Frequency responses of age-structured populations: Pacific salmon as an example

Increasing evidence of the effects of changing climate on physical ocean conditions and long-term changes in fish populations adds to the need to understand the effects of stochastic forcing on marine populations. Cohort resonance is of particular interest because it involves selective sensitivity to specific time scales of environmental variability, including that of mean age of reproduction, and, more importantly, very low frequencies (i.e., trends). We present an age-structured model for two Pacific salmon species with environmental variability in survival rate and in individual growth rate, hence spawning age distribution. We use computed frequency response curves and analysis of the linearized dynamics to obtain two main results. First, the frequency response of the population is affected by the life history stage at which variability affects the population; varying growth rate tends to excite periodic resonance in age structure, while varying survival tends to excite low-frequency fluctuation with more effect on total population size. Second, decreasing adult survival strengthens the cohort resonance effect at all frequencies, a finding that addresses the question of how fishing and climate change will interact.Comment: much revised: the version accepted by Theoretical Population Biolog

Optimal wind patterns for biological production in shelf ecosystems driven by coastal upwelling

Major upwelling systems around the world provide marine productivity and fishery yield out of proportion to their area. Upwelling winds have the counteracting effects that stronger winds upwell more nutrients to the surface for higher production, but they also transport that production off continental shelves where it may not be consumed by shelf-dwelling species. Because the patterns of wind fluctuations vary in these systems, we determined the conditions for maximal biological production using a simple conveyor belt model. The conditions are that: (1) the average cross-shelf velocity produced by the winds be the value that provides the maximum production with constant winds and (2) that the wind pattern be periodic with period equal to the cross-shelf transport time that results from maximizing production with constant winds. Examination of an example using winds in central California indicated wind patterns optimal for phytoplankton occurred more frequently than those for zooplankton

Using Open Journal Systems to Move from Paper Production to Online Open Access

The Canadian Journal of Sociology is an independent, peer-reviewed publication, originally constituted as a charitable organization in 1975. From 1975 to 2008, CJS was printed quarterly and mailed to its subscribers. The move to Open Access and the Open Journal System has meant some adjustments philosophically and pragmatically. In outlining them below, we hope to guide other journals who may be contemplating the same move. While we focus on our use of the Open Journal System, the comments are easily transferrable to other programs and situations

Infective endocarditis in intravenous drug abusers: an update

Infective endocarditis despite advances in diagnosis remains a common cause of hospitalization, with high morbidity and mortality rates. Through literature review it is possible to conclude that polymicrobial endocarditis occurs mainly in intravenous drug abusers with predominance in the right side of the heart, often with tricuspid valve involvement. This fact can be associated with the type of drug used by the patients; therefore, knowledge of the patient's history is critical for adjustment of the therapy. It is also important to emphasize that the most common combinations of organisms in polymicrobial infective endocarditis are: Staphylococcus aureus, Streptococcus pneumonia and Pseudomonas aeruginosa, as well as mixed cultures of Candida spp. and bacteria. A better understanding of the epidemiology and associated risk factors are required in order to develop an efficient therapy, although PE studies are difficult to perform due to the rarity of cases and lack of prospective cohorts.This work was supported by Portuguese Foundation for Science and Technology (FCT) through the grants SFRH/BPD/47693/2008, SFRH/BPD/20987/2004 and SFRH/BPD/72632/2010 attributed to Claudia Sousa, Claudia Botelho and Diana Rodrigues, respectively

Piecewise-Linear Models of Genetic Regulatory Networks: Theory and Example

International audienceThe experimental study of genetic regulatory networks has made tremendous progress in recent years resulting in a huge amount of data on the molecular interactions in model organisms. It is therefore not possible anymore to intuitively understand how the genes and interactions together influence the behavior of the system. In order to answer such questions, a rigorous modeling and analysis approach is necessary. In this chapter, we present a family of such models and analysis methods enabling us to better understand the dynam-ics of genetic regulatory networks. We apply such methods to the network that underlies the nutritional stress response of the bacterium E. coli. The functioning and development of living organisms is controlled by large and complex networks of genes, proteins, small molecules, and their interactions, so-called genetic regulatory networks. The study of these networks has recently taken a qualitative leap through the use of modern genomic techniques that allow for the simultaneous measurement of the expression levels of all genes of an organism. This has resulted in an ever growing description of the interactions in the studied genetic regulatory networks. However, it is necessary to go beyond the simple description of the interactions in order to understand the behavior of these networks and their relation with the actual functioning of the organism. Since the networks under study are usually very large, an intuitive approach for their understanding is out of ques-tion. In order to support this work, mathematical and computer tools are necessary: the unambiguous description of the phenomena that mathematical models provide allows for a detailed analysis of the behaviors at play, though they might not exactly represent the exact behavior of the networks. In this chapter, we will be mostly interested in the modeling of the genetic reg-ulatory networks by means of differential equations. This classical approach allows precise numerical predictions of deterministic dynamic properties of genetic regu-latory networks to be made. However, for most networks of biological interest the application of differential equations is far from straightforward. First, the biochemi-cal reaction mechanisms underlying the interactions are usually not or incompletel

