A Topological Characterization Of Knots and Links Arising From Site-Specific Recombination

We develop a topological model of knots and links arising from a single (or multiple processive) round(s) of recombination starting with an unknot, unlink, or (2,m)-torus knot or link substrate. We show that all knotted or linked products fall into a single family, and prove that the size of this family grows linearly with the cube of the minimum number of crossings. Additionally, we prove that the only possible products of an unknot substrate are either clasp knots and links or (2,m)-torus knots and links. Finally, in the (common) case of (2,m)-torus knot or link substrates whose products have minimal crossing number m+1, we prove that the types of products are tightly prescribed, and use this to examine previously uncharacterized experimental data.Comment: 18 pages, 3 tables, 18 figures. See also arXiv:0707.3775v1 for biological evidence for and applications of the model developed her

Calibrating whole house thermal models against a coheating test

This paper presents the methodology, along with some of the initial findings and observations from tests performed on two dwellings, of differing construction and form, in which a coheating test was performed using the dwelling's central heating system; this method is referred to as integrated coheating. Data obtained during the integrated coheating tests using a dwelling's heating system have been compared with data obtained during electric coheating of the same dwelling. In one instance, integrated coheating test data from one dwelling was compared to a similar adjoining control dwelling that was simultaneously subject to an electric coheating test. The results show a good agreement between the heat loss coefficients (HLC) obtained using a dwelling's own heating system and those obtained through electrical coheating. Initial analysis suggests the HLC estimate obtained from integrated coheating is likely to be more representative of how a dwelling performs in-use. The findings question the appropriateness of comparing current steady-state HLC predictions to those derived from in-use monitoring data. Integrated coheating has the potential to provide a more cost-effective and informative indication of whole house heat loss than electric coheating, as it enables in situ quantification of both fabric and heating system performance

X-ray reflection from the inner disc of the AGN Ton S180

We analyse a long archival XMM-Newton observation of the narrow-line Seyfert 1 galaxy Ton S180, using the latest reflection models to explore the high quality X-ray spectrum. We find that the iron line is relatively narrow and sharp, and the soft excess is extremely smooth. We cannot find an acceptable reflection model that describes both components, and conclude that the soft excess cannot be produced by relativistic reflection. Fitting the 3-10 keV band with relativistic reflection to model the iron line strongly prefers low spin values (< 0.4), with the exact value depending on the model and not well constrained. We then model the broad- band spectrum with a two-component Comptonization continuum plus relativistic reflection. This gives a much better fit than a pure reflection model, which again prefers a low spin value. The photon index of the reflection component is intermediate between the two Comptoniza- tion components, suggesting that both illuminate the disk a similar amount and therefore both contribute to the reflection

Measurement tools and process indicators of patient safety culture in primary care. A mixed methods study by the LINNEAUS collaboration on patient safety in primary care.

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordBACKGROUND: There is little guidance available to healthcare practitioners about what tools they might use to assess the patient safety culture. OBJECTIVE: To identify useful tools for assessing patient safety culture in primary care organizations in Europe; to identify those aspects of performance that should be assessed when investigating the relationship between safety culture and performance in primary care. METHODS: Two consensus-based studies were carried out, in which subject matter experts and primary healthcare professionals from several EU states rated (a) the applicability to their healthcare system of several existing safety culture assessment tools and (b) the appropriateness and usefulness of a range of potential indicators of a positive patient safety culture to primary care settings. The safety culture tools were field-tested in four countries to ascertain any challenges and issues arising when used in primary care. RESULTS: The two existing tools that received the most favourable ratings were the Manchester patient safety framework (MaPsAF primary care version) and the Agency for healthcare research and quality survey (medical office version). Several potential safety culture process indicators were identified. The one that emerged as offering the best combination of appropriateness and usefulness related to the collection of data on adverse patient events. CONCLUSION: Two tools, one quantitative and one qualitative, were identified as applicable and useful in assessing patient safety culture in primary care settings in Europe. Safety culture indicators in primary care should focus on the processes rather than the outcomes of care.The research leading to these results has received funding from the European Community’s Seventh Framework Programme FP7/2008 – 2012 under grant agreement no. 223424

Grazer diversity, functional redundancy, and productivity in seagrass beds: An experimental test

