Summary goodness‐of‐fit statistics for binary generalized linear models with noncanonical link functions

Generalized linear models (GLM) with a canonical logit link function are the primary modeling technique used to relate a binary outcome to predictor variables. However, noncanonical links can offer more flexibility, producing convenient analytical quantities (e.g., probit GLMs in toxicology) and desired measures of effect (e.g., relative risk from log GLMs). Many summary goodness‐of‐fit (GOF) statistics exist for logistic GLM. Their properties make the development of GOF statistics relatively straightforward, but it can be more difficult under noncanonical links. Although GOF tests for logistic GLM with continuous covariates (GLMCC) have been applied to GLMCCs with log links, we know of no GOF tests in the literature specifically developed for GLMCCs that can be applied regardless of link function chosen. We generalize the Tsiatis GOF statistic originally developed for logistic GLMCCs, (), so that it can be applied under any link function. Further, we show that the algebraically related Hosmer–Lemeshow () and Pigeon–Heyse (J²) statistics can be applied directly. In a simulation study, , , and J² were used to evaluate the fit of probit, log–log, complementary log–log, and log models, all calculated with a common grouping method. The statistic consistently maintained Type I error rates, while those of and J² were often lower than expected if terms with little influence were included. Generally, the statistics had similar power to detect an incorrect model. An exception occurred when a log GLMCC was incorrectly fit to data generated from a logistic GLMCC. In this case, had more power than or J².     

Different fates of deposited and in a temperate forest in northeast China: a 15N tracer study

Increasing atmospheric reactive nitrogen (N) deposition due to human activities could change N cycling in terrestrial ecosystems. However, the differences between the fates of deposited and are still not fully understood. Here, we investigated the fates of deposited and , respectively, via the application of ¹⁵NH₄NO₃ and NH₄¹⁵NO₃ in a temperate forest ecosystem. Results showed that at 410 days after tracer application, most was immobilized in litter layer (50 ± 2%), while a considerable amount of penetrated into 0–5 cm mineral soil (42 ± 2%), indicating that litter layer and 0–5 cm mineral soil were the major N sinks of and , respectively. Broad‐leaved trees assimilated more ¹⁵N under NH₄¹⁵NO₃ treatment compared to under ¹⁵NH₄NO₃ treatment, indicating their preference for –N. At 410 days after tracer application, 16 ± 4% added ¹⁵N was found in aboveground biomass under treatment, which was twice more than that under treatment (6 ± 1%). At the same time, approximately 80% added ¹⁵N was recovered in soil and plants under both treatments, which suggested that this forest had high potential for retention of deposited N. These results provided evidence that there were great differences between the fates of deposited and , which could help us better understand the mechanisms and capability of forest ecosystems as a sink of reactive nitrogen.     

High‐throughput identification of protein mutant stability computed from a double mutant fitness landscape

The effect of a mutation on protein stability is traditionally measured by genetic construction, expression, purification, and physical analysis using low‐throughput methods. This process is tedious and limits the number of mutants able to be examined in a single study. In contrast, functional fitness effects can be measured in a high‐throughput manner by various deep mutational scanning tools. Using protein GB 1, we have recently demonstrated the feasibility of estimating the mutational stability effect ( G) of single‐substitution based on the functional fitness profile of all double‐substitutions. The principle is to identify genetic backgrounds that have an exhausted stability margin. The functional effect of an additional substitution on these genetic backgrounds can then be used to compute the mutational G based on the biophysical relationship between functional fitness and thermodynamic stability. However, to identify such genetic backgrounds, the approach described in our previous study required a benchmark dataset, which is a set of known mutational G. In this study, a benchmark‐independent approach is developed. The genetic backgrounds of interest are identified using k‐means clustering with the integration of structural information. We further demonstrated that a reasonable approximation of G can also be obtained without taking structural information into account. In summary, this study describes a novel method for computing G from double‐substitution functional fitness profiles alone, without relying on any known mutational G as a benchmark.     

