Age Validation and Reproductive Biology of Bluefish, \u3ci\u3ePomatomus saltatrix,\u3c/i\u3e Along the East Coast of United States

I describe a new preparation technique that increases readability of otoliths, along with criteria for the interpretation of otolith microstructure of bluefish, Pomatomus saltatrix, collected from Florida to New York during 2001-2003 (n = 2652). I validated annulus formation in otoliths for ages 1 to 8 using marginal increment analysis and thus extended validation by four years to include the preponderance of age classes in the catch. Although otoliths are typically superior for ageing, bluefish are routinely aged with scales; thus a side-by-side comparison of otoliths versus scales is necessary before otoliths can supplant scales. When compared, precision was highest with sectioned otoliths, exceeding 87% across all years, and exceeding 99% within 1 year up to ages 13. In contrast, scales tended to over age age-1 through age-5, and under aged age-7 and older in comparison with sectioned otoliths. Having demonstrated the value ofotoliths, I used ages estimated from them to evaluate age distribution of various gears used in the fishery and calculated growth parameters and batch fecundity. When I evaluated my coast wide collections, I noted that gears caught different age ranges yet there were no significant differences in the von Bertalanffy growth parameters compared by sex, year, and between the South Atlantic and Middle Atlantic Bights using likelihood-ratio tests. The estimated Atlantic von Bertalanffy model growth parameters were Linf = 815.3mm ± 15.3, k = 0.311 ± 0.03, t0 = -.301 ± 0.18. Histology, trends in gonadosomatic index, and oocyte diameter frequencies were used to determine bluefish spawning locations and patterns. Bluefish are multiple spawners with indeterminate fecundity. The presence of all stages of development in fully mature ovaries indicates that bluefish have asynchronous oocyte development. Mean age at first maturity for bluefish provided evidence for larger sizes than previously estimated with females maturing at 1.90 years and 480 mm. Histological samples showed imminent spawning in Florida and North Carolina during March to April, and from April to August in Virginia to New York, supporting the hypothesis of continuous spawning from South Atlantic Bight to Middle Atlantic Bight. My estimates of fecundity at size are lower than previously published results

Attainability of Accurate Age Frequencies for Ocean Quahogs (Arctica islandica) Using Large Datasets: Protocol, Reader Precision, and Error Assessment

Ocean quahogs (Arctica islandica) are the longest lived bivalve on Earth. Individuals on the deep continental shelf off Georges Bank can survive for centuries, and in the colder, boreal waters of Iceland, ages over 500 y can be reached. Ocean quahog landings in the United States represent a $24 million industry, yet assessment models operate with no age data because of the substantial sample size required to develop adequate population age distributions for such a long-lived species, the unknown error associated with age estimates, and the extensive time and financial investment required to create production-scale age datasets. Inclusion of age data for this species requires precision metrics to evaluate aging uncertainty such as percent agreement, percent error, coefficient of variation, and tests of bias. To move forward using error-validated age-composition data, a 3-fold error protocol was developed using a large dual-reader dataset (n = 610) from Georges Bank. First, a proxy age-validation study was performed to corroborate an aging method, followed by error evaluation in the context of age-reader bias, precision, and error frequency. Error thresholds were established for each of the three error methods. Georges Bank samples ranged from 33 to 261 y of age and met the predetermined error thresholds for bias (conditionally because of significant and nonsignificant results), precision (average coefficient of variation less than 7%), and error frequency (less than 10%). Consequently, age estimates were deemed acceptable to support age frequency analyses. Precision and bias error were greatest for the youngest animals and, in the context of age-reader bias, error rates were higher for young male ocean quahogs than for young females. Improved age validation of young, sex-differentiated A. islandica will constrain aging error and guide refinement of both aging and age-error protocols

Coloration avec préférences : complexité, inégalités valides et vérification formelle

National audienceNous nous intéressons à un problème de coloration avec préférences minimale CPM dans les graphes triangulés. Cette étude s'inscrit dans le projet CompCert qui a pour objectif la certification, à l'aide de méthodes formelles, d'un compilateur optimisant du langage C. L'une des optimisations du compilateur certifié est l'allocation des registres du processeur. Optimiser cette allocation de registres revient à résoudre le problème CPM auquel nous nous intéressons. Nous montrons un résultat de complexité concernant CPM et proposons l'amélioration d'une méthode de coupes permettant la résolution de ce problème. Ce travail est une jonction entre la recherche opérationnelle et les méthodes formelles, dans la mesure où nous vérifions formellement par ailleurs la résolution du problème en prouvant correct le développement, hormis la recherche effectuée par le solveur dont la vérification consiste à déterminer a posteriori si la solution proposée est bien correcte

