Fifty years of appreciation, 1895-1945 : a record of our progress during the past half century.

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Delineating environmental envelopes to improve mapping of species distributions, via a hurdle model with CART &/or MaxEnT

Species distribution modelling (SDM) typically analyses species’ presence together with some form of absence information. Ideally absences comprise observations or are inferred from comprehensive sampling. When such information is not available, then pseudo-absences are often generated from the background locations within the study region of interest containing the presences, or else absence is implied through the comparison of presences to the whole study region, e.g. as is the case in Maximum Entropy (MaxEnt) or Poisson point process modelling. However, the choice of which absence information to include can be both challenging and highly influential on SDM predictions (e.g. Oksanen and Minchin, 2002). In practice, the use of pseudo- or implied absences often leads to an imbalance where absences far outnumber presences. This leaves analysis highly susceptible to ‘naughty-noughts’: absences that occur beyond the envelope of the species, which can exert strong influence on the model and its predictions (Austin and Meyers, 1996). Also known as ‘excess zeros’, naughty noughts can be estimated via an overall proportion in simple hurdle or mixture models (Martin et al., 2005). However, absences, especially those that occur beyond the species envelope, can often be more diverse than presences. Here we consider an extension to excess zero models. The two-staged approach first exploits the compartmentalisation provided by classification trees (CTs) (as in O’Leary, 2008) to identify multiple sources of naughty noughts and simultaneously delineate several species envelopes. Then SDMs can be fit separately within each envelope, and for this stage, we examine both CTs (as in Falk et al., 2014) and the popular MaxEnt (Elith et al., 2006). We introduce a wider range of model performance measures to improve treatment of naughty noughts in SDM. We retain an overall measure of model performance, the area under the curve (AUC) of the Receiver-Operating Curve (ROC), but focus on its constituent measures of false negative rate (FNR) and false positive rate (FPR), and how these relate to the threshold in the predicted probability of presence that delimits predicted presence from absence. We also propose error rates more relevant to users of predictions: false omission rate (FOR), the chance that a predicted absence corresponds to (and hence wastes) an observed presence, and the false discovery rate (FDR), reflecting those predicted (or potential) presences that correspond to absence. A high FDR may be desirable since it could help target future search efforts, whereas zero or low FOR is desirable since it indicates none of the (often valuable) presences have been ignored in the SDM. For illustration, we chose Bradypus variegatus, a species that has previously been published as an exemplar species for MaxEnt, proposed by Phillips et al. (2006). We used CTs to increasingly refine the species envelope, starting with the whole study region (E0), eliminating more and more potential naughty noughts (E1–E3). When combined with an SDM fit within the species envelope, the best CT SDM had similar AUC and FPR to the best MaxEnt SDM, but otherwise performed better. The FNR and FOR were greatly reduced, suggesting that CTs handle absences better. Interestingly, MaxEnt predictions showed low discriminatory performance, with the most common predicted probability of presence being in the same range (0.00-0.20) for both true absences and presences. In summary, this example shows that SDMs can be improved by introducing an initial hurdle to identify naughty noughts and partition the envelope before applying SDMs. This improvement was barely detectable via AUC and FPR yet visible in FOR, FNR, and the comparison of predicted probability of presence distribution for pres/absence.

Propagation of an isothermal shock in stellar envelopes

We have studied in this paper the propagation of an isothermal shock in the radiative envelopes of the Bosman-Crespin model for a hot star and Boury’s model for a giant star. A spherically symmetric disturbance is supposed to be originated at or outside the surface of the convective core. We have used Whitham’s rule to study the variation in the shock strength and the shock velocity after modifying it for inclusion of pressure, energy and flux of radiation. We find the shock increases in strength as it propagates through the envelopes of decreasing density, pressure and temperature. The velocity of the shock decreases for very weak initial shock strengths, for intermediate initial shock strength it first decreases and then increases, while for large initial shock strength, it always increases. This aspect of the problem throws some light on the stability of the models under consideration.

Real-Time Bayesian Analysis of Ground Motion Envelopes for Earthquake Early Warning

Current earthquake early warning systems usually make magnitude and location predictions and send out a warning to the users based on those predictions. We describe an algorithm that assesses the validity of the predictions in real-time. Our algorithm monitors the envelopes of horizontal and vertical acceleration, velocity, and displacement. We compare the observed envelopes with the ones predicted by Cua & Heaton's envelope ground motion prediction equations (Cua 2005). We define a "test function" as the logarithm of the ratio between observed and predicted envelopes at every second in real-time. Once the envelopes deviate beyond an acceptable threshold, we declare a misfit. Kurtosis and skewness of a time evolving test function are used to rapidly identify a misfit. Real-time kurtosis and skewness calculations are also inputs to both probabilistic (Logistic Regression and Bayesian Logistic Regression) and nonprobabilistic (Least Squares and Linear Discriminant Analysis) models that ultimately decide if there is an unacceptable level of misfit. This algorithm is designed to work at a wide range of amplitude scales. When tested with synthetic and actual seismic signals from past events, it works for both small and large events.

Process envelopes for stabilisation/solidification of contaminated soil using lime-slag blend.

PURPOSE: Stabilisation/solidification (S/S) has emerged as an efficient and cost-effective technology for the treatment of contaminated soils. However, the performance of S/S-treated soils is governed by several intercorrelated variables, which complicates the optimisation of the treatment process design. Therefore, it is desirable to develop process envelopes, which define the range of operating variables that result in acceptable performance. METHODS: In this work, process envelopes were developed for S/S treatment of contaminated soil with a blend of hydrated lime (hlime) and ground granulated blast furnace slag (GGBS) as the binder (hlime/GGBS = 1:4). A sand contaminated with a mixture of heavy metals and petroleum hydrocarbons was treated with 5%, 10% and 20% binder dosages, at different water contents. The effectiveness of the treatment was assessed using unconfined compressive strength (UCS), permeability, acid neutralisation capacity and contaminant leachability with pH, at set periods. RESULTS: The UCS values obtained after 28 days of treatment were up to ∼800 kPa, which is quite low, and permeability was ∼10(-8) m/s, which is higher than might be required. However, these values might be acceptable in some scenarios. The binder significantly reduced the leachability of cadmium and nickel. With the 20% dosage, both metals met the waste acceptance criteria for inert waste landfill and relevant environmental quality standards. CONCLUSIONS: The results show that greater than 20% dosage would be required to achieve a balance of acceptable mechanical and leaching properties. Overall, the process envelopes for different performance criteria depend on the end-use of the treated material.

Cement-fly ash stabilisation/solidification of contaminated soil: Performance properties and initiation of operating envelopes

This study was aimed at evaluating the mechanical and pH-dependent leaching performance of a mixed contaminated soil treated with a mixture of Portland cement (CEMI) and pulverised fuel ash (PFA). It also sought to develop operating envelopes, which define the range(s) of operating variables that result in acceptable performance. A real site soil with low contaminant concentrations, spiked with 3000mg/kg each of Cd, Cu, Pb, Ni and Zn, and 10,000mg/kg of diesel, was treated with one part CEMI and four parts PFA (CEMI:PFA=1:4) using different binder and water contents. The performance was assessed over time using unconfined compressive strength (UCS), hydraulic conductivity, acid neutralisation capacity (ANC) and pH-dependent leachability of contaminants. With binder dosages ranging from 5% to 20% and water contents ranging from 14% to 21% dry weight, the 28-day UCS was up to 500kPa and hydraulic conductivity was around 10-8m/s. With leachant pH extremes of 7.2 and 0.85, leachability of the contaminants was in the range: 0.02-3500mg/kg for Cd, 0.35-1550mg/kg for Cu, 0.03-92mg/kg for Pb, 0.01-3300mg/kg for Ni, 0.02-4010mg/kg for Zn, and 7-4884mg/kg for total petroleum hydrocarbons (TPHs), over time. Design charts were produced from the results of the study, which show the water and/or binder proportions that could be used to achieve relevant performance criteria. The charts would be useful for the scale-up and design of stabilisation/solidification (S/S) treatment of similar soil types impacted with the same types of contaminants. © 2013 Elsevier Ltd.

