Experimental Design Principles to Choose the Number of Monte Carlo Replicates for Stochastic Ecological Models

Ecologists often rely on computer models as virtual laboratories to evaluate alternative theories, make predictions, perform scenario analysis, and to aid in decision-making. The application of ecological models can have real-world consequences that drive ecological theory development and science-based decision and policy-making, so it is imperative that the conclusions drawn from ecological models have a strong, credible quantitative basis. In particular it is important to establish whether any predicted change in a model output has ecological and statistical significance. Ecological models may include stochastic components, using probability distributions to represent some modeled processes. An individual run of a stochastic ecological model is a random draw from an infinitely large population, requiring replicate simulations to estimate the distribution of model outcomes. An important consideration is the number of Monte Carlo replicates necessary to draw useful conclusions from the model analysis. A simple framework is presented that borrows from well-understood techniques for experimental design, including confidence interval estimation and sample size power analysis. The desired precision of interval estimates for model prediction, or the minimum desired detectable effect size between scenarios, is established by the researcher in the context of the model objectives and the ecological system. The number of replicates required to achieve that level of precision or detectable effect is computed given an estimate of the variability in the model outcomes of interest. If the number of replicates is computationally prohibitive, then the expected precision or detectable effect for that sample size should be reported. An example is given for a stochastic model of fire spread integrated with an eco-hydrological model. © 2018 Elsevier B.V

Structure of cellulose microfibrils in primary cell-walls from collenchyma

In the primary walls of growing plant cells, the glucose polymer cellulose is assembled into long microfibrils a few nanometers in diameter. The rigidity and orientation of these microfibrils control cell expansion; therefore, cellulose synthesis is a key factor in the growth and morphogenesis of plants. Celery (Apium graveolens) collenchyma is a useful model system for the study of primary wall microfibril structure because its microfibrils are oriented with unusual uniformity, facilitating spectroscopic and diffraction experiments. Using a combination of x-ray and neutron scattering methods with vibrational and nuclear magnetic resonance spectroscopy, we show that celery collenchyma microfibrils were 2.9 to 3.0 nm in mean diameter, with a most probable structure containing 24 chains in cross section, arranged in eight hydrogen-bonded sheets of three chains, with extensive disorder in lateral packing, conformation, and hydrogen bonding. A similar 18-chain structure, and 24-chain structures of different shape, fitted the data less well. Conformational disorder was largely restricted to the surface chains, but disorder in chain packing was not. That is, in position and orientation, the surface chains conformed to the disordered lattice constituting the core of each microfibril. There was evidence that adjacent microfibrils were noncovalently aggregated together over part of their length, suggesting that the need to disrupt these aggregates might be a constraining factor in growth and in the hydrolysis of cellulose for biofuel production

Identification and frequency of consumption of wild edible plants over a year in central Tunisia: a mixed-methods approach

Objective: To identify wild plants used as food and assess their frequency of consumption over a year in a region of Tunisia where agriculture is undergoing a major transformation from smallholder farming to an intensive high-input agricultural system. Design: Qualitative ethnobotanical study followed by a survey of women's frequency of consumption of wild plants conducted using FFQ at quarterly intervals. Setting: Sidi Bouzid governorate of central Tunisia. Participants: Mixed-gender group of key informants (n 14) and focus group participants (n 43). Survey sample of women aged 20-49 years, representative at governorate level (n 584). Results: Ethnobotanical study: thirty folk species of wild edible plants corresponding to thirty-five taxa were identified by key informants, while twenty folk species (twenty-five taxa) were described by focus groups as commonly eaten. Population-based survey: 98 % of women had consumed a wild plant over the year, with a median frequency of 2 d/month. Wild and semi-domesticated fennel (Foeniculum vulgare Mill. and Anethum graveolens) was the most frequently consumed folk species. Women in the upper tertile of wild plant consumption frequency were more likely to be in their 30s, to live in an urban area, to have non-monetary access to foods from their extended family and to belong to wealthier households. Conclusions: In this population, wild edible plants, predominantly leafy vegetables, are appreciated but consumed infrequently. Their favourable perception, however, offers an opportunity for promoting their consumption which could play a role in providing healthy diets and mitigating the obesity epidemic that is affecting the Tunisian population

Forage type influences milk yield and ruminal responses to wheat adaptation in late-lactation dairy cows

peer-reviewedThe effects of different wheat adaptation strategies on ruminal fluid pH, dry matter intake (DMI) and energy-corrected milk (ECM) were measured in 28 late-lactation dairy cows. Cows were fed either perennial ryegrass (PRG) hay or alfalfa hay and had no previous wheat adaptation. Wheat was gradually substituted for forage in 3 even increments, over 6 or 11 d, until wheat made up 40% of DMI (∼8 kg of dry matter/cow per day). We found no differences in DMI between adaptation strategies (6 or 11 d) within forage type; however, cows fed alfalfa hay consumed more overall and produced more ECM. The rate of ruminal pH decline after feeding, as well as the decrease in mean, minimum, and maximum ruminal pH with every additional kilogram of wheat was greater for cows fed alfalfa hay. Cows fed alfalfa hay and on the 6-d adaptation strategy had the lowest mean and minimum ruminal fluid pH on 3 consecutive days and were the only treatment group to record pH values below 6.0. Despite ruminal pH declining to levels typically considered low, no other measured parameters indicated compromised fermentation or acidosis. Rather, cows fed alfalfa hay and adapted to wheat over 6 d had greater ECM yields than cows on the 11-d strategy. This was due to the 6-d adaptation strategy increasing the metabolizable energy intake in a shorter period than the 11-d strategy, as substituting wheat for alfalfa hay caused a substantial increase in the metabolizable energy concentration of the diet. We found no difference in ECM between adaptation strategies when PRG hay was fed, as there was no difference in metabolizable energy intake. The higher metabolizable energy concentration and lower intake of the PRG hay meant the increase in metabolizable energy intake with the substitution of wheat was less pronounced for cows consuming PRG hay compared with alfalfa hay. Neither forage type nor adaptation strategy affected time spent ruminating. The higher intakes likely contributed to the lower ruminal pH values from the alfalfa hay treatments. However, both forages allowed the rumen contents to resist the large declines in ruminal pH typically seen during rapid grain adaptation. Depending on the choice of base forage, rapid grain introduction may not result in poor adaptation. In situations where high-energy grains are substituted for a low-energy, high-fiber basal forage, rapid introduction could prove beneficial over gradual strategies

A simple model for magnetism in itinerant electron systems

A new lattice model of interacting electrons is presented. It can be viewed as a classical Hubbard model in which the energy associated to electron itinerance is proportional to the total number of possible electron jumps. Symmetry properties of the Hubbard model are preserved. In the half-filled band with strong interaction the model becomes the Ising model. The main features of the magnetic behavior of the model in the one-dimensional and mean-field cases are studied.Comment: 9 pages, 3 figures, to be published in Physica

Characterization of meta-Cresol Purple for spectrophotometric pH measurements in saline and hypersaline media at sub-zero temperatures

Accurate pH measurements in polar waters and sea ice brines require pH indicator dyes characterized at near-zero and below-zero temperatures and high salinities. We present experimentally determined physical and chemical characteristics of purified meta-Cresol Purple (mCP) pH indicator dye suitable for pH measurements in seawater and conservative seawater-derived brines at salinities (S) between 35 and 100 and temperatures (T) between their freezing point and 298.15 K (25 °C). Within this temperature and salinity range, using purified mCP and a novel thermostated spectrophotometric device, the pH on the total scale (pHT) can be calculated from direct measurements of the absorbance ratio R of the dye in natural samples as pHT=−log(kT2e2)+log(R−e11−Re3e2) Based on the mCP characterization in these extended conditions, the temperature and salinity dependence of the molar absorptivity ratios and − log(kT2e2) of purified mCP is described by the following functions: e1 = −0.004363 + 3.598 × 10−5T, e3/e2 = −0.016224 + 2.42851 × 10−4T + 5.05663 × 10−5(S − 35), and − log(kT2e2) = −319.8369 + 0.688159 S −0.00018374 S2 + (10508.724 − 32.9599 S + 0.059082S2) T−1 + (55.54253 − 0.101639 S) ln T −0.08112151T. This work takes the characterisation of mCP beyond the currently available ranges of 278.15 K ≤ T ≤ 308.15 K and 20 ≤ S ≤ 40 in natural seawater, thereby allowing high quality pHT measurements in polar systems

Evaluation of the n-alkane technique for estimating herbage dry matter intake of dairy cows offered herbage harvested at two different stages of growth in summer and autumn

peer-reviewedThe n-alkane technique for estimating herbage dry matter intake (DMI) of dairy cows was investigated in this experiment. Eight Holstein-Friesian dairy cows were offered perennial ryegrass ad libitum that had been harvested at two different herbage masses and during two different seasons, in order to assess the effect of herbage mass and season on the accuracy of the n-alkane technique. Two pre-harvested herbage mass treatments (low, target 1500 kg DM/ha versus high, target 4000 kg DM/ha, measured above 4 cm), were investigated in a crossover factorial arrangement within each of two seasons (summer versus autumn), in Ireland. Each season consisted of two periods, each 12 days in length. Cows were housed in individual metabolism stalls to allow for accurate determination of measured DMI. Herbage DMI was estimated, with the n-alkane technique, by dosing cows twice daily with a C32 n-alkane. Pre-harvest herbage mass and season did not affect the n-alkane estimated DMI, although lack of season and herbage mass effects may have been masked by variation that occurred between swards within the same herbage mass and season. However, there were a number of differences between summer and autumn in the fecal recovery rates of a number of n-alkanes suggesting that the effect of season requires further investigation prior to the application of recovery rates from literature values when investigating diet selection and botanical composition. Overall, the n-alkane technique provided good estimates of DMI; the discrepancy had a standard deviation due to sward of 1.2 and 1.0 kg DM/cow per day, and hence potential bias of up to twice this, and a measurement error standard deviation of 1.3 and 1.0 kg DM/cow per day, for the C33/C32 and C31/C32 n-alkane pair methods respectively. Two n-alkane pairs were tested, and C33/C32 n-alkane provided the most precise estimates of DMI, compared with the C31/C32 n-alkane pair. This research provides some strong evidence for future use of the n-alkane technique including that the accuracy of the technique has not been influenced by contemporary changes to herbage management, is not affected by seasonal changes, and overall is an accurate and precise technique for estimating DMI.This research was funded by Teagasc Core Funding (Ireland) and the Irish Dairy Levy Research fund (Ireland). The Department of Economic Development, Jobs, Transport and Resources (Australia), Dairy Australia (Australia) and The University of Melbourne (Australia) supported the travel costs in order to conduct this research

Chemical and isotopic characteristics of the coso east flankhydrothermal fluids: implications for the location and nature of the heatsource

Fluids have been sampled from 9 wells and 2 fumaroles fromthe East Flank of the Coso hydrothermal system with a view toidentifying, if possible, the location and characteristics of the heatsource inflows into this portion of the geothermal field. Preliminaryresults show that there has been extensive vapor loss in the system, mostprobably in response to production. Wells 38A-9, 51-16 and 83A-16 showthe highest CO2-CO-CH4-H2 chemical equilibration temperatures, rangingbetween 300-340oC, and apart from 38A-9, the values are generally inaccordance with the measured temperatures in the wells. Calculatedtemperatures for the fractionation of 13C between CO2 and CH4 are inexcess of 400oC in fluids from wells 38A-9, 64-16-RD2 and 51A-16,obviously pointing to equilibrium conditions from deeper portions of thereservoir. Given that the predominant reservoir rock lithologies in theCoso system are relatively silicic (granitic to dioritic), the isotopicsignatures appear to reflect convective circulation and equilibrationwithin rocks close to the plastic-brittle transition. 3He/4He signatures,in conjunction with relative volatile abundances in the Coso fluids,point to a possibly altered mantle source for the heat sourcefluids

SU(N) Antiferromagnets and Strongly Coupled QED: Effective Field Theory for Josephson Junctions Arrays

We review our analysis of the strong coupling of compact QED on a lattice with staggered Fermions. We show that, for infinite coupling, compact QED is exactly mapped in a quantum antiferromagnet. We discuss some aspects of this correspondence relevant for effective field theories of Josephson junctions arrays.Comment: 33 pages,latex,Proceedings of "Common Trends in Condensed Matter and High Energy Physics",DFUPG 1/9