A Polynomial Translation of pi-calculus FCPs to Safe Petri Nets

We develop a polynomial translation from finite control pi-calculus processes to safe low-level Petri nets. To our knowledge, this is the first such translation. It is natural in that there is a close correspondence between the control flows, enjoys a bisimulation result, and is suitable for practical model checking.Comment: To appear in special issue on best papers of CONCUR'12 of Logical Methods in Computer Scienc

The Role of Organic Matter in the Fate and Transport of Antibiotic Resistance, Metals, and Nutrients in the Karst of Northwest Arkansas

Organic matter (OM) in the environment acts as a nutrient, but may also act as a transport vector for harmful chemical compounds and bacteria. Acetate is a labile form of OM produced during fermentation in anaerobic lagoons used to store animal fecal-waste from concentrated animal feeding operations (CAFOs). Dry and liquid fertilizers from CAFOs pose a threat to groundwater by introducing excessive amounts of nutrients (e.g. OM, nitrate and ammonia), metals, and antibiotic compounds. In the epikarst of Northern Arkansas in the Buffalo River watershed additional input of labile dissolved organic carbon (DOC) from liquid CAFO waste-fertilizers was hypothesized to increase microbial activity along groundwater flowpaths. In addition, high metal and antibiotic concentrations associated with increasing concentrations of DOC were hypothesized to be detrimental to microbial processes, with exception given to resistant bacteria species. Laboratory microcosm experiments were conducted to characterize microbial DIC production and denitrification. The microcosms were treated with acetate, nitrate, phosphate, and/or various metal species to characterize concentration effects on microbial activity. Field studies were used to calibrate laboratory conditions, and to compare biomass production and composition. Isotopes of dissolved inorganic carbon (δ13C-DIC), nitrate (δ15N-NO3), and dissolved oxygen (DO) were used to assess microbial responses to increasing DOC concentrations. Fatty acid methyl ester (FAME) analysis was used to characterize biomass produced during the experiments. Conversion of DOC-DIC and decreasing NO3 concentrations were observed in the microcosms. Microbial productivity was greatest when DOC concentrations were 10 times greater than NO3 concentrations. When metals were added to the microcosms, microbial activity was inhibited with exception being microcosms containing metal concentrations below 10 µg/L. FAME biomarkers indicated gram-negative bacteria were present in biomass samples from the spring orifice and metal-treated microcosms, but microcosms amended with nutrients and DOC displayed indicators of predominantly gram-positive bacteria. Critical findings of this study were: bacteria species transported in spring discharge were resistant to antibiotics and metals, high concentrations of DOC and nitrate increase biological productivity in epikarst and metal exposure inhibits nitrate removal and causes ecological shifts in biofilms selecting for resistant bacteria strains

Strategic incompatibility in ATM markets

We test whether firms use incompatibility strategically, using data from ATM markets. High ATM fees degrade the value of competitors’ deposit accounts, and can in principle serve as a mechanism for siphoning depositors away from competitors or for creating deposit account differentiation. Our empirical framework can empirically distinguish surcharging motivated by this strategic concern from surcharging that simply maximizes ATM profit considered as a stand-alone operation. The results are consistent with such behavior by large banks, but not by small banks. For large banks, the effect of incompatibility seems to operate through higher deposit account fees rather than increased deposit account base

Evaluation of potential drug–drug interactions among patients with chronic kidney disease in northeastern Nigeria

Background: Potential drug–drug interactions (pDDIs) may not manifest clinically in patients who are treated with multiple pharmaceutical agents, but when they do they can produce adverse outcomes. In patients with chronic kidney disease (CKD), the frequent use of multiple agents to manage this condition and its complications puts these patients at increased risk for DDIs. We determined the prevalence of pDDIs in CKD patients in two Nigerian hospitals and investigated possible predictors of pDDIs.Methods: This cross-sectional study involved patients with CKD who attended the nephrology unit of the University of Maiduguri Teaching Hospital and the medical outpatients clinic of the State Specialist Hospital in Maiduguri, Nigeria. We collected prescriptions, clinical data and laboratory data from the medical files of patients seen between January 2013 and December 2017. Descriptive and inferential statistics were used to analyse the data.Results: The study included 201 patients. A total of 273 pDDIs were identified in 166 patients (83%). These pDDIs included 30 unique drug interactions, the most common being between ferrous sulphate and calcium carbonate (seen in 46% of patients with pDDIs), followed by lisinopril and furosemide (8%). The proportion of clinically significant interactions was only 2%. There was a positive association between pDDIs and the total number of drugs prescribed (P < 0.001).Conclusions: A high prevalence of pDDIs was documented among Nigerian patients with CKD. The bulk of the interactions were related to the co-prescription of ferrous sulphate and calcium carbonate. The total number of drugs prescribed was a significant predictor of pDDIs. We recommend routine screening of prescriptions of CKD patients for potential pDDIs