Impact of Hydroxylation and Hydration on the Reactivity of α‐Fe2O3 (0001) and (102) Surfaces under Environmental and Electrochemical Conditions

Hematite (α‐Fe₂O₃) is widely used as a catalytic electrode material in photo‐electrochemical water oxidation, where its surface compositions and stabilities can strongly impact the redox reaction process. Here, its surface configurations in environmental or electrochemical conditions are assessed via density functional theory (DFT) calculations conducted at the Perdew, Burke, and Ernzerhof (PBE)+U level. The most energetically favorable surface domains of α‐Fe₂O₃ (0001) and (102) are predicted by constructing the surface phase diagrams in the framework of first‐principle thermodynamics. The relative surface stabilities are investigated as a function of partial pressures of oxygen and water, temperature, solution pH, and electrode potential not only for perfect bulk terminations but also for defect‐containing surfaces having various degrees of hydroxylation and hydration. In order to assess the impact on the redox reactions of the surface planes as well as of the extent of surface hydration/hydroxylation, the thermodynamics of the four‐step oxygen evolution reaction (OER) mechanism are examined in detail for different models of the α‐Fe₂O₃ (0001) and (102) surfaces. Importantly, the results underline that the nature of the surface termination and the degree of near‐surface hydroxylation give rise to significant variations in the OER overpotentials.     

pKa predictions for proteins,RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa

We developed a Poisson‐Boltzmann based approach to calculate the values of protein ionizable residues (Glu, Asp, His, Lys and Arg), nucleotides of RNA and single stranded DNA. Two novel features were utilized: the dielectric properties of the macromolecules and water phase were modeled via the smooth Gaussian‐based dielectric function in DelPhi and the corresponding electrostatic energies were calculated without defining the molecular surface. We tested the algorithm by calculating values for more than 300 residues from 32 proteins from the PPD dataset and achieved an overall RMSD of 0.77. Particularly, the RMSD of 0.55 was achieved for surface residues, while the RMSD of 1.1 for buried residues. The approach was also found capable of capturing the large shifts of various single point mutations in staphylococcal nuclease (SNase) from ‐cooperative dataset, resulting in an overall RMSD of 1.6 for this set of pKa's. Investigations showed that predictions for most of buried mutant residues of SNase could be improved by using higher dielectric constant values. Furthermore, an option to generate different hydrogen positions also improves predictions for buried carboxyl residues. Finally, the calculations on two RNAs demonstrated the capability of this approach for other types of biomolecules. Proteins 2015; 83:2186–2197. © 2015 Wiley Periodicals, Inc.     

Sensitivity analysis of effective population size to demographic parameters in house sparrow populations

The ratio between the effective and the census population size, , is an important measure of the long‐term viability and sustainability of a population. Understanding which demographic processes that affect most will improve our understanding of how genetic drift and the probability of fixation of alleles is affected by demography. This knowledge may also be of vital importance in management of endangered populations and species. Here, we use data from 13 natural populations of house sparrow (Passer domesticus) in Norway to calculate the demographic parameters that determine . Using the global variance‐based Sobol’ method for the sensitivity analyses, we found that was most sensitive to demographic variance, especially among older individuals. Furthermore, the individual reproductive values (that determine the demographic variance) were most sensitive to variation in fecundity. Our results draw attention to the applicability of sensitivity analyses in population management and conservation. For population management aiming to reduce the loss of genetic variation, a sensitivity analysis may indicate the demographic parameters towards which resources should be focused. The result of such an analysis may depend on the life history and mating system of the population or species under consideration, because the vital rates and sex–age classes that is most sensitive to may change accordingly.     

Nanodiamond‐Embedded p‐Type Copper(I) Oxide Nanocrystals for Broad‐Spectrum Photocatalytic Hydrogen Evolution

Copper(I) oxide (Cu₂O) is an attractive photocatalyst because of its abundance, low toxicity, environmental compatibility, and narrow direct band gap, which allows efficient light harvesting. However, Cu₂O exhibits poor photocatalytic performance and photostability because of its short electron diffusion length and low hole mobility. Here, it is demonstrated that nanodiamond (ND) can greatly improve the photocatalytic hydrogen evolution reaction (HER) of the p‐type photocatalyst Cu₂O nanocrystals by nanocomposition. Compared with pure Cu₂O nanocrystals, this composite shows a tremendous improvement in HER performance and photostability. HER rates of 100.0 mg NDs‐Cu₂O nanocrystals are 1597 and 824 under the simulated solar light irradiation (AM 1.5, 100 mW cm^?2) and visible light irradiation (420–760 nm, 77.5 mW cm^?2), respectively. The solar‐to‐hydrogen conversion efficiency of this composite is 0.85%, which is nearly ten times higher than that of pure Cu₂O. The quantum efficiency of the composite is high, with values of 0.17% at and 0.23% at . The broad spectral response of ND provides numerous carriers for the subsequent reactions. The electron‐donating ability of ND and suitable band structures of the two components promote electron injection from ND to Cu₂O. These results suggest the broad applicability of ND to ameliorate the photoelectric properties of semiconductors.     

Purging putative siblings from population genetic data sets: a cautionary view

Interest has surged recently in removing siblings from population genetic data sets before conducting downstream analyses. However, even if the pedigree is inferred correctly, this has the potential to do more harm than good. We used computer simulations and empirical samples of coho salmon to evaluate strategies for adjusting samples to account for family structure. We compared performance in full samples and sibling‐reduced samples of estimators of allele frequency (), population differentiation () and effective population size (). Results: (i) unless simulated samples included large family groups together with a component of unrelated individuals, removing siblings generally reduced precision of and ; (ii) based on the linkage disequilibrium method was largely unbiased using full random samples but became increasingly upwardly biased under aggressive purging of siblings. Under nonrandom sampling (some families over‐represented), using full samples was downwardly biased; removing just the right ‘Goldilocks’ fraction of siblings could produce an unbiased estimate, but this sweet spot varied widely among scenarios; (iii) weighting individuals based on the inferred pedigree (to produce a best linear unbiased estimator, BLUE) maximized precision of when the inferred pedigree was correct but performed poorly when the pedigree was wrong; (iv) a variant of sibling removal that leaves intact small sibling groups appears to be more robust to errors in inferences about family structure. Our results illustrate the complex challenges posed by presence of family structure, suggest that no single optimal solution exists and argue for caution in adjusting population genetic data sets for the presence of putative siblings without fully understanding the consequences.     

Estimators for QST and coalescence times

Comparisons of to can provide insights into the evolutionary processes that lead to differentiation, or lack thereof, among the phenotypes of different groups (e.g., populations, species), and these comparisons have been performed on a variety of taxa, including humans. Here, I show that for neutrally evolving (i.e., by genetic drift, mutation, and gene flow alone) quantitative characters, the two commonly used estimators have somewhat different interpretations in terms of coalescence times, particularly when the number of groups that have been sampled is small. A similar situation occurs for estimators. Consequently, when observations come from only a small number of groups, which is not an unusual situation, it is important to match estimators appropriately when comparing to .     

Nest occurrence and survival of King Rails in fire‐managed coastal marshes in North Carolina and Virginia

Prescribed burning maintains marsh habitat, but its impact on breeding King Rails (Rallus elegans) is poorly understood. This practice may serve as a means to enhance populations of a species whose numbers are declining in the southeastern United States. We used call‐broadcast surveys and nest searches to categorize the state of occupied plots by the presence or non‐presence of nesting activity in the Back Bay region, North Carolina and Virginia, in 2010. We also used nest video surveillance to estimate nest survival in 2009 and 2010. The probabilities that a surveyed plot was occupied (¹) and contained an active nest (²) were higher in recently burned marsh plots (0–1 year‐since‐burn [YSB]) than in plots with ≥2 YSB at Mackay Island and Back Bay National Wildlife Refuges (NWRs). Highest probabilities were recorded in 0–1 YSB plots at Mackay Island NWR ( = 0.96 ± 0.04, = 0.75 ± 0.18), and the lowest in ≥2 YSB plots at Back Bay NWR ( = 0.21 ± 0.10, = 0.03 ± 0.04). Nest survival from egg laying to hatching (31 d) was 0.48 (95% confidence interval [CI] = 0.06–0.83), with an estimated 0.79 (95% CI = 0.29–0.96) survival rate for the incubation stage (21 d). These nest survival estimates for King Rails in fire‐managed marshes were similar to estimates for other populations. Measures of vegetation cover, proxies for concealment, did not differ between nest sites and unused sites, even within recently burned marshes. This lack of differences in vegetation structure suggests that regrowth occurs rapidly during the period between burning (winter months) and the onset of reproduction (late April). Thus, recently burned marshes may benefit nesting King Rails by providing nest concealment. In addition, burned marshes may enhance availability of many invertebrates. Although we found that the probability that surveyed plots contained active nests was higher in recently burned marsh plots, estimates of fledging success are needed before marsh burns can be considered an effective means of fostering population growth.     