Structure characterization of the central repetitive domain of high molecular weight gluten proteins. II. Characterization in solution and in the dry state

The structure of the central repetitive domain of high molecular weight (HMW) wheat gluten proteins was characterized in solution and in the dry state using HMW proteins Bx6 and Bx7 and a subcloned, bacterially expressed part of the repetitive domain of HMW Dx5. Model studies of the HMW consensus peptides PGQGQQ and GYYPTSPQQ formed the basis for the data analysis. In solution, the repetitive domain contained a continuous nonoverlapping series of both type I and type II β-turns at positions predicted from the model studies; type II β-turns occurred at QPGQ and QQGY sequences and type I β-turns at YPTS and SPQQ. The subcloned part of the HMW Dx5 repetitive domain sometimes migrated as two bands on SDS-PAGE; we present evidence that this may be caused by a single amino acid insertion that disturbs the regular structure of β-turns. The type I β-turns are lost when the protein is dried on a solid surface, probably by conversion to type II β-turns. The homogeneous type II β-turn distribution is compatible with the formation of a β-spiral structure, which provides the protein with elastic properties. The β-turns and thus the β-spiral are stabilized by hydrogen bonds within and between turns. Reformation of this hydrogen bonding network after, e.g., mechanical disruption may be important for the elastic properties of gluten proteins

A Vulnerability Assessment of Fish and Invertebrates to Climate Change on the Northeast U.S. Continental Shelf

Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These methods combine the exposure of a species to a stressor (climate change and decadal variability) and the sensitivity of species to the stressor. These two components are then combined to estimate an overall vulnerability. Quantitative data are used when available, but qualitative information and expert opinion are used when quantitative data is lacking. Here we conduct a climate vulnerability assessment on 82 fish and invertebrate species in the Northeast U.S. Shelf including exploited, forage, and protected species. We define climate vulnerability as the extent to which abundance or productivity of a species in the region could be impacted by climate change and decadal variability. We find that the overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability. In addition, the majority of species included in the assessment have a high potential for a change in distribution in response to projected changes in climate. Negative effects of climate change are expected for approximately half of the species assessed, but some species are expected to be positively affected (e.g., increase in productivity or move into the region). These results will inform research and management activities related to understanding and adapting marine fisheries management and conservation to climate change and decadal variability

Chikungunya Virus Infection during Pregnancy, Réunion, France, 2006

Except for prenatal hospital admissions for those infected, this virus had no effect on outcomes

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

On the Maximum Affinity Coloring : Complexity in Bipartite Conflict Graphs and Links with Multiway Cut

National audienceThe maximum affinity K-coloring problem is a generalization of the classical K- coloring problem that enables to model that two vertices should be, if possible, colored with the same color. Such vertices are linked with another kind of edges, called affinities. Almost all the algorithms used in practice use local criteria to determine whether an affinity can be satisfied (i.e. its endpoints can be colored with the same color) or not. These criteria only rely on the colorability of the graph and do not take care of the global configuration of affinities.This paper has two objectives. First, highlight a problem that models many applications and on which much work has to be done. Second, point out that affinities have to be considered more globally than they currently are in the literature.We first describe complexity results, mostly in 2-colorable graphs. In partic- ular, we show that the problem is NP-hard in these graphs for K = 2, meaning that the problem is hard even if coloring the graph is easy. Then we prove that any affinity of a graph can be satisfied while preserving the K-colorability in partial (K ? 1)-trees. Finally, we prove that, in partial (K ? 1)-trees, an optimal affinity coloring can be found by solving a minimum multiway cut instance and a classical K-coloring instance separately

Vérification formelle d'un algorithme d'allocation de registres par coloration de graphe

Cette publication a fait l'objet d'une invitation aux 1ères Journées Nationales du GDR GPL,du 28 au 30 Janvier 2009, à Toulouse (France), où elle a été présentée de nouveau.International audienceLe travail présenté dans cet article est à l'interface entre la recherche opérationnelle et les méthodes formelles. Il s'inscrit dans le cadre du projet CompCert ayant pour but le développement et la vérification formelle, utilisant l'assistant de preuve Coq, d'un compilateur du langage C potentiellement utilisable pour la production de logiciels embarqués critiques. Nous nous intéressons dans cet article à l'allocation de registres, qui consiste à optimiser l'utilisation des registres du processeur. Nous proposons d'aborder cette optimisation en la modélisant par un problème dit de coloration avec préférences dont nous vérifions formellement la résolution. Cette vérification prend deux formes : preuve de correction de la spécification Coq pour la première partie de l'algorithme et validation a posteriori pour la seconde