Application of data consistency tests and new parameter estimation methods to microbial growth on corn dust in batch culture

The microorganism Candida utilis was grown on both filtered and unfiltered substrate obtained from enzymatic hydrolysis of starch in corn dust. For growth on filtered substrate, the average integrated biomass energetic yield value based on biomass-substrate data was η = 0.55 and for growth on unfiltered substrate an average yield value of η = 0.59 was obtained. Material and energy balances showed that the presence of unfiltered corn residue in the media had no significant effect on the yields. Statistical methods were developed and used to obtain best estimates of the growth parameters. Values of the biomass energetic yield corrected for maintenance (η_max = 0.619) and the maintenance coefficient (m_e = 0.043) were obtained for growth on filtered substrate. Values of η_max = 0.741 and m_e = 0.142 were obtained for the growth on unfiltered substrate. The consistency of data and parameter estimates was relatively good for filtered substrate; however, parameter estimates for unfiltered substrate were not consistent. Growth experiments without filtration of the products of starch hydrolysis resulted in protein-enriched products with about 39.73% protein.     

Transformation of the ϕ-ψ plot for proteins to a new representation with local helicity and peptide torsional angles as variables

A new representation of protein structure is obtained by the angular coordinate transformations η_i = (?_i+1?ψ_i)/2 and ξ_i = ?_i+1+ψ_i with careful mathematical attention to the cyclical boundary conditions of all of the variables involved. From published ?-ψ data it is possible to obtain a new η-ξ plot. As the angle ξ_i is varied from – 180° through 0° to + 180° in this plot, the local helicity of the polypeptide chain changes continuously and contiguously without sudden reversals in handedness. The variable, η_i, gives the torsional position of the ith peptide group. Some peptide groups in proteins, such as the second peptide residue in a type II β-turn, are nonhydrogen-bonded and can undergo considerable torsional oscillation. In such cases the η angle should be represented by a line whose length reflects the allowed dynamical variations in the peptide torsional position. Certain peptide residues in proteins may be able to undergo a complete torsional rotation of 360°. Such residues would be represented on the η-ξ plot as a straight line across the plot parallel to the abscissa. Other examples of the possible usefulness of this plot are also given.     

Growth efficiency of thielavia terrestris mycelial structures

The growth energetic efficiency (η) of two mycelial forms of Thielavia terrestris (pellets and diffused form) was studied by different methods. η Values determined by the pulse method are similar for the two forms, but the values determined by C balance for pellets were lower than those for diffused mycelium. These balance data prove that pellets yield more extracellular products than the diffused mycelium form, which is also confirmed by experimental data for different amounts of carbon in the culture fluid. Growth efficiency can be determined by various methods based on the principles of mass and energy balance. The estimates most frequently used are the biomass and substrate balances. However, growth efficiency determination according to oxygen balance (particularly by the pulse method) is simpler and more accurate; as it makes possible the immediate fixation of changes in the physiological condition of microorganisms and the determination of complex substrate utilization efficiency [1]. Earlier the possible use of this method for evaluating the growth efficiency of heterotrophic bacteria [2], hyphalic and yeast forms of microscopic fungi [3] was shown. The aim of the present study is the comparative investigation of the growth efficiency of two mycelial structures (hyphalic and pellets) by different methods as well as by pulse additions.     

QUANTIFICATION OF THE RELATIVE ABUNDANCE OF THE TOXIC DINOFLAGELLATE,KARENIA BREVIS (DINOPHYTA), USING UNIQUE PHOTOPIGMENTS1