Investigating the consequences of interference between multiple CD8+ T cell escape mutations in early HIV infection

During early human immunodeficiency virus (HIV) infection multiple CD8+ T cell responses are elicited almost simultaneously. These responses exert strong selective pressures on different parts of HIV's genome, and select for mutations that escape recognition and are thus beneficial to the virus. Some studies reveal that the later these escape mutations emerge, the more slowly they go to fixation. This pattern of escape rate decrease(ERD) can arise by distinct mechanisms. In particular, in large populations with high beneficial mutation rates interference among different escape strains – an effect that can emerge in evolution with asexual reproduction and results in delayed fixation times of beneficial mutations compared to sexual reproduction – could significantly impact the escape rates of mutations. In this paper, we investigated how interference between these concurrent escape mutations affects their escape rates in systems with multiple epitopes, and whether it could be a source of the ERD pattern. To address these issues, we developed a multilocus Wright-Fisher model of HIV dynamics with selection, mutation and recombination, serving as a null-model for interference. We also derived an interference-free null model assuming initial neutral evolution before immune response elicitation. We found that interference between several equally selectively advantageous mutations can generate the observed ERD pattern. We also found that the number of loci, as well as recombination rates substantially affect ERD. These effects can be explained by the underexponential decline of escape rates over time. Lastly, we found that the observed ERD pattern in HIV infected individuals is consistent with both independent, interference-free mutations as well as interference effects. Our results confirm that interference effects should be considered when analyzing HIV escape mutations. The challenge in estimating escape rates and mutation-associated selective coefficients posed by interference effects cannot simply be overcome by improved sampling frequencies or sizes. This problem is a consequence of the fundamental shortcomings of current estimation techniques under interference regimes. Hence, accounting for the stochastic nature of competition between mutations demands novel estimation methodologies based on the analysis of HIV strains, rather than mutation frequencies

An Alternative to the Advection Dispersion Model for Interpreting Dye Tracing Studies in Fractured-Rock and Karst Aquifers

Due to the complexity of groundwater fl ow in fractured-rock and karst aquifers, solute transport models for these aquifers are typically stochastic models based on tracer transport studies. Water and tracers do not fl ow at one single advective velocity but experience a wide range of velocities, from rapid fl ow in conduits to near stagnant conditions in adjacent voids. This variance of velocities is referred to as dispersion and is traditionally described mathematically by the advection-dispersion equation (ADE). Analytical solutions to the ADE are available and are referred to as advection-dispersion models (ADM).The ADM is fitted to the tracer data by varying the parameters until a best-fit is achieved between the experimental residence time distribution (RTD) and the model RTD. The major shortcomings of this approach are due to the symmetry of the ADM and its associated prediction of finite concentrations at zero time and its inability to reflect the long upper tail typical in experimental RTD data. This paper presents an alternative conceptual approach to the ADM for modeling solute transport in fractured-rock and karst aquifers. In this approach the variance in fl ow velocities and fl ow path lengths are addressed directly by treating them as random, gamma distributed variables and deriving the RTD from a transformation of random variables based on the ratio of length to velocity and representing the RTD as a conditional probability distribution of time. The resulting four parameter (Gamma-RTD) model is relatively easily parameterized since the fl ow path length is tightly distributed about the known straight line distance between the injection point and the effluent. The model is demonstrated and contrasted to the ADM below by applying it to tracer data from a quantitative tracer study at Mammoth Cave National Park. The results indicate that the Gamma-RTD is superior to the ADM in modeling the shape as well as the area of the experimental RTD