Analyzing large-scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon.

Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0-8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological factors (e.g., competition) were more important than genetic considerations (e.g., inbreeding depression) in determining the response to supplementation

Development of a new laser Doppler velocimeter for the Ames High Reynolds Channel No. 2

A new two-channel laser Doppler velocimeter developed for the Ames High Reynolds Channel No. 2 is described. Design features required for the satisfactory operation of the optical system in the channel environment are discussed. Fiber optics are used to transmit the megahertz Doppler signal to the photodetectors located outside the channel pressure vessel, and provision is made to isolate the optical system from pressure and thermal strain effects. Computer-controlled scanning mirrors are used to position the laser beams in the channel flow. Techniques used to seed the flow with 0.5-micron-diam polystyrene spheres avoiding deposition on the test-section windows and porous boundary-layer removal panels are described. Preliminary results are presented with a discussion of several of the factors affecting accuracy

Eggshell pigment composition covaries with phylogeny but not with life history or with nesting ecology traits of British passerines

No single hypothesis is likely to explain the diversity in eggshell coloration and patterning across birds, suggesting that eggshell appearance is most likely to have evolved to fulfill many nonexclusive functions. By controlling for nonindependent phylogenetic associations between related species, we describe this diversity using museum eggshells of 71 British breeding passerine species to examine how eggshell pigment composition and concentrations vary with phylogeny and with life-history and nesting ecology traits. Across species, concentrations of biliverdin and protoporphyrin, the two main pigments found in eggshells, were strongly and positively correlated, and both pigments strongly covaried with phylogenetic relatedness. Controlling for phylogeny, cavity-nesting species laid eggs with lower protoporphyrin concentrations in the shell, while higher biliverdin concentrations were associated with thicker eggshells for species of all nest types. Overall, these relationships between eggshell pigment concentrations and the biology of passerines are similar to those previously found in nonpasserine eggs, and imply that phylogenetic dependence must be considered across the class in further explanations of the functional significance of avian eggshell coloration

A modified gas-trapping method for high-throughput metabolic experiments in Drosophila melanogaster

Metabolism is often studied in animal models, with the Drosophila melanogaster fruit fly model offering ease of genetic manipulation and high-throughput studies. Fly metabolism is typically studied using end-point assays that are simple but destructive, and do not provide information on the utilization of specific nutrients. To address these limitations, we adapted existing gas-trapping protocols to measure the oxidation of radiolabeled substrates (such as glucose) in multi-well plates. This protocol is cost effective, simple, and offers precise control over experimental diet and measurement time, thus being amenable to high-throughput studies. Furthermore, it is nondestructive, enabling time-course experiments and multiplexing with other parameters. Overall, this protocol is useful for merging fly genetics with metabolic studies to understand whole organism responses to different macronutrients

Antibacterial Properties of a Tri-Sodium Citrate Modified Glass Polyalkenoate Cement

Primary deep infection following joint replacement surgery accounts for 7% of all revisions. Glass polyalkenoate cements (GPCs) have previously been shown to exhibit antibacterial properties. The present study had two objectives. The first was to determine if addition of tri-sodium citrate (TSC) to the powder phase of an Al-free GPC (0.04 SrO-0.12 CaO-0.36 ZnO-0.48 SiO2, by mole fraction) enhanced the resultant cement\u27s antibacterial properties against three strains of bacteria that are commonly found in periprosthetic sites following total joint replacements (TJRs); namely, E. coli, B. fragilis, and S. epidermidis. Four cement sets were prepared, which contained 0 wt% TSC (control), 5 wt% TSC, 10 wt% TSC, and 15 wt% TSC. All the TSC-modified cements were found to exhibit large inhibition zones against all the bacterial strains, especially the cement containing 15 wt% TSC against E. coli. The antibacterial properties of the TSC containing GPCs are attributed to the release of Zn and Na ions from the cements and the presence of the TSC. The second objective was to investigate if, when a modified GPC is embedded in a bovine bone model, ionic transfer occurs. It was found that Zn ions migrated from the cement to the surrounding bone, particularly at the cement-bone interface. This is a desirable outcome as Zn ions are known to play a vital role in both bone metabolism and the regeneration of healthy bone. The present results point to the potential clinical benefits of using TSC-modified GPCs in TJRs. © 2009 Wiley Periodicals, Inc

Employment relations and social stratification in contemporary urban China: does Goldthorpe’s class theory still work?