Diagnostic photopigment analysis is a useful tool for determining the presence and relative abundance of algal groups in natural phytoplankton assemblages. This approach is especially useful when a genus has a unique photopigment composition. The toxic dinoflagellate Karenia brevis (Davis) G. Hansen & Moestrup comb. nov. shares the diagnostic pigment gyroxanthin‐diester with only a few other dinoflagellates and lacks peridinin, one of the major diagnostic pigments of most dinoflagellate species. In this study, measurements of gyroxanthin‐diester and other diagnostic pigments of K. brevis were incorporated into the initial pigment ratio matrix of the chemical taxonomy program (CHEMTAX) to resolve the relative contribution of K. brevis biomass in mixed estuarine phytoplankton assemblages from Florida and Galveston Bay, Texas. The phytoplankton community composition of the bloom in Galveston Bay was calculated based on cell enumerations and biovolumetric measurements in addition to chl a‐specific photopigment estimates of biomass (HPLC and CHEMTAX). The CHEMTAX and biovolume estimates of the phytoplankton community structure were not significantly different and suggest that the HPLC–CHEMTAX approach provides reasonable estimates of K. brevis biomass in natural assemblages. The gyroxanthin‐diester content per cell of K. brevis from Galveston Bay was significantly higher than in K. brevis collected from the west coast of Florida. This pigment‐based approach provides a useful tool for resolving spatiotemporal distributions of phytoplankton in the presence of K. brevis blooms, when an appropriate initial ratio matrix is applied.     

Blue Moon Approach to Rare Events

The "Blue Moon" ensemble is a computationally efficient molecular dynamics method to estimate the rate constants of rare activated events when the process can be described by a reaction coordinate ξ(r), a well-defined function in configuration space. By means of holonomic constraints a number of values of ξ(r) can be prescribed along the relevant path to identify the "bottleneck" region first and to sample an ensemble of starting conditions to generate activated trajectories. These MD trajectories sample phase space according to a biased configurational distribution. With a suitable re-weighting of averages from such ensemble of trajectories one can characterize completely rare events.     

Genetic and environmental variations in quantitative characters in fishes: a comparative analysis of monoclonal triploid and bisexual tetraploid spined loaches (<Emphasis Type="Italic">Cobitis</Emphasis>, Cobitidae)

The heritability estimates of 25 external morphometric characters and 23 craniometric indices are obtained by use of variances in monoclonal all-female triploids and bisexual tetraploids of spined loaches (genus Cobitis, Cobitidae) collected from the same breeding biotope. Most of studied traits demonstrate low heritability confirming previous conclusion on the similarity between external morphometric characters and craniological indices in relative effects of genetic and environmental components in their total phenotypic variation. Low heritability estimates in most of external morphological traits correspond to their low diagnostic value in Cobitis species. As a whole, in spite of certain deviations, studies on clonal forms do not refute the concept on higher heritability estimates in diagnostically significant traits in comparison with traits without diagnostic values in the same taxonomic group. Low heritability in most morphometric traits more probably is resulted from their low additive genetic variation caused by strong selection of evolutionary developed specific body shape in spined loaches, because strong selection should reduce the genetic variance in body proportions to minimal size. Sex differences observed in heritability estimates should be interpreted as a result of linkage of several additive genes controlling these traits to sex chromosomes. A few characters demonstrating high heritability estimates up to 0.492–0.580 are of great interest for taxonomic and phylogenetic studies in genus Cobitis and related taxa.     

Correct and logical inference on efficacy in subgroups and their mixture for binary outcomes

Targeted therapies are becoming more common. In targeted therapy development, suppose its companion diagnostic test divides patients into a marker‐positive subgroup and its complementary marker‐negative subgroup. To find the right patient population for the therapy to target, inference on efficacy in the marker‐positive and marker‐negative subgroups as well as efficacy in the overall mixture population are all of interest. Depending on the type of clinical endpoints, inference on mixture population can be nontrivial and commonly used efficacy measures may not be suitable for a mixture population. Correlations among estimates of efficacy in the marker‐positive, marker‐negative, and overall mixture population play a crucial role in using an earlier phase study to inform on the design of a confirmatory study (e.g., determination of sample size). This article first shows that when the clinical endpoint is binary (such as respond or not), odds ratio is inappropriate as an efficacy measure in this setting, but relative response (RR) is appropriate. We show a safe way of calculating estimated correlations is to consider mixing subgroup response probabilities within each treatment arm first, and then derive the joint distribution of RR estimates. We also show, if one calculates RR within each subgroup first, how wrong the correlations can be if the Delta method derivation fails to take randomness of estimating the mixing coefficient into account.     

