), with more physiotherapists and SLTs in UK (16.8%, 16.8%; Vs. FR 6.5%, 2.3%), and more nurses in France (22.1% Vs. UK 10.8%). More HCPs were qualified to degree level in France (75.2%; UK 48.5%, p<0.001). In terms of knowledge, all HCPs agreed that AT helps people complete otherwise difficult or impossible tasks (UK 86.2%; FR 94.3%) and that successful AT adoption always depends on support from carers, family and professionals (UK 52.7%; FR 66.2%). There were some notable differences between countries that require further exploration. For example, more French HCPs thought that AT is provided by trial and error (84.7%, UK 45.5%, p<0.001), while more UK HCPs believed that AT promotes autonomous living (93.4%; FR 42.8%, p<0.001). Also, more French HCPs considered that AT refers exclusively to technologically-advanced electronic devices (71.8%, UK 28.8%, p<0.001). In both countries, top AT prescribers were OTs, physiotherapists and SLTs. Respondents had little/no knowledge in comparing/choosing AT (UK 86.8%; FR 76.7%) and stated they would benefit from interdisciplinary clinical standards (UK 80.8%; FR 77.1%). A third of HCPs did not know if AT users had access to adequate resources/support (UK 34.1%; FR 27.5%) and rated themselves as capable to monitor continued effective use of AT (UK 38.9%; FR 34.8%). Conclusion: Knowledge and application of AT was varied between the two countries due to differences in health care provision and support mechanisms. Survey findings suggest that HCPs recognised the value of AT for users’ improved care, but had low confidence in their ability to choose appropriate AT solutions and monitor continued use, and would welcome AT interdisciplinary clinical standards

MO-ParamILS: A Multi-objective Automatic Algorithm Configuration Framework

International audienceAutomated algorithm configuration procedures play an increasingly important role in the development and application of algorithms for a wide range of computationally challenging problems. Until very recently, these configuration procedures were limited to optimising a single performance objective, such as the running time or solution quality achieved by the algorithm being configured. However, in many applications there is more than one performance objective of interest. This gives rise to the multi-objective automatic algorithm configuration problem, which involves finding a Pareto set of configurations of a given target algorithm that characterises trade-offs between multiple performance objectives. In this work, we introduce MO-ParamILS, a multi-objective extension of the state-of-the-art single-objective algorithm configuration framework ParamILS, and demonstrate that it produces good results on several challenging bi-objective algorithm configuration scenarios compared to a base-line obtained from using a state-of-the-art single-objective algorithm configurator

Sedentary and Physically Active Behavior Patterns Among Low-Income African-American and White Adults Living in the Southeastern United States

Increased sedentary behavior and lack of physical activity are associated with increased risk for many chronic diseases. Differences in leisure-time physical activity between African American and white adults have been suggested to partially explain racial disparities in chronic disease outcomes, but expanding the definition of physical activity to include household and occupational activities may reduce or even eliminate racial differences in total physical activity. The objective of this study was to describe patterns of active and sedentary behaviors in black and white adults and to examine these behaviors across demographic measures. Sedentary and physically active behaviors were obtained from a validated physical activity questionnaire in 23,021 black men, 9,899 white men, 32,214 black women, and 15,425 white women (age 40–79) at enrollment into the Southern Community Cohort Study. Descriptive statistics for sedentary time; light, moderate, and vigorous household/occupational activity; sports/exercise; total activity; and meeting current physical activity recommendations via sports/exercise were examined for each race-sex group. Adjusted means were calculated using multiple linear regression models across demographic measures. Study participants spent approximately 60% of waking time in sedentary behaviors. Blacks reported more television viewing time than whites (45 minutes for females, 15 minutes for males), but when sitting time was expressed as a proportion of overall awake time, minimal racial differences were found. Patterns of light, moderate, and vigorous household/occupational activity were similar in all race/sex groups. 2008 Physical Activity Guidelines for Americans were followed by 16% of women and 25% of men independent of race. Overall, black and white men and women in this study spent the majority of their daily time in sedentary behaviors and less than one-fourth followed current guidelines for physical activity. These results indicate that public health campaigns should focus on both reducing sedentary behavior and increasing physical activity in all adult US populations

Euclid: Fast two-point correlation function covariance through linear construction

We present a method for fast evaluation of the covariance matrix for a two-point galaxy correlation function (2PCF) measured with the Landy-Szalay estimator. The standard way of evaluating the covariance matrix consists in running the estimator on a large number of mock catalogs, and evaluating their sample covariance. With large random catalog sizes (random-to-data objects' ratio M >> 1) the computational cost of the standard method is dominated by that of counting the data-random and random-random pairs, while the uncertainty of the estimate is dominated by that of data-data pairs. We present a method called Linear Construction (LC), where the covariance is estimated for small random catalogs with a size of M = 1 and M = 2, and the covariance for arbitrary M is constructed as a linear combination of the two. We show that the LC covariance estimate is unbiased. We validated the method with PINOCCHIO simulations in the range r = 20-200 h(-1) Mpc. With M = 50 and with 2h(-1) Mpc bins, the theoretical speedup of the method is a factor of 14. We discuss the impact on the precision matrix and parameter estimation, and present a formula for the covariance of covariance.Peer reviewe

PHIL photoinjector test line

LAL is now equiped with its own platform for photoinjectors tests and Research and Developement, named PHIL (PHotoInjectors at LAL). This facility has two main purposes: push the limits of the photoinjectors performances working on both the design and the associated technology and provide a low energy (MeV) short pulses (ps) electron beam for the interested users. Another very important goal of this machine will be to provide an opportunity to form accelerator physics students, working in a high technology environment. To achieve this goal a test line was realised equipped with an RF source, magnets and beam diagnostics. In this article we will desrcibe the PHIL beamline and its characteristics together with the description of the first two photoinjector realised in LAL and tested: the ALPHAX and the PHIN RF Guns