The role of a cytosolic superoxide dismutase in barley–pathogen interactions

Reactive oxygen species (ROS), including superoxide ( / ) and hydrogen peroxide (H₂O₂), are differentially produced during resistance responses to biotrophic pathogens and during susceptible responses to necrotrophic and hemi‐biotrophic pathogens. Superoxide dismutase (SOD) is responsible for the catalysis of the dismutation of / to H₂O₂, regulating the redox status of plant cells. Increased SOD activity has been correlated previously with resistance in barley to the hemi‐biotrophic pathogen Pyrenophora teres f. teres (Ptt, the causal agent of the net form of net blotch disease), but the role of individual isoforms of SOD has not been studied. A cytosolic CuZnSOD, HvCSD1, was isolated from barley and characterized as being expressed in tissue from different developmental stages. HvCSD1 was up‐regulated during the interaction with Ptt and to a greater extent during the resistance response. Net blotch disease symptoms and fungal growth were not as pronounced in transgenic HvCSD1 knockdown lines in a susceptible background (cv. Golden Promise), when compared with wild‐type plants, suggesting that cytosolic / contributes to the signalling required to induce a defence response to Ptt. There was no effect of HvCSD1 knockdown on infection by the hemi‐biotrophic rice blast pathogen Magnaporthe oryzae or the biotrophic powdery mildew pathogen Blumeria graminis f. sp. hordei, but HvCSD1 also played a role in the regulation of lesion development by methyl viologen. Together, these results suggest that HvCSD1 could be important in the maintenance of the cytosolic redox status and in the differential regulation of responses to pathogens with different lifestyles.     

A practical approach in bioreactor scale‐up and process transfer using a combination of constant P/V and vvm as the criterion

Bioreactor scale‐up is a critical step in the production of therapeutic proteins such as monoclonal antibodies (MAbs). With the scale‐up criterion such as similar power input per volume or O₂ volumetric mass transfer coefficient ( ), adequate oxygen supply and cell growth can be largely achieved. However, CO₂ stripping in the growth phase is often inadequate. This could cascade down to increased base addition and osmolality, as well as residual lactate increase and compromised production and product quality. Here we describe a practical approach in bioreactor scale‐up and process transfer, where bioreactor information may be limited. We evaluated the sparger and (CO₂ volumetric mass transfer coefficient) from a range of bioreactor scales (3–2,000 L) with different spargers. Results demonstrated that for oxygen is not an issue when scaling from small‐scale to large‐scale bioreactors at the same gas flow rate per reactor volume (vvm). Results also showed that sparging CO₂ stripping, , is dominated by the gas throughput. As a result, a combination of a minimum constant vvm air or N₂ flow with a similar specific power was used as the general scale‐up criterion. An equation was developed to determine the minimum vvm required for removing CO₂ produced from cell respiration. We demonstrated the effectiveness of using such scale‐up criterion with five MAb projects exhibiting different cell growth and metabolic characteristics, scaled from 3 to 2,000 L bioreactors across four sites. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1146–1159, 2017     

speed‐ne: Software to simulate and estimate genetic effective population size (Ne) from linkage disequilibrium observed in single samples

The genetic effective population size, N_e, can be estimated from the average gametic disequilibrium () between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. speed‐ne is a suite of matlab computer code functions to estimate from with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed‐ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of estimators under various population genetic scenarios. speed‐ne was validated with data simulated under both time‐forward and time‐backward coalescent models of genetic drift. Three classes of estimators were compared with simulated data to examine several general questions: what are the impacts of microsatellite null alleles on , how should missing data be treated, and does disequilibrium contributed by reduced recombination among some loci in a sample impact . Estimators differed greatly in precision in the scenarios examined, and a widely employed estimator exhibited the largest variances among replicate data sets. speed‐ne implements several jackknife approaches to estimate confidence intervals, and simulated data showed that jackknifing over loci and jackknifing over individuals provided ~95% confidence interval coverage for some estimators and should be useful for empirical studies. speed‐ne provides an open‐source extensible tool for estimation of from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare estimators.     

Metallic Photonic Crystal Absorber‐Emitter for Efficient Spectral Control in High‐Temperature Solar Thermophotovoltaics

A high‐temperature stable solar absorber based on a metallic 2D photonic crystal (PhC) with high and tunable spectral selectivity is demonstrated and optimized for a range of operating temperatures and irradiances. In particular, a PhC absorber with solar absorptance 0.86 and thermal emittance = 0.26 at 1000 K, using high‐temperature material properties, is achieved resulting in a thermal transfer efficiency more than 50% higher than that of a blackbody absorber. Furthermore, an integrated double‐sided 2D PhC absorber/emitter pair is demonstrated for a high‐performance solar thermophotovoltaic (STPV) system. The 2D PhC absorber/emitter is fabricated on a double‐side polished tantalum substrate, characterized, and tested in an experimental STPV setup along with a flat Ta absorber and a nearly blackbody absorber composed of an array of multiwalled carbon nanotubes (MWNTs). At an irradiance of 130 kW m^?2 the PhC absorber enables more than a two‐fold improvement in measured STPV system efficiency (3.74%) relative to the nearly blackbody absorber (1.60%) and higher efficiencies are expected with increasing operating temperature. These experimental results show unprecedented high efficiency, demonstrating the importance of the high selectivity of the 2D PhC absorber and emitter for high‐temperature energy conversion.     