Joint Estimation of Diagnostic Accuracy Measures for Paired Organs – Application in Ophthalmology

Diagnostic studies in ophthalmology frequently involve binocular data where pairs of eyes are evaluated, through some diagnostic procedure, for the presence of certain diseases or pathologies. The simplest approach of estimating measures of diagnostic accuracy, such as sensitivity and specificity, treats eyes as independent, consequently yielding incorrect estimates, especially of the standard errors. Approaches that account for the inter‐eye correlation include regression methods using generalized estimating equations and likelihood techniques based on various correlated binomial models. The paper proposes a simple alternative statistical methodology of jointly estimating measures of diagnostic accuracy for binocular tests based on a flexible model for correlated binary data. Moments' estimation of model parameters is outlined and asymptotic inference is discussed. The resulting estimates are straightforward and easy to obtain, requiring no special statistical software but only elementary calculations. Results of simulations indicate that large‐sample and bootstrap confidence intervals based on the estimates have relatively good coverage properties when the model is correctly specified. The computation of the estimates and their standard errors are illustrated with data from a study on diabetic retinopathy.     

Some Theoretical Aspects of Analysis in Half Diallel

The analysis of F₁ and F₂ half diallel has been discussed as compared to full diallel without reciprocal effects given by MATHER and JINKS (1971). In practice, mostly the half diallel (one-way) crosses are prepared and erroreously analysed using the least square estimates of full diallel without reciprocal effects. The H₁ and H₂, however, appeared to be over estimated when full diallel without reciprocal effects estimates were used in place of those of half diallel. Least square estimates were also obtained assuming heterogeneity of error components between parents and F₁/F₂ families.     

Effects of sampling close relatives on some elementary population genetics analyses

Many molecular ecology analyses assume the genotyped individuals are sampled at random from a population and thus are representative of the population. Realistically, however, a sample may contain excessive close relatives (ECR) because, for example, localized juveniles are drawn from fecund species. Our knowledge is limited about how ECR affect the routinely conducted elementary genetics analyses, and how ECR are best dealt with to yield unbiased and accurate parameter estimates. This study quantifies the effects of ECR on some popular population genetics analyses of marker data, including the estimation of allele frequencies, F‐statistics, expected heterozygosity (H_e), effective and observed numbers of alleles, and the tests of Hardy–Weinberg equilibrium (HWE) and linkage equilibrium (LE). It also investigates several strategies for handling ECR to mitigate their impact and to yield accurate parameter estimates. My analytical work, assisted by simulations, shows that ECR have large and global effects on all of the above marker analyses. The naïve approach of simply ignoring ECR could yield low‐precision and often biased parameter estimates, and could cause too many false rejections of HWE and LE. The bold approach, which simply identifies and removes ECR, and the cautious approach, which estimates target parameters (e.g., H_e) by accounting for ECR and using naïve allele frequency estimates, eliminate the bias and the false HWE and LE rejections, but could reduce estimation precision substantially. The likelihood approach, which accounts for ECR in estimating allele frequencies and thus target parameters relying on allele frequencies, usually yields unbiased and the most accurate parameter estimates. Which of the four approaches is the most effective and efficient may depend on the particular marker analysis to be conducted. The results are discussed in the context of using marker data for understanding population properties and marker properties.     