Recruitment Constraints in Singapore's Fluted Giant Clam (Tridacna squamosa) Populations - A Dispersal Model Approach

10.1371/journal.pone.0058819PLoS ONE83

Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals

This is the final version of the article. Available from Springer Nature via the DOI in this record.Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of thirteen and eight microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland, and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Unsurprisingly, historical patterns of gene flow appeared more complex, though again southwest Britain appeared an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as ‘Vulnerable’, and for the designation and management of European MPAs.We thank Natural England (project No. RP0286, contract No. SAE 03-02-146), the NERC (grant No. NE/L002434/1) and the University of Exeter for funding this research. Additional funding for sample collection, travel and microsatellite development was provided by the EU Framework 7 ASSEMBLE programme, agreement no. 227799, and NERC grant No. NBAF-362

High interannual variability in connectivity and genetic pool of a temperate clingfish matches oceanographic transport predictions

Adults of most marine benthic and demersal fish are site-attached, with the dispersal of their larval stages ensuring connectivity among populations. In this study we aimed to infer spatial and temporal variation in population connectivity and dispersal of a marine fish species, using genetic tools and comparing these with oceanographic transport. We focused on an intertidal rocky reef fish species, the shore clingfish Lepadogaster lepadogaster, along the southwest Iberian Peninsula, in 2011 and 2012. We predicted high levels of self-recruitment and distinct populations, due to short pelagic larval duration and because all its developmental stages have previously been found near adult habitats. Genetic analyses based on microsatellites countered our prediction and a biophysical dispersal model showed that oceanographic transport was a good explanation for the patterns observed. Adult sub-populations separated by up to 300 km of coastline displayed no genetic differentiation, revealing a single connected population with larvae potentially dispersing long distances over hundreds of km. Despite this, parentage analysis performed on recruits from one focal site within the Marine Park of Arrabida (Portugal), revealed self-recruitment levels of 2.5% and 7.7% in 2011 and 2012, respectively, suggesting that both long-and short-distance dispersal play an important role in the replenishment of these populations. Population differentiation and patterns of dispersal, which were highly variable between years, could be linked to the variability inherent in local oceanographic processes. Overall, our measures of connectivity based on genetic and oceanographic data highlight the relevance of long-distance dispersal in determining the degree of connectivity, even in species with short pelagic larval durations

Audible Image Description as an Accommodation in Statewide Assessments for Students with Visual and Print Disabilities.

Introduction:Although image description has been identified as an accommodation for presentations conducted in the classroom, only a few U.S. states have approved it for use in high-stakes assessments. This study examined the use of audible image description as an assessment accommodation for students with visual and print disabilities by investigating student comprehension under multiple conditions. Methods: Students in three western states in grades three through eight who had visual (n= 117) or print (n= 178) disabilities participated in an abbreviated test constructed of retired assessment questions in English language arts, mathematics, and science, that were aligned with each state's instructional standards, under conditions with and without standardized description of graphic images. The study used a within-subjects block design to collect and compare comprehension data under conditions where audible image description was both used and not used in an abbreviated test. Results: Results indicated that students who read braille were more likely to respond correctly under the audible image description condition, and students with visual and print disabilities who used print were equally likely to respond correctly regardless of condition. Discussion: Braille readers were more likely to obtain a correct answer when audible image description accompanied the question. Audible image description did not affect the likelihood of a correct response from students with print disabilities or students with visual disabilities who read print. Implications for practitioners: Audible image description is an accommodation that may help braille readers perform better on tests. Although the Partnership for Assessment of Readiness for College and Careers (PARCC) and Smarter Balanced consortia are taking steps to include image (or picture) descriptions in their assessment accommodations, teachers may want to develop a standard method for describing images and familiarize their braille readers to the strategy by including it in instruction and in classroom tests. Readers are referred to the National Center on Accessible Media’s online guidelines for image description