Comparisons of operating envelopes for contaminated soil stabilised/solidified with different cementitious binders

This work initiated the development of operating envelopes for stabilised/solidified contaminated soils. The operating envelopes define the range of operating variables for acceptable performance of the treated soils. The study employed a soil spiked with 3,000 mg/kg each of Cd, Cu, Pb, Ni and Zn, and 10,000 mg/kg of diesel. The binders used for treatment involved Portland cement (CEMI), pulverised fuel ash (PFA), ground granulated blast furnace slag (GGBS) and hydrated lime (hlime). The specific binder formulations were CEMI, CEMI/PFA = 1:4, CEMI/GGBS = 1:9 and hlime/GGBS = 1:4. The water contents employed ranged from 13 % to 21 % (dry weight), while binder dosages ranged from 5 % to 20 % (w/w). We monitored the stabilised/solidified soils for up to 84 days using different performance tests. The tests include unconfined compressive strength (UCS), hydraulic conductivity, acid neutralisation capacity (ANC) and pH-dependent leachability of contaminants. The water content range resulted in adequate workability of the mixes but had no significant effect on leachability of contaminants. We produced design charts, representing operating envelopes, from the results generated. The charts establish relationships between water content, binder dosage and UCS; and binder dosage, leachant pH and leachability of contaminants. The work also highlights the strengths and weaknesses of the different binder formulations. © 2013 Springer-Verlag Berlin Heidelberg.

Infection of monkeys by simian-human immunodeficiency viruses with transmitted/founder clade C HIV-1 envelopes.

Simian-human immunodeficiency viruses (SHIVs) that mirror natural transmitted/founder (T/F) viruses in man are needed for evaluation of HIV-1 vaccine candidates in nonhuman primates. Currently available SHIVs contain HIV-1 env genes from chronically-infected individuals and do not reflect the characteristics of biologically relevant HIV-1 strains that mediate human transmission. We chose to develop clade C SHIVs, as clade C is the major infecting subtype of HIV-1 in the world. We constructed 10 clade C SHIVs expressing Env proteins from T/F viruses. Three of these ten clade C SHIVs (SHIV KB9 C3, SHIV KB9 C4 and SHIV KB9 C5) replicated in naïve rhesus monkeys. These three SHIVs are mucosally transmissible and are neutralized by sCD4 and several HIV-1 broadly neutralizing antibodies. However, like natural T/F viruses, they exhibit low Env reactivity and a Tier 2 neutralization sensitivity. Of note, none of the clade C T/F SHIVs elicited detectable autologous neutralizing antibodies in the infected monkeys, even though antibodies that neutralized a heterologous Tier 1 HIV-1 were generated. Challenge with these three new clade C SHIVs will provide biologically relevant tests for vaccine protection in rhesus macaques.

Hydrocarbon Anions in Interstellar Clouds and Circumstellar Envelopes

The recent detection of the hydrocarbon anion C$_6$H$^-$ in the interstellar medium has led us to investigate the synthesis of hydrocarbon anions in a variety of interstellar and circumstellar environments. We find that the anion/neutral abundance ratio can be quite large, on the order of at least a few percent, once the neutral has more than five carbon atoms. Detailed modeling shows that the column densities of C$_6$H$^-$ observed in IRC+10216 and TMC-1 can be reproduced. Our calculations also predict that other hydrocarbon anions, such as C$_{4}$H$^{-}$ and C$_8$H$^-$, are viable candidates for detection in IRC+10216, TMC-1 and photon-dominated regions such as the Horsehead Nebula.

Maximal C*-algebras of quotients and injective envelopes of C*-algebras

A new C*-enlargement of a C*-algebra A nested between the local multiplier algebra of A and its injective envelope is introduced. Various aspects of this maximal C*-algebra of quotients are studied, notably in the setting of AW*-algebras. As a by-product we obtain a new example of a type I C*-algebra such that its second iterated local multiplier algebra is strictly larger than its local multiplier algebra.