Assessment of Flood Risk Under Future Climate Conditions

Global climate change is predicted to have impacts on the frequency and severity of flood events. In this study, output from Global Circulation Models (GCMs) for a range of possible future climate scenarios was used to force hydrologic models for four case study watersheds built using the Soil and Water Assessment Tool (SWAT). GCM output was applied with either the delta change method or a bias correction. Potential changes in flood risk are assessed based on modeling results and possible relationships to watershed characteristics. Differences in model outputs when using the two different methods of adjusting GCM output are also compared. Preliminary results indicate that watersheds exhibiting higher proportions of runoff in streamflow are more vulnerable to changes in flood risk. The delta change method appears to be more useful when simulating extreme events as it better preserves daily climate variability as opposed to using bias corrected GCM output

Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations

3D-2D crossover in the naturally layered superconductor (LaSe)1.14(NbSe2)

The temperature and angular dependencies of the resistive upper critical magnetic field $B_{c2}$ reveal a dimensional crossover of the superconducting state in the highly anisotropic misfit-layer single crystal of (LaSe)$_{1.14}$(NbSe$_2$) with the critical temperature $T_c$ of 1.23 K. The temperature dependence of the upper critical field $B_{c2\parallel ab}(T)$ for a field orientation along the conducting $(ab)$-planes displays a characteristic upturn at 1.1 K and below this temperature the angular dependence of $B_{c2}$ has a cusp around the parallel field orientation. Both these typical features are observed for the first time in a naturally crystalline layered system.Comment: 7 pages incl. 3 figure

Supplementary report to the final report of the coral reef expert group: S8. Monitoring site planner - choosing where to monitor coral reefs on the Great Barrier Reef

[Extract] In this project we develop a multi-criteria analysis and optimisation tool, called the Monitoring Site Planner, to assist in the evaluation of the existing and new proposed coral reef monitoring programs for the Great Barrier Reef (the Reef). This tool allows the performance of a given monitoring survey design (a set of reefs that will be monitored) to be evaluated against a set of performance criteria. This tool can be run as an interactive web application that is available for use from https://tools.eatlas.org.au/msp.An accessible copy of this report is not yet available from this repository, please contact [email protected] for more information

Top-dressing durum with nitrogen to manage protein

Non-Peer ReviewedGrain protein is an important factor in determining the quality of durum wheat (Triticum turidum L.). Durum markets pay a premium for protein content of 13% or higher. During the 1990's, the average protein content of durum produced on the Canadian prairies has been 12.5% or less, leaving a sizable proportion of the durum crop unsuitable for the premium market. The overall objective of this project is to determine the effect and relative efficiency of top-dressed N on grain protein, quality, yield, and economic return of durum wheat. Nitrogen at three rates (20,40 and 60 kg N ha-1) was top-dressed on durum at 4 growth stages; before germination (during seeding), five leaf, flag leaf and flowering. The study was done over three years at two locations (Indian Head and Swift Current, SK). Four cultivars were used. Increasing the rate of top-dressed nitrogen increased the protein content of the durum. Applying all the nitrogen at seeding provided the most consistent increases in protein. However, when the yield potential increased during the growing season due to above normal spring and summer precipitation, protein levels in the durum seed increased when nitrogen was top-dressed during the growing season

Inferring Energy Bounds via Static Program Analysis and Evolutionary Modeling of Basic Blocks

The ever increasing number and complexity of energy-bound devices (such as the ones used in Internet of Things applications, smart phones, and mission critical systems) pose an important challenge on techniques to optimize their energy consumption and to verify that they will perform their function within the available energy budget. In this work we address this challenge from the software point of view and propose a novel parametric approach to estimating tight bounds on the energy consumed by program executions that are practical for their application to energy verification and optimization. Our approach divides a program into basic (branchless) blocks and estimates the maximal and minimal energy consumption for each block using an evolutionary algorithm. Then it combines the obtained values according to the program control flow, using static analysis, to infer functions that give both upper and lower bounds on the energy consumption of the whole program and its procedures as functions on input data sizes. We have tested our approach on (C-like) embedded programs running on the XMOS hardware platform. However, our method is general enough to be applied to other microprocessor architectures and programming languages. The bounds obtained by our prototype implementation can be tight while remaining on the safe side of budgets in practice, as shown by our experimental evaluation.Comment: Pre-proceedings paper presented at the 27th International Symposium on Logic-Based Program Synthesis and Transformation (LOPSTR 2017), Namur, Belgium, 10-12 October 2017 (arXiv:1708.07854). Improved version of the one presented at the HIP3ES 2016 workshop (v1): more experimental results (added benchmark to Table 1, added figure for new benchmark, added Table 3), improved Fig. 1, added Fig.

A generalized Robinson-Foulds distance for labeled trees.

The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the type of the branching event (e.g. speciation, duplication, transfer, etc). We extend RF to trees with labeled internal nodes by including a node flip operation, alongside edge contractions and extensions. We explore properties of this extended RF distance in the case of a binary labeling. In particular, we show that contrary to the unlabeled case, an optimal edit path may require contracting "good" edges, i.e. edges shared between the two trees. We provide a 2-approximation algorithm which is shown to perform well empirically. Looking ahead, computing distances between labeled trees opens up a variety of new algorithmic directions.Implementation and simulations available at https://github.com/DessimozLab/pylabeledrf

A generalized Robinson-Foulds distance for labeled trees

Background: The Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the type of the branching event (e.g. speciation, duplication, transfer, etc). Results: We extend RF to trees with labeled internal nodes by including a node flip operation, alongside edge contractions and extensions. We explore properties of this extended RF distance in the case of a binary labeling. In particular, we show that contrary to the unlabeled case, an optimal edit path may require contracting “good” edges, i.e. edges shared between the two trees. Conclusions: We provide a 2-approximation algorithm which is shown to perform well empirically. Looking ahead, computing distances between labeled trees opens up a variety of new algorithmic directions. Implementation and simulations available at https://github.com/DessimozLab/pylabeledrf

Diagnostic test interpretation and referral delay in patients with interstitial lung disease.

BACKGROUND:Diagnostic delays are common in patients with interstitial lung disease (ILD). A substantial percentage of patients experience a diagnostic delay in the primary care setting, but the factors underpinning this observation remain unclear. In this multi-center investigation, we assessed ILD reporting on diagnostic test interpretation and its association with subsequent pulmonology referral by a primary care physician (PCP). METHODS:A retrospective cohort analysis of patients referred to the ILD programs at UC-Davis and University of Chicago by a PCP within each institution was performed. Computed tomography (CT) of the chest and abdomen and pulmonary function test (PFT) were reviewed to identify the date ILD features were first present and determine the time from diagnostic test to pulmonology referral. The association between ILD reporting on diagnostic test interpretation and pulmonology referral was assessed, as was the association between years of diagnostic delay and changes in fibrotic features on longitudinal chest CT. RESULTS:One hundred and forty-six patients were included in the final analysis. Prior to pulmonology referral, 66% (n = 97) of patients underwent chest CT, 15% (n = 21) underwent PFT and 15% (n = 21) underwent abdominal CT. ILD features were reported on 84, 62 and 33% of chest CT, PFT and abdominal CT interpretations, respectively. ILD reporting was associated with shorter time to pulmonology referral when undergoing chest CT (1.3 vs 15.1 months, respectively; p = 0.02), but not PFT or abdominal CT. ILD reporting was associated with increased likelihood of pulmonology referral within 6 months of diagnostic test when undergoing chest CT (rate ratio 2.17, 95% CI 1.03-4.56; p = 0.04), but not PFT or abdominal CT. Each year of diagnostic delay was associated with a 1.8% increase in percent fibrosis on chest CT. Patients with documented dyspnea had shorter time to chest CT acquisition and pulmonology referral than patients with documented cough and lung crackles. CONCLUSIONS:Determinants of ILD diagnostic delays in the primary care setting include underreporting of ILD features on diagnostic testing and prolonged time to pulmonology referral even when ILD is reported. Interventions to modulate these factors may reduce ILD diagnostic delays in the primary care setting