Modeling the spatial and temporal heterogeneity of deforestation‐driven carbon emissions: the INPE‐EM framework applied to the Brazilian Amazon

We present a generic spatially explicit modeling framework to estimate carbon emissions from deforestation (INPE‐EM). The framework incorporates the temporal dynamics related to the deforestation process and accounts for the biophysical and socioeconomic heterogeneity of the region under study. We build an emission model for the Brazilian Amazon combining annual maps of new clearings, four maps of biomass, and a set of alternative parameters based on the recent literature. The most important results are as follows: (a) Using different biomass maps leads to large differences in estimates of emission; for the entire region of the Brazilian Amazon in the last decade, emission estimates of primary forest deforestation range from 0.21 to 0.26 Pg C yr^?1. (b) Secondary vegetation growth presents a small impact on emission balance because of the short duration of secondary vegetation. In average, the balance is only 5% smaller than the primary forest deforestation emissions. (c) Deforestation rates decreased significantly in the Brazilian Amazon in recent years, from 27 Mkm² in 2004 to 7 Mkm² in 2010. INPE‐EM process‐based estimates reflect this decrease even though the agricultural frontier is moving to areas of higher biomass. The decrease is slower than a non‐process instantaneous model would estimate as it considers residual emissions (slash, wood products, and secondary vegetation). The average balance, considering all biomass, decreases from 0.28 in 2004 to 0.15 Pg C yr^?1 in 2009; the non‐process model estimates a decrease from 0.33 to 0.10 Pg C yr^?1. We conclude that the INPE‐EM is a powerful tool for representing deforestation‐driven carbon emissions. Biomass estimates are still the largest source of uncertainty in the effective use of this type of model for informing mechanisms such as REDD+. The results also indicate that efforts to reduce emissions should focus not only on controlling primary forest deforestation but also on creating incentives for the restoration of secondary forests.     

Inheritance of size and shape in a natural population of collared flycatchers,Ficedula albicollis

Four external skeletal and three feather dimensions were measured on adult collared flycatchers (Ficedula albicollis) and their adult offspring. By using mid-offspring-midparent regressions, all traits were found to be heritable with an arithmetic mean heritability of 0.46. Heritability estimates from full-sib analyses were about 1.5 times higher (mean 0.67), indicating that variation in traits was affected by shared nest environment among full-sibs. The overall body size as measured by principal component one (PC1) was found to be heritable (h² = 0.40). However, this multivariate measure of heritability was not significant in offspring-father comparison, while highly so in offspring-mother comparison (h² = 0.60). Low offspring-father resemblance was evident also in univariate estimates of heritability. Possible causes of this (extra-pair copulations, maternal effects, sex-linked variance) are discussed. Genetic correlations among seven traits were estimated to be low (mean 0.22), and of similar magnitude or higher than phenotypic correlations (mean 0.18). All genetic correlations were positive. Genetic and phenotypic correlations as well as covariances were fairly similar to each other (r = 0.85 and r = 0.87, respectively). Environmental correlations did not follow the pattern of genetic correlations (r = 0.11), but were more similar to phenotypic correlations (r = 0.60). Given the low genetic correlations and moderate heritabilities, the overall conclusion is that the external morphology of collared flycatchers is largely under additive genetic control and that there is a strong potential for evolutionary change in morphology even under complex multivariate selection.     

DNA damage induced Pol η recruitment takes place independently of the cell cycle phase

When DNA is damaged in cells progressing through S phase, replication blockage can be avoided by TLS (Translesion DNA synthesis). This is an auxiliary replication mechanism that relies on the function of specialized polymerases that accomplish DNA damage bypass. Intriguingly, recent evidence has linked TLS polymerases to processes that can also take place outside S phase such as nucleotide excision repair (NER). Here we show that Pol η is recruited to UV-induced DNA lesions in cells outside S phase including cells permanently arrested in G1. This observation was confirmed by different strategies including global UV irradiation, local UV irradiation and local multi-photon laser irradiation of single nuclei in living cells. The potential connection between Pol η recruitment to DNA lesions outside S phase and NER was further evaluated. Interestingly, the recruitment of Pol η to damage sites outside S phase did not depend on active NER, as UV-induced focus formation occurred normally in XPA, XPG and XPF deficient fibroblasts. Our data reveals that the re-localization of the TLS polymerase Pol η to photo-lesions might be temporally and mechanistically uncoupled from replicative DNA synthesis and from DNA damage processing.     

Analysis of the separation of gadolinium isotopes by the ICR method

The problem of separating gadolinium isotopes is discussed. The parameters of isotope separation in a plasma by the ICR method are estimated for a device with given operating parameters. The mean transverse energy 〈E_⊥〉 of the heated ions of the ¹⁵⁷Gd isotope and the heating efficiency η are calculated as functions of the frequency of the RF electric field in the plasma. The dependence of the heating efficiency η on the longitudinal temperature of the plasma flow is investigated. The issue of how the concentration of the target isotope ions at the collector plate depends on the longitudinal coordinate measured from the front edge of the plate is analyzed for different values of the frequency detuning parameter. The extraction coefficient Г for the target isotope is calculated as a function of the distance b between the collector plates for different frequency detunings.     

Corrosion and Alloy Engineering in Rational Design of High Current Density Electrodes for Efficient Water Splitting

Alongside rare‐earth metals, Ni, Fe, Co, Cu are some of the critical materials that will be in huge demand thanks to growth in clean‐energy sector. Herein scrap stainless steel wires (SSW) from worn‐out tires are employed as a support material for catalyst integration in the hydrogen evolution reaction (HER). In addition, SSW by corrosion engineering is exercised as an in situ formed freestanding robust electrode for the oxygen evolution reaction (OER). By superficial corrosion of SSW, inherent active species are unmasked in the form of Ni/FeOOH nanocrystallites displaying efficient water oxidation by reaching 500 mA cm^?2 at low overpotential (η₅₀₀) of 287 mV in 1 m KOH. Similarly, cathode scrap SSW with active (alloy) coatings of MoNi₄ catalyzes the HER at η_‐200 = 77 mV, with a low activation energy (E_a = 16.338 kJ mol^?1) and high durability of 150 h. Promisingly, when used in industrial conditions, 5 m KOH, 343 K, these electrodes demonstrate abnormal activity by yielding high anodic and cathodic current density of 1000 mA cm^?2 at η = 233 mV and η = 161 mV, respectively. This work may inspire researchers to explore and reutilize high‐demand metals from scrap for addressing critical material shortfalls in clean‐energy technologies.     

Aging three-spined sticklebacks Gasterosteus aculeatus: comparison of estimates from three structures

In order to assess the accuracy and reliability of age estimates from calcified structures in the three-spined stickleback Gasterosteus aculeatus, we evaluated intra and inter-reader repeatability from three structures: otoliths, gill covers and pelvic spines). Average age estimates were also compared between the structures. The overall intra-reader repeatability of age estimates were highest for otoliths (69%), lowest for gill covers (53%) and intermediate for spine cross-sections (63%). Although four of the seven readers had the highest intra-reader repeatability score for spine cross-sections, the inter-reader variance in this structure was much higher than in others. Otoliths were the easiest in terms of their pre-analysis treatment and exchange of materials (as digital images) between readers. In addition, otoliths are more well-studied compared with the other structures with respect to their development through ontogenesis; hence, age estimates based on otoliths should be the most reliable. Therefore, our recommendation is that whenever possible, analysis of otoliths should be the preferred approach for aging G. aculeatus.     

Polyelectrolyte theory. I. Counterion accumulation,site-binding,and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations

We have computed the Poisson-Boltzmann distribution of counterions around polyelectrolytes in solutions containing finite salt concentrations. The polyelectrolytes considered here are highly charged in the sense that ξ > 1, ξ being the linear charge density parameter for cylinders, which is generalized by us to other shapes. Contrary to the situation at zero salt concentration, the counterion distribution is not strongly shape dependent, being similar for cylinders or spheres which have the same superficial charge density and radius of curvature R_c. The distribution resembles that in the neighborhood of a plane with the same charge density. Three regions are distinguished. (1) In the “inner region” which extends up to a distance R_c/2ξ from the surface, the counterion distribution is essentially salt independent. The counterion concentration in the immediate vicinity of the polyelectrolyte surface (CIV) is quite high, typically 1–10M, and proportional to the square of the surface charge density, which is its main determinant. (2) An intermediate region extends out to a distance where the electrostatic potential is equal to κT/e. This distance is comparable to λ for plane and cylinder, and smaller for the sphere. (3) In the outer region, the distribution is hardly influenced by the details of the inner region, on which it cannot, therefore, give much information. Colligative properties are dependent on the distribution in the outer region and are fairly well predicted even by a rudimentary theory. The large value of the CIV implies that site binding must often be significant. It can be computed by applying the mass-action law to site-bound counterions in equilibrium with the counterions in the neighborhood, whose concentration is the CIV, the relevant equilibrium constant being that for the binding of counterions to isolated monomer sites. Because the CIV is insensitive to salt concentration, this will also be the case for site binding. With the graphs provided, one can compute the extent of sitebinding within the Poisson-Boltzmann framework. The “condensation radius,” i.e., the radius encompassing a counterionic charge 1 ? ξ^?1 around a cylinder, is found to be large. It varies with salt concentration and tends to infinity as the salt is diluted. Neither this radius nor the charge fraction 1 ? ξ^?1 of condensation theory plays any special role in the counterion distribution. The “finite-salt” results apply to salt concentrations, typically as low as 1–10 mM. This encompasses, among others, all experiments on biological polyelectrolytes.     

Field evaluation of abundance estimates under binomial and multinomial N-mixture models

Assessing and modelling abundance from animal count data is a very common task in ecology and management. Detection is arguably never perfect, but modern hierarchical models can incorporate detection probability and yield abundance estimates that are corrected for imperfect detection. Two variants of these models rely on counts of unmarked individuals, or territories (binomial N-mixture models, or binmix), and on detection histories based on territory-mapping data (multinomial N-mixture models or multimix). However, calibration studies which evaluate these two N-mixture model approaches are needed. We analysed conventional territory-mapping data (three surveys in 2014 and four in 2015) using both binmix and multimix models to estimate abundance for two common avian cavity-nesting forest species (Great Tit Parus major and Eurasian Blue Tit Cyanistes caeruleus). In the same study area, we used two benchmarks: occupancy data from a dense nestbox scheme and total number of detected territories. To investigate variance in estimates due to the territory assignment, three independent ornithologists conducted territory assignments. Nestbox occupancy yields a minimum number of territories, as some natural cavities may have been used, and binmix model estimates were generally higher than this benchmark. Estimates using the multimix model were slightly more precise than binmix model estimates. Depending on the person assigning the territories, the multimix model estimates became quite different, either overestimating or underestimating the ‘truth’. We conclude that N-mixture models estimated abundance reliably, even for our very small sample sizes. Territory-mapping counts depended on territory assignment and this carried over to estimates under the multimix model. This limitation has to be taken into account when abundance estimates are compared between sites or years. Whenever possible, accounting for such hidden heterogeneity in the raw data of bird surveys, via including a ‘territory editor’ factor, is recommended. Distributing the surveys randomly (in time and space) to editors may also alleviate this problem.     

中国柿树科植物一新记录种——长柱柿(英文)

报道中国柿科(Ebenaceae)柿属植物一新记录种——长柱柿(Diospyros brandisiana Kurz),并描述了该新记录种的形态特征和生境分布。该种为该属中国分布的唯一具老茎生花的种类。凭证标本存放于中国科学院昆明植物研究所标本馆(KUN)。