Comparative effects of ammonium,nitrate and urea on growth and photosynthetic efficiency of three bloom‐forming cyanobacteria

相似文献   

Identifying important conservation areas for the clouded leopard Neofelis nebulosa in a mountainous landscape: Inference from spatial modeling techniques

The survival of large carnivores is increasingly precarious due to extensive human development that causes the habitat loss and fragmentation. Habitat selection is influenced by anthropogenic as well as environmental factors, and understanding these relationships is important for conservation management. We assessed the environmental and anthropogenic variables that influence site use of clouded leopard Neofelis nebulosa in Bhutan, estimated their population density, and used the results to predict the species’ site use across Bhutan. We used a large camera‐trap dataset from the national tiger survey to estimate for clouded leopards, for the first time in Bhutan, (1) population density using spatially explicit capture–recapture models and (2) site‐use probability using occupancy models accounting for spatial autocorrelation. Population density was estimated at (0.10 SD) and (0.12 SE) per 100 km². Clouded leopard site use was positively associated with forest cover and distance to river while negatively associated with elevation. Mean site‐use probability (from the Bayesian spatial model) was (0.076 SD). When spatial autocorrelation was ignored, the probability of site use was overestimated, (0.066 SD). Predictive mapping allowed us to identify important conservation areas and priority habitats to sustain the future of these elusive, ambassador felids and associated guilds. Multiple sites in the south, many of them outside of protected areas, were identified as habitats suitable for this species, adding evidence to conservation planning for clouded leopards in continental South Asia.     

Superoxide anion radical scavenging property of catecholamines

The direct effect of the four catecholamines (adrenaline, noradrenaline, dopamine and isoproterenol) on superoxide anion radicals () was investigated. The reaction between 18‐crown‐6‐ether and potassium superoxide in dimethylsulfoxide was used as a source of . The reactivity of catecholamines with was examined using chemiluminescence, reduction of nitroblue tetrazolium and electron paramagnetic resonance spin‐trapping techniques. 5,5‐Dimethyl‐1‐pyrroline‐N‐oxide was included as the spin trap. The results showed that the four catecholamines were effective and efficient in inhibiting chemiluminescence accompanying the potassium superoxide/18‐crown‐6‐ether system in a dose‐dependent manner over the range 0.05–2 mm in the following order: adrenaline > noradrenaline > dopamine > isoproterenol, with, IC₅₀ = 0.15 ± 0.02 mm 0.21 ± 0.03 mm , 0.27 ± 0.03 mm and 0.50 ± 0.04 mm , respectively. The catecholamines examined also exhibited a strong scavenging effect towards when evaluated this property by the inhibition of nitroblue tetrazolium reduction (56–73% at 1 m concentration). A very similar capacity of scavenging was monitored in the 5,5‐dimethyl‐1‐pyrroline‐N‐oxide spin‐trapping assay. The results suggest that catecholamines tested may involve a direct effect on scavenging radicals. Copyright © 2013 John Wiley & Sons, Ltd.     

Optimal design of the Wilcoxon–Mann–Whitney‐test

In scientific research, many hypotheses relate to the comparison of two independent groups. Usually, it is of interest to use a design (i.e., the allocation of sample sizes m and n for fixed ) that maximizes the power of the applied statistical test. It is known that the two‐sample t‐tests for homogeneous and heterogeneous variances may lose substantial power when variances are unequal but equally large samples are used. We demonstrate that this is not the case for the nonparametric Wilcoxon–Mann–Whitney‐test, whose application in biometrical research fields is motivated by two examples from cancer research. We prove the optimality of the design in case of symmetric and identically shaped distributions using normal approximations and show that this design generally offers power only negligibly lower than the optimal design for a wide range of distributions.     

Effects of chronic elevated nitrate concentrations on the structure and function of river biofilms

相似文献