Monitoring Partially Synchronous Distributed Systems using SMT Solvers

In this paper, we discuss the feasibility of monitoring partially synchronous distributed systems to detect latent bugs, i.e., errors caused by concurrency and race conditions among concurrent processes. We present a monitoring framework where we model both system constraints and latent bugs as Satisfiability Modulo Theories (SMT) formulas, and we detect the presence of latent bugs using an SMT solver. We demonstrate the feasibility of our framework using both synthetic applications where latent bugs occur at any time with random probability and an application involving exclusive access to a shared resource with a subtle timing bug. We illustrate how the time required for verification is affected by parameters such as communication frequency, latency, and clock skew. Our results show that our framework can be used for real-life applications, and because our framework uses SMT solvers, the range of appropriate applications will increase as these solvers become more efficient over time.Comment: Technical Report corresponding to the paper accepted at Runtime Verification (RV) 201

What you know can influence what you are going to know (especially for older adults)

Stimuli related to an individual's knowledge/experience are often more memorable than abstract stimuli, particularly for older adults. This has been found when material that is congruent with knowledge is contrasted with material that is incongruent with knowledge, but there is little research on a possible graded effect of congruency. The present study manipulated the degree of congruency of study material with participants’ knowledge. Young and older participants associated two famous names to nonfamous faces, where the similarity between the nonfamous faces and the real famous individuals varied. These associations were incrementally easier to remember as the name-face combinations became more congruent with prior knowledge, demonstrating a graded congruency effect, as opposed to an effect based simply on the presence or absence of associations to prior knowledge. Older adults tended to show greater susceptibility to the effect than young adults, with a significant age difference for extreme stimuli, in line with previous literature showing that schematic support in memory tasks particularly benefits older adults

Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in <i>C. elegans</i>

Parkinson's disease (PD), the second most prevalent neurodegenerative disease after Alzheimer's disease, is linked to the gradual loss of dopaminergic neurons in the substantia nigra. Disease loci causing hereditary forms of PD are known, but most cases are attributable to a combination of genetic and environmental risk factors. Increased incidence of PD is associated with rural living and pesticide exposure, and dopaminergic neurodegeneration can be triggered by neurotoxins such as 6-hydroxydopamine (6-OHDA). In C. elegans, this drug is taken up by the presynaptic dopamine reuptake transporter (DAT-1) and causes selective death of the eight dopaminergic neurons of the adult hermaphrodite. Using a forward genetic approach to find genes that protect against 6-OHDA-mediated neurodegeneration, we identified tsp-17, which encodes a member of the tetraspanin family of membrane proteins. We show that TSP-17 is expressed in dopaminergic neurons and provide genetic, pharmacological and biochemical evidence that it inhibits DAT-1, thus leading to increased 6-OHDA uptake in tsp-17 loss-of-function mutants. TSP-17 also protects against toxicity conferred by excessive intracellular dopamine. We provide genetic and biochemical evidence that TSP-17 acts partly via the DOP-2 dopamine receptor to negatively regulate DAT-1. tsp-17 mutants also have subtle behavioral phenotypes, some of which are conferred by aberrant dopamine signaling. Incubating mutant worms in liquid medium leads to swimming-induced paralysis. In the L1 larval stage, this phenotype is linked to lethality and cannot be rescued by a dop-3 null mutant. In contrast, mild paralysis occurring in the L4 larval stage is suppressed by dop-3, suggesting defects in dopaminergic signaling. In summary, we show that TSP-17 protects against neurodegeneration and has a role in modulating behaviors linked to dopamine signaling

Framing access to medicines in developing countries: an analysis of media coverage of Canada's Access to Medicines Regime

<p>Abstract</p> <p>Background</p> <p>In September 2003, the Canadian government committed to developing legislation that would facilitate greater access to affordable medicines for developing countries. Over the course of eight months, the legislation, now known as Canada's Access to Medicines Regime (CAMR), went through a controversial policy development process and the newspaper media was one of the major venues in which the policy debates took place. The purpose of this study was to examine how the media framed CAMR to determine how policy goals were conceptualized, which stakeholder interests controlled the public debate and how these variables related to the public policy process.</p> <p>Methods</p> <p>We conducted a qualitative content analysis of newspaper coverage of the CAMR policy and implementation process from 2003-2008. The primary theoretical framework for this study was framing theory. A total of 90 articles from 11 Canadian newspapers were selected for inclusion in our analysis. A team of four researchers coded the articles for themes relating to access to medicines and which stakeholders' voice figured more prominently on each issue. Stakeholders examined included: the research-based industry, the generic industry, civil society, the Canadian government, and developing country representatives.</p> <p>Results</p> <p>The most frequently mentioned themes across all documents were the issues of drug affordability, intellectual property, trade agreements and obligations, and development. Issues such as human rights, pharmaceutical innovation, and economic competitiveness got little media representation. Civil society dominated the media contents, followed far behind by the Canadian government, the research-based and generic pharmaceutical industries. Developing country representatives were hardly represented in the media.</p> <p>Conclusions</p> <p>Media framing obscured the discussion of some of the underlying policy goals in this case and failed to highlight issues which are now significant barriers to the use of the legislation. Using the media to engage the public in more in-depth exploration of the policy issues at stake may contribute to a more informed policy development process. The media can be an effective channel for those stakeholders with a weaker voice in policy deliberations to raise public attention to particular issues; however, the political and institutional context must be taken into account as it may outweigh media framing effects.</p

Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms

Rate variation in genes from all three genomes has been observed frequently in plant lineages with a parasitic and mycoheterotrophic mode of life. While the loss of photosynthetic ability leads to a relaxation of evolutionary constraints in genes involved in the photosynthetic apparatus, it remains to be determined how prevalent increased substitution rates are in nuclear DNA of non-photosynthetic angiosperms. In this study we infer rates of molecular evolution of 18S rDNA of all parasitic and mycoheterotorphic plant families (except Lauraceae and Polygalaceae) using relative rate tests. In several holoparasitic and mycoheterotrophic plant lineages extremely high substitution rates are observed compared to other photosynthetic angiosperms. The position and frequency of these substitutions have been identified to understand the mutation dynamics of 18S rRNA in achlorophyllous plants. Despite the presence of significantly elevated substitution rates, very few mutations occur in major functional and structural regions of the small ribosomal molecule, providing evidence that the efficiency of the translational apparatus in non-photosynthetic plants has not been affected

Intraspecific Inversions Pose a Challenge for the trnH-psbA Plant DNA Barcode

BACKGROUND: The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. METHODOLOGY/PRINCIPAL FINDINGS: Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. CONCLUSIONS/SIGNIFICANCE: Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding

How predation and landscape fragmentation affect vole population dynamics

Background: Microtine species in Fennoscandia display a distinct north-south gradient from regular cycles to stable populations. The gradient has often been attributed to changes in the interactions between microtines and their predators. Although the spatial structure of the environment is known to influence predator-prey dynamics of a wide range of species, it has scarcely been considered in relation to the Fennoscandian gradient. Furthermore, the length of microtine breeding season also displays a north-south gradient. However, little consideration has been given to its role in shaping or generating population cycles. Because these factors covary along the gradient it is difficult to distinguish their effects experimentally in the field. The distinction is here attempted using realistic agent-based modelling. Methodology/Principal Findings: By using a spatially explicit computer simulation model based on behavioural and ecological data from the field vole (Microtus agrestis), we generated a number of repeated time series of vole densities whose mean population size and amplitude were measured. Subsequently, these time series were subjected to statistical autoregressive modelling, to investigate the effects on vole population dynamics of making predators more specialised, of altering the breeding season, and increasing the level of habitat fragmentation. We found that fragmentation as well as the presence of specialist predators are necessary for the occurrence of population cycles. Habitat fragmentation and predator assembly jointly determined cycle length and amplitude. Length of vole breeding season had little impact on the oscillations. Significance: There is good agreement between our results and the experimental work from Fennoscandia, but our results allow distinction of causation that is hard to unravel in field experiments. We hope our results will help understand the reasons for cycle gradients observed in other areas. Our results clearly demonstrate the importance of landscape fragmentation for population cycling and we recommend that the degree of fragmentation be more fully considered in future analyses of vole dynamics

Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (∼450 bp) representing ∼100 morphospecies from ∼650 collections of Agaricomycotina using several sets of new primers. Large introns (∼1500 bp) at variable locations were detected in ∼5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (∼30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms

Exploring dietitians' salient beliefs about shared decision-making behaviors

<p>Abstract</p> <p>Background</p> <p>Shared decision making (SDM), a process by which health professionals and patients go through the decision-making process together to agree on treatment, is a promising strategy for promoting diet-related decisions that are informed and value based and to which patients adhere well. The objective of the present study was to identify dietitians' salient beliefs regarding their exercise of two behaviors during the clinical encounter, both of which have been deemed essential for SDM to take place: (1) presenting patients with all dietary treatment options for a given health condition and (2) helping patients clarify their values and preferences regarding the options.</p> <p>Methods</p> <p>Twenty-one dietitians were allocated to four focus groups. Facilitators conducted the focus groups using a semistructured interview guide based on the Theory of Planned Behavior. Discussions were audiotaped, transcribed verbatim, coded, and analyzed with NVivo8 (QSR International, Cambridge, MA) software.</p> <p>Results</p> <p>Most participants stated that better patient adherence to treatment was an advantage of adopting the two SDM behaviors. Dietitians identified patients, physicians, and the multidisciplinary team as normative referents who would approve or disapprove of their adoption of the SDM behaviors. The most often reported barriers and facilitators for the behaviors concerned patients' characteristics, patients' clinical situation, and time.</p> <p>Conclusions</p> <p>The implementation of SDM in nutrition clinical practice can be guided by addressing dietitians' salient beliefs. Identifying these beliefs also provides the theoretical framework needed for developing a quantitative survey questionnaire to further study the determinants of dietitians' adoption of SDM behaviors.</p