Population structure, mortality and growth of Pinna nobilis Linnaeus, 1758 (Mollusca, Bivalvia) at different depths in Moraira bay (Alicante, Western Mediterranean)

An investigation to characterize the causes of Pinna nobilis population structure in Moraira bay (Western Mediterranean) was developed. Individuals of two areas of the same Posidonia meadow, located at different depths (A1, -13 and A2, -6 m), were inventoried, tagged, their positions accurately recorded and monitored from July 1997 to July 2002. On each area, different aspects of population demography were studied (i.e. spatial distribution, size structure, displacement evidences, mortality, growth and shell orientation). A comparison between both groups of individuals was carried out, finding important differences between them. In A1, the individuals were more aggregated and mean and maximum size were higher (A1, 10.3 and A2, 6 individuals/100 m(2); A1, x = 47.2 +/- 9.9; A2, x = 29.8 +/- 7.4 cm, P < 0.001, respectively). In A2, growth rate and mortality were higher, the latter concentrated on the largest individuals, in contrast to A1, where the smallest individuals had the higher mortality rate [A1, L = 56.03(1 - e(-0.17t)); A2, L = 37.59(1 - e(-0.40t)), P < 0.001; mean annual mortality A1: 32 dead individuals out of 135, 23.7% and A2: 16 dead individuals out of 36, 44.4%, and total mortality coefficients (z), z(A1(-30)) = 0.28, z(A1(31-45)) = 0.05, z(A1(46-)) = 0.08; z(A2(-30)) = 0.15, z(A2(31-45)) = 0.25]. A common shell orientation N-S, coincident with the maximum shore exposure, was observed in A2. Spatial distribution in both areas showed not enough evidence to discard a random distribution of the individuals, despite the greater aggregation on the deeper area (A1) (A1, chi(2) = 0.41, df = 3, P > 0.5, A2, chi(2)= 0.98, df = 2 and 0.3 < P < 0.5). The obtained results have demonstrated that the depth-related size segregation usually shown by P. nobilis is mainly caused by differences in mortality and growth among individuals located at different depths, rather than by the active displacement of individuals previously reported in the literature. Furthermore, dwarf individuals are observed in shallower levels and as a consequence, the relationship between size and age are not comparable even among groups of individuals inhabiting the same meadow at different depths. The final causes of the differences on mortality and growth are also discussed.

Effect of individual variability on estimation of population parameters from length-frequency data

We consider estimation of mortality rates and growth parameters from length-frequency data of a fish stock when there is individual variability in the von Bertalanffy growth parameter L-infinity and investigate the possible bias in the estimates when the individual variability is ignored. Three methods are examined: (i) the regression method based on the Beverton and Holt's (1956, Rapp. P.V. Reun. Cons. Int. Explor. Mer, 140: 67-83) equation; (ii) the moment method of Powell (1979, Rapp. PV. Reun. Int. Explor. Mer, 175: 167-169); and (iii) a generalization of Powell's method that estimates the individual variability to be incorporated into the estimation. It is found that the biases in the estimates from the existing methods are, in general, substantial, even when individual variability in growth is small and recruitment is uniform, and the generalized method performs better in terms of bias but is subject to a larger variation. There is a need to develop robust and flexible methods to deal with individual variability in the analysis of length-frequency data.

Variable Size Population NSGA-II: VPNSGA-II

Multi-objective optimization is an active field of research with broad applicability in aeronautics. This report details a variant of the original NSGA-II software aimed to improve the performances of such a widely used Genetic Algorithm in finding the optimal Pareto-front of a Multi-Objective optimization problem for the use of UAV and aircraft design and optimsaiton. Original NSGA-II works on a population of predetermined constant size and its computational cost to evaluate one generation is O(mn^2 ), being m the number of objective functions and n the population size. The basic idea encouraging this work is that of reduce the computational cost of the NSGA-II algorithm by making it work on a population of variable size, in order to obtain better convergence towards the Pareto-front in less time. In this work some test functions will be tested with both original NSGA-II and VPNSGA-II algorithms; each test will be timed in order to get a measure of the computational cost of each trial and the results will be compared.

Canadian Stroke Best Practice Recommendations: Mood, Cognition and Fatigue Following Stroke practice guidelines, update 2015

Every year, approximately 62 000 people with stroke and transient ischemic attack are treated in Canadian hospitals, and the evidence suggests one-third or more will experience vascular-cognitive impairment, and/or intractable fatigue, either alone or in combination. The 2015 update of the Canadian Stroke Best Practice Recommendations: Mood, Cognition and Fatigue Module guideline is a comprehensive summary of current evidence-based recommendations for clinicians in a range of settings, who provide care to patients following stroke. The three consequences of stroke that are the focus of the this guideline (poststroke depression, vascