The growth of the common two-banded seabream, Diplodus vulgaris (Teleostei, Sparidae), in Canarian waters, estimated by reading otoliths and by back-calculation

The yearly nature of increment formation in the otoliths of 1–9‐year‐old seabream, Diplodus vulgaris (E. Geoffrey Saint‐Hilaire 1817), from the Canary Islands was validated. The marginal increment method showed that the opaque rings were formed in summer, and the translucent rings in winter. The Brody Proportional Hypothesis and the power length–radius relationship used to back‐calculate the growth trajectories of D. vulgaris showed that this growth model could provide reasonable growth estimates in this species. Growth back‐calculation and growth estimates obtained by direct otolith readings were similar. Data on age and size used to estimate the parameters of the von Bertalanffy growth model for D. vulagris from the Canary Islands showed that males and females had similar growth rates.     

Age and growth of the tropical oviparous shark,Chiloscyllium punctatum in Indonesian waters

The brown-banded bamboo shark, Chiloscyllium punctatum, is the most common shark caught in coastal commercial fisheries throughout Southeast Asia, yet there is a lack of the life-history information necessary for reliable stock assessments. The authors estimated growth rates and age at maturity using analysis of growth bands in vertebral centra. They trialled four different techniques to enhance the visibility and improve identification of the putative annual growth bands necessary for age estimation. The authors found that the burn method on whole vertebral centra provided the most readable and consistent results for age analysis. The logistic model was chosen as the best-fit growth model for age estimation of 330 individual C. punctatum from Indonesia. Several age verification methods, including marginal increment ratio and length-frequency analysis, were performed with the support of age validation through the use of calcein-labelled vertebrae from two sharks maintained in captivity. This study found that C. punctatum from Indonesian waters is a fast-growing species that can grow up to 18 cm year⁻¹, reach an estimated maximum total length of 1 m, mature at c. 6.5 years and live for up to 14 years.     

Is the marginal otolith increment width a reliable recent growth index for larval and juvenile herring?

Marginal otolith increment width analysis was performed on field‐collected larval and juvenile spring‐spawned herring Clupea harengus that experienced variable feeding conditions and high temperatures that were above the optimum for growth. Although drastic zooplankton biomass reduction had a significant effect on increment width, a delay of a few days in the otolith response was observed. More importantly, a very clear, positive temperature effect on marginal increment width was demonstrated in fish characterized by temperature independent somatic growth. These results indicate that under natural conditions it may be impossible to distinguish increment width changes related to variation in feeding conditions from changes caused by temperature fluctuations. Therefore, it was concluded that marginal otolith increment width analysis could not be used as a recent growth index ( I _G) for herring larvae and juveniles exposed to drastic temperature fluctuations. The implication of these results is significant not only for the use of marginal increments as a recent growth index, but also if growth rate backcalculation is to be used as a research method.     

A critical appraisal of marginal increment analysis for assessing temporal periodicity in band formation among tropical sharks

Marginal increment ratio (MIR) analyses were conducted as part of age and growth studies on three coastal/semi-oceanic species, the smalltail shark, Carcharhinus porosus, daggernose shark, Isogomphodon oxyrhynchus and the night shark C. signatus, and two ubiquitous oceanic species, blue shark, Prionace glauca, and whitetip shark, C. longimanus, collected in equatorial areas off Brazil with the aim of establishing the interspecific temporal nature of vertebral band formation. Monthly variations in marginal bands were analyzed using mean MIR on the entire sample as the standard method for all species. Reasons for the inconclusive results regarding these species are critically appraised with respect to three main sources of bias that are associated with marginal increment analysis (MIA). Bias due to insufficient sample sizes may have hampered the analysis for I. oxyrhynchus and C. longimanus due to movements from shallow waters to seamounts for the former species and to extensive migrations for the latter. Bias due to data collection over too long a period is thought to have influenced monthly mean MIR for C. porosus and P. glauca. For the latter, individuals from different age groups lay down rings at different times, making band deposition inconsistent between individuals. Finally, bias due to births occurring over too long a period was the prevalent cause for confounding MIR values among I. oxyrhynchus and C. signatus species, whose birth period lasts several months and leads to different ages within the same cohort. Other approaches used for MIA in C. signatus and P.␣glauca led to distinct times of band formation by age-groups when compared to MIR applied on the entire sample. For the daggernose shark, delays in events related to the reproductive cycle from one year to the next were also found to confound MIR. Requirements for the use of MIR implying a band width that displays a sinusoidal cycle when temporally plotted (month or season) were not fulfilled for any of these species. The method has been of little utility for detecting the periodicity of band deposition among sharks from the tropics. This emphasizes the need for supplying information on the temporal periodicity of pair deposition based on other methods.     

Models for circular-linear and circular-circular data constructed from circular distributions based on nonnegative trigonometric sums

Johnson and Wehrly (1978, Journal of the American Statistical Association 73, 602-606) and Wehrly and Johnson (1980, Biometrika 67, 255-256) show one way to construct the joint distribution of a circular and a linear random variable, or the joint distribution of a pair of circular random variables from their marginal distributions and the density of a circular random variable, which in this article is referred to as joining circular density. To construct flexible models, it is necessary that the joining circular density be able to present multimodality and/or skewness in order to model different dependence patterns. Fernández-Durán (2004, Biometrics 60, 499-503) constructed circular distributions based on nonnegative trigonometric sums that can present multimodality and/or skewness. Furthermore, they can be conveniently used as a model for circular-linear or circular-circular joint distributions. In the current work, joint distributions for circular-linear and circular-circular data constructed from circular distributions based on nonnegative trigonometric sums are presented and applied to two data sets, one for circular-linear data related to the air pollution patterns in Mexico City and the other for circular-circular data related to the pair of dihedral angles between consecutive amino acids in a protein.     

Organization of the subumbrellar musculature in the ephyra,juvenile, and adult stages of Aurelia aurita Medusae

We used fluorescently labeled phalloidin to examine the subumbrellar musculature of the scyphozoan jellyfish Aurelia aurita in a developmental series from ephyra to adult medusa. In the ephyra, the swim musculature includes a disc‐like sheet of circular muscle, in addition to two radial bands of muscle in each of the eight ephyral arms. The radial muscle bands join with the circular muscle, and both circular and radial muscle act together during each swim contraction. As the ephyra grows into a juvenile medusa, arms tissue is resorbed as the bell tissue grows outward, so eventually, the ephyral arms disappear. During this process, the circular muscle disc also grows outward and the radial muscle bands of the arms also disappear. At this time, a marginal gap appears at the bell margin, which is devoid of circular muscle cells, but has a loose arrangement of radial muscle fibers. This marginal gap is preserved as the medusa grows, and contributes to the floppy nature of the bell margin. Radial distortions in the circular muscle layer involve muscle fibers that run in random directions, with a primarily radial orientation. These are believed to be remnants of the radial muscle of the ephyral arms, and the distortions decrease in number and extent as the medusa grows. Since the mechanics of swimming changes from drag‐based paddling in the ephyra to marginal rowing in the adult medusa, the development of the marginal gap and the presence of radial distortions should be considered in terms of this mechanical transition.     

Identifying marginal supplying countries of wood products via trade network analysis

Purpose

The consequential inventory modeling approach for life cycle assessment implies that an increase in the demand for a specific product is met by the marginal suppliers within the market. The identification of marginal suppliers is however complicated by difficulties in defining appropriate geographical market delimitations. In this study, an advanced system thinking approach is proposed to address this challenge in the identification of marginal supplying countries of wood products.

Methods

Groups of countries which represent geographical markets are identified from trade data by using a network analysis-based clustering technique. Within these markets, marginal supplying countries are selected based on positive historical increments. The analysis covers 12 different products and all countries in the world using trade data for the period 1998–2013.

Results and discussion

Global indices allow differentiating how product-specific trade networks are separated into communities and how interconnected these networks are. Large differences between products and minor differences between trade years are observed. Communities identified for each product tend to overlap with existing geographical regions and seem thus realistic. By combining this information with product-specific production increment rankings, marginal supplying countries of wood products were identified.

Conclusions

The identified geographical market delimitation is a key for proper consequential life cycle assessment (LCA) inventory modeling in areas such as timber-based construction and biomass-based energy production. The method can in principle be applied to any product for which trade network data are available and ideally should be accompanied by a detailed analysis of technological constrains within the identified supplying country.

     

Age and growth of the sandbar shark, Carcharhinus plumbeus, in Hawaiian waters through vertebral analysis

Age and growth estimates were determined for the sandbar shark, Carcharhinus plumbeus, from Oahu, Hawaii in the central Pacific Ocean. Age estimates were obtained through vertebral centra analysis of 187 sharks. We verified our age estimates through marginal increment analysis of centra and oxytetracycline marking methods of at liberty sandbar sharks. Sizes of sampled sharks ranged from 46 to 147 cm pre-caudal length. Four growth models were fitted to length-at-age data; two forms of the von Bertalanffy growth model, the Gompertz growth model, and a logistic growth model. Males and females exhibited statistically significant differences in growth, indicating that females grow slower and attain larger sizes than males. Growth parameter estimates revealed slower growth rates than previously estimated (based on captive specimens) for Hawaiian sandbar sharks. The von Bertalanffy growth model using empirical length-at-birth provided the best biological and statistical fit to the data. This model gave parameter estimates of L _∞ = 138.5 cm PCL and k = 0.12 year⁻¹ for males and L _∞ = 152.8 cm PCL, k = 0.10 year⁻¹ for females. Male and female sandbar sharks mature at approximately 8 and 10 years of age, respectively.     

Age estimation and validation for South Pacific albacore Thunnus alalunga

Validated estimates of age are presented for albacore Thunnus alalunga, sampled from a large part of the south‐western Pacific Ocean, based on counts of annual opaque growth zones from transverse sections of otoliths. Counts of daily increments were used to estimate the location of the first opaque growth zone, which was completed before the first assumed birthday. The periodicity of opaque zones was estimated by marginal increment analysis and an oxytetracycline mark–recapture experiment. Both validation methods indicated that opaque zones formed over the austral summer and were completed by autumn to winter (April to August). The direct comparison of age estimates obtained from otoliths and dorsal‐fin spines of the same fish indicated bias, which was assumed to be due to poor increment clarity and resorption of early growth zones in spines, resulting in imprecise age estimates. As such, age estimates from otoliths are considered to be more accurate than those from spines for T. alalunga. This is consistent with results for a growing number of tropical and temperate tuna Thunnini species. It is recommend that validated counts of annual growth zones from sectioned otoliths is used as the preferred method for estimating age‐based parameters for assessment and management advice for these important stocks.     

Direct ageing of Thunnus thynnus from the eastern Atlantic Ocean and western Mediterranean Sea using dorsal fin spines

This study deals with important methodology issues that affect age estimates of eastern Atlantic bluefin tuna Thunnus thynnus using dorsal fin spines. Nearly 3800 spine sections were used from fish caught in the north‐east Atlantic Ocean and western Mediterranean Sea over a 21 year period. Edge type and marginal increment analyses indicated a yearly periodicity of annulus formation with the translucent bands (50% of occurrence) appearing from October to May. Nucleus vascularization seriously affected specimens older than 6 years, with the disappearance of 40–50% of the presumed annuli by that age. An alternate sectioning location was a clear improvement and this finding is an important contribution to the methodology of using this structure for ageing the full‐length range of eastern T. thynnus. Finally, there were no significant differences between the coefficients of von Bertalanffy growth model estimated from mean length at age data (L_∞ = 327·4; k = 0·097; t₀ = ?0·838) and those estimated from the growth curves accepted for the eastern and western T. thynnus management units.     

A goodness-of-fit test for the marginal Cox model for correlated interval-censored failure time data

The marginal Cox model approach is perhaps the most commonly used method in the analysis of correlated failure time data (Cai, 1999; Cai and Prentice, 1995; Lin, 1994; Wei, Lin and Weissfeld, 1989). It assumes that the marginal distributions for the correlated failure times can be described by the Cox model and leaves the dependence structure completely unspecified. This paper discusses the assessment of the marginal Cox model for correlated interval-censored data and a goodness-of-fit test is presented for the problem. The method is applied to a set of correlated interval-censored data arising from an AIDS clinical trial.     

A note on key factor analysis

Various aspects of a model for key factor analysis (Manly , 1977a) are discussed. Equations for estimating the parameters of the model are given. The jackknife method is suggested for obtaining standard errors for estimators. The case of circular populations (where the adults in one generation produce all the individuals alive at the start of the next, generation) is considered. A computer program is described. Varley et al.'s (1973) data on the winter moth is used for illustrative purposes.     

On the occurrence of false positives in tests of migration under an isolation‐with‐migration model

The population genetic study of divergence is often carried out using a Bayesian genealogy sampler, like those implemented in ima2 and related programs, and these analyses frequently include a likelihood ratio test of the null hypothesis of no migration between populations. Cruickshank and Hahn (2014, Molecular Ecology, 23, 3133–3157) recently reported a high rate of false‐positive test results with ima2 for data simulated with small numbers of loci under models with no migration and recent splitting times. We confirm these findings and discover that they are caused by a failure of the assumptions underlying likelihood ratio tests that arises when using marginal likelihoods for a subset of model parameters. We also show that for small data sets, with little divergence between samples from two populations, an excellent fit can often be found by a model with a low migration rate and recent splitting time and a model with a high migration rate and a deep splitting time.     

Circular dichroism of the alkyl amino acids in the vacuum ultraviolet

The circular dichroism and absorption for five alkyl amino acids as zwitterions has now been measured to 160 nm. Two bands are found, the nπ* at long wavelengths and ππ* at short wavelengths. In an effort to extract conformal information from the circular dichroism measurmenths, the circular dichroism spectra for these molecules is calculated using an independent systems apporach. It is found that the signs calculated using these methods are quite reliable, but that reliable magnitudes must await more accurate data to use in the calculations. Comparing the signs for both the measured and calculated circular dichriosm it if possible to determine the region inhabited by the carboxylate anion chromophore of these amino acid zwitterions. The greatest failure of the calculations is that thay are unable to explain the sigmoidal shape of the nπ* transition in proline. The problems facing workers trying to make calculations to relate circular dichroism measurements to conformation are discussed.     

Circular dichroism of corticotropin, fragment 1-24, and model compounds. An assessment of the contributions of the peptide chromophore and armoatic residues.

The far-ultraviolet circular dichroic spectrum of the 39-residue peptide hormone porcine corticotropin and the biologically active fragment corticotropin 1–24 is negative from 250 nm to 195 nm in water, but in 6M guanidinium chloride a positive band appears at about 225 nm. The temperature and guanidinium chloride dependence of this spectral transition indicates the absence of any stable ordered secondary structure in corticotropin and the spectrum is seen to be in only partial agreement with results using the model peptide chromophore, Ala-Ala-Ala. Using oligopeptides containing aromatic amino acid residues sandwiched between glycyl residues, it is shown that the shape and intensity of the corticotropin 225 nm positive band which appears in 6M guanidinium chloride is in agreement with the far-ultraviolet transitions of the aromatic chromophores in the hormone. Curve resolution of the near-ultraviolet circular dichroic spectrum of corticotropin and comparison of the rotational strengths of the phenylalanyl and tyrosyl bands reveals no evidence for increased rotational freedom in 6M guanidinium hydrochloride. Spectral changes are observed, however, in the transitions arising from the single tryptophan. This study suggests that corticotropin in aqueous solution may serve as a better model for the circular dichroic spectrum of the aperiodic regions in globular proteins than either synthetic homopolypeptides or reference proteins for which spectral and X-ray diffraction data are available.     

Otolith characteristics and age determination of an endemic Ptychobarbus dipogon (Regan, 1905) (Cyprinidae: Schizothoracinae) in the Yarlung Tsangpo River, Tibet

We describe the microincrements, checks and annuli in the lapilli of the schizothoracine Ptychobarbus dipogon, an endemic species of the Tibetan plateau. We collected samples in the Yarlung Tsangpo River and its tributaries on a monthly basis (from April 2004 to August 2006). We describe the shape features of the three pairs of otoliths and document the full trajectory of lapillus development. We found that five to seven checks were clearly visible in the opaque zone of the first annulus. The pattern of 21–23 daily growth increments within each check might be explained as a lunar-induced deposition. We counted between 137 and 154 increments within the first annulus. Annuli appeared as a sequence of gradually declining increment widths, whereas false rings were characterized by abrupt checks. Our oldest estimates were 23⁺years for males and 44⁺ for females. The time of annulus completion was clearly between March and April each year using monthly marginal increments analysis. We consider the factors responsible for daily increment formation as an endogenous circadian rhythm. Environmental information, such as strong sunlight and cold water temperatures in the Tibetan Plateau, could reinforce the endogenous daily cycle. Our results provided important data addressing the ecology and population dynamics of P. dipogon.     

Thermodynamics of the Trp‐cage miniprotein unfolding in urea

The thermodynamic properties of unfolding of the Trp‐cage mini protein in the presence of various concentrations of urea have been characterized using temperature‐induced unfolding monitored by far‐UV circular dichroism spectroscopy. Analysis of the data using a two‐state model allowed the calculation of the Gibbs energy of unfolding at 25°C as a function of urea concentration. This in turn was analyzed by the linear extrapolation model that yielded the dependence of Gibbs energy on urea concentration, i.e. the m‐value for Trp‐cage unfolding. The m‐value obtained from the experimental data, as well as the experimental heat capacity change upon unfolding, were correlated with the structural parameters derived from the three dimensional structure of Trp‐cage. It is shown that the m‐value can be predicted well using a transfer model, while the heat capacity changes are in very good agreement with the empirical models based on model compounds studies. These results provide direct evidence that Trp‐cage, despite its small size, is an excellent model for studies of protein unfolding and provide thermodynamic data that can be used to compare with atomistic computer simulations. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

Stochastic compartmental modeling and parameter estimation with application to cancer treatment follow-up studies

In this paper we use marginal probabilities to derive expressions for the means, variances and covariances ofm-compartment systems. We also present an efficient algorithm for the estimation of the parameters of the system using time series data when measurements are available fromk of them compartments. An application of the analysis and parameter estimation procedure for a model representing the results of a cancer treatment follow-up study is given. Supported in part by NSF Grant Number DCR74-17282.     

PORGUENIA PERUVIANA GEN. ET SP. NOV., A MARINE CENTRIC DIATOM WITH AN UNUSUAL OCELLUS1

A new diatom genus and species, Porguenia peruviana Sullivan, is described from an Eocene marine deposit from the Paracas Peninsula, Peru. The valve outline is circular and the areolation is best described as pseudoloculate; spines of any type are lacking. A ring of elongated, densely packed rimoportulae is situated on the secondary marginal ridge. Externally, each rimoportula consists of a long, flattened, fluted upper portion supported by a shorter cylindrical stalk. The processes are winged and exhibit various degrees of curvature of the major axis. Typically, six reniform ocelli of unusual structure are situated centrifugally to the ring of rimoportulae and interrupt the true marginal ridge. Because the perforation plate differs from that of all other ocellus-bearing diatoms, a new term has been introduced for this structure, the diaphoron. The placement and structure of this newly discovered “perforation plate” do not allow Porguenia to be placed in any circumscribed family, although the Triceratiaceae would appear at present to be the most closely related family.     

Multiple two-sample testing under arbitrary covariance dependency with an application in imaging mass spectrometry

Large-scale hypothesis testing has become a ubiquitous problem in high-dimensional statistical inference, with broad applications in various scientific disciplines. One relevant application is constituted by imaging mass spectrometry (IMS) association studies, where a large number of tests are performed simultaneously in order to identify molecular masses that are associated with a particular phenotype, for example, a cancer subtype. Mass spectra obtained from matrix-assisted laser desorption/ionization (MALDI) experiments are dependent, when considered as statistical quantities. False discovery proportion (FDP) estimation and  control under arbitrary dependency structure among test statistics is an active topic in modern multiple testing research. In this context, we are concerned with the evaluation of associations between the binary outcome variable (describing the phenotype) and multiple predictors derived from MALDI measurements. We propose an inference procedure in which the correlation matrix of the test statistics is utilized. The approach is based on multiple marginal models. Specifically, we fit a marginal logistic regression model for each predictor individually. Asymptotic joint normality of the stacked vector of the marginal regression coefficients is established under standard regularity assumptions, and their (limiting) correlation matrix is estimated. The proposed method extracts common factors from the resulting empirical correlation matrix. Finally, we estimate the realized FDP of a thresholding procedure for the marginal p-values. We demonstrate a practical application of the proposed workflow to MALDI IMS data in an oncological context.