Concern over the accelerating loss of biodiversity has stimulated renewed interest in relationships among species richness, species composition, and the functional properties of ecosystems. Mechanistically, the degree of functional differentiation or complementarity among individual species determines the form of such relationships and is thus important to distinguishing among alternative hypotheses for the effects of diversity on ecosystem processes. Although a growing number of studies have reported relationships between plant diversity and ecosystem processes, few have explicitly addressed how functional diversity at higher trophic levels influences ecosystem processes. We used mesocosm experiments to test the impacts of three herbivorous crustacean species (Gammarus mucronatus, Idotea baltica, and Erichsonella attenuata) on plant biomass accumulation, relative dominance of plant functional groups, and herbivore secondary production in beds of eelgrass (Zostera marina), a dominant feature of naturally low-diversity estuaries throughout the northern hemisphere. By establishing treatments with all possible combinations of the three grazer species, we tested the degree of functional redundancy among grazers and their relative impacts on productivity. Grazer species composition strongly influenced eelgrass biomass accumulation and grazer secondary production, whereas none of the processes we studied was clearly related to grazer species richness over the narrow range (0–3 species) studied. In fact, all three measured ecosystem processes—epiphyte grazing, and eelgrass and grazer biomass accumulation— reached highest values in particular single-species treatments. Experimental deletions of individual species from the otherwise-intact assemblage confirmed that the three grazer species were functionally redundant in impacting epiphyte accumulation, whereas secondary production was sensitive to deletion of G. mucronatus, indicating its unique, nonredundant role in influencing this variable. In the field, seasonal abundance patterns differed markedly among the dominant grazer species, suggesting that complementary grazer phenologies may reduce total variance in grazing pressure on an annual basis. Our results show that even superficially similar grazer species can differ in both sign and magnitude of impacts on ecosystem processes and emphasize that one must be cautious in assuming redundancy when assigning species to functional groups

Genome-wide profiling of uncapped mRNA

Gene transcripts are under extensive posttranscriptional regulation, including the regulation of their stability. A major route for mRNA degradation produces uncapped mRNAs, which can be generated by decapping enzymes, endonucleases, and small RNAs. Profiling uncapped mRNA molecules is important for the understanding of the transcriptome, whose composition is determined by a balance between mRNA synthesis and degradation. In this chapter, we describe a method to profile these uncapped mRNAs at the genome scale

A physiologically-motivated compartment-based model of the effect of inhaled hypertonic saline on mucociliary clearance and liquid transport in cystic fibrosis

Background: Cystic Fibrosis (CF) lung disease is characterized by liquid hyperabsorption, airway surface dehydration, and impaired mucociliary clearance (MCC). Herein, we present a compartment-based mathematical model of the airway that extends the resolution of functional imaging data. Methods: Using functional imaging data to inform our model, we developed a system of mechanism-motivated ordinary differential equations to describe the mucociliary clearance and absorption of aerosolized radiolabeled particle and small molecules probes from human subjects with and without CF. We also utilized a novel imaging metric in vitro to gauge the fraction of airway epithelial cells that have functional ciliary activity. Results: This model, and its incorporated kinetic rate parameters, captures the MCC and liquid dynamics of the hyperabsorptive state in CF airways and the mitigation of that state by hypertonic saline treatment. Conclusions: We postulate, based on the model structure and its ability to capture clinical patient data, that patients with CF have regions of airway with diminished MCC function that can be recruited with hypertonic saline treatment. In so doing, this model structure not only makes a case for durable osmotic agents used in lung-region specific treatments, but also may provide a possible clinical endpoint, the fraction of functional ciliated airway

Centenarians today: New insights on selection from the 5-COOP study

The number of oldest old grew tremendously over the past few decades. However, recent studies have disclosed that the pace of increase strongly varies among countries. The present study aims to specify the level of mortality selection among the nonagenarians and centenarians living currently in five low mortality countries, Denmark, France, Japan, Switzerland, and Sweden, part of the 5-Country Oldest Old Project (5-COOP). All data come from the Human Mortality Database, except for the number of centenarians living in Japan. We disclosed three levels of mortality selection, a milder level in Japan, a stronger level in Denmark and Sweden and an intermediary level in France and Switzerland. These divergences offer an opportunity to study the existence of a trade-off between the level of mortality selection and the functional health status of the oldest old survivors which will be seized by the 5-COOP project. © 2010 Jean-Marie Robine et al.published_or_final_versio

Diversity and temperature indirectly reduce CO2 concentrations in experimental freshwater communities.

Biodiversity loss and climate warming are occurring in concert, with potentially profound impacts on ecosystem functioning. We currently know very little about the combined effects of these changes on the links between the community structure, dynamics and the resulting in situ CO2 concentrations in freshwater ecosystems. Here we aimed to determine both individual and combined effects of temperature and non-resource diversity (species inedible for a given consumer) on CO2 concentration. Our analysis further aimed to establish both direct effects on CO2 concentrations and potential indirect effects that occur via changes to the phytoplankton and zooplankton biomasses. Our results showed that there were no interactive effects of changes in temperature and diversity on CO2 concentration in the water. Instead, independent increases in either temperature or non-resource diversity resulted in a substantial reduction in CO2 concentrations, particularly at the highest non-resource diversity. The effects of non-resource diversity and warming on CO2 were indirect, resulting largely from the positive impacts on total biomass of primary producers. Our study is the first to experimentally partition the impacts of temperature and diversity on the consumer-resource dynamics and associated changes to CO2 concentrations. It provides new mechanistic insights into the role of diverse plankton communities for ecosystem functioning and their importance in regulating CO2 dynamics under ongoing climate warming