Goldthorpe’s class theory suggests that social class arises from employment relations in industrialised societies. This article assesses whether class in urban China can be approached from the same perspective by addressing three issues: 1) whether employment relations can capture China’s class structure, 2) how differently class is shaped by occupational structure in China, and 3) how useful class is to help us understand income inequality. Based on a recent Chinese social survey, the analysis finds three clusters of Chinese employees that fit into the ‘service’, ‘intermediate’ and ‘labour contract’ class typologies suggested by Goldthorpe’s class theory. Also, there is evidence that class links to occupational structures in a similar way between Chinese and Western societies. Finally class, when directly measured from employment relations, displays a reasonable degree of explanatory power for inter-class income inequality whereas the Goldthorpe class classification fails to differentiate between intermediate and labour class positions

Nursing teamwork in the care of older people: A mixed methods study

Healthcare is increasingly complex and requires the ability to adapt to changing demands. Teamwork is essential to delivering high quality care and is central to nursing. The aims of this study were to identify the processes that underpin nursing teamwork and how these affect the care of older people, identify the relationship between perceived teamwork and perceived quality of care, and explore in depth the experience of working in nursing teams. The study was carried out in three older people's wards in a London teaching hospital. Nurses and healthcare assistants completed questionnaires (n=65) on known dynamics of teamwork (using the Nursing Teamwork Survey) together with ratings of organisational quality (using an adapted AHRQ HSPS scale). A sample (n=22; 34%) was then interviewed about their perceptions of care, teamwork and how good outcomes are delivered in everyday work. Results showed that many care difficulties were routinely encountered, and confirmed the importance of teamwork (e.g. shared mental models of tasks and team roles and responsibilities, supported by leadership) in adapting to challenges. Perceived quality of teamwork was positively related to perceived quality of care. Work system variability and the external environment influenced teamwork, and confirmed the importance of team adaptive capacity. The CARE model shows the centrality of teamwork in adapting to variable demand and capacity to deliver care processes, and the influence of broader system factors on teamworking

DNA damage response (DDR) pathway engagement in cisplatin radiosensitization of non-small cell lung cancer

Non-small cell lung cancers (NSCLC) are commonly treated with a platinum-based chemotherapy such as cisplatin (CDDP) in combination with ionizing radiation (IR). Although clinical trials have demonstrated that the combination of CDDP and IR appear to be synergistic in terms of therapeutic efficacy, the mechanism of synergism remains largely uncharacterized. We investigated the role of the DNA damage response (DDR) in CDDP radiosensitization using two NSCLC cell lines. Using clonogenic survival assays, we determined that the cooperative cytotoxicity of CDDP and IR treatment is sequence dependent, requiring administration of CDDP prior to IR (CDDP-IR). We identified and interrogated the unique time and agent-dependent activation of the DDR in NSCLC cells treated with cisplatin-IR combination therapy. Compared to treatment with CDDP or IR alone, CDDP-IR combination treatment led to persistence of γH2Ax foci, a marker of DNA double-strand breaks (DSB), for up to 24h after treatment. Interestingly, pharmacologic inhibition of DDR sensor kinases revealed the persistence of γ-H2Ax foci in CDDP-IR treated cells is independent of kinase activation. Taken together, our data suggest that delayed repair of DSBs in NSCLC cells treated with CDDP-IR contributes to CDDP radiosensitization and that alterations of the DDR pathways by inhibition of specific DDR kinases can augment CDDP-IR cytotoxicity by a complementary mechanism

A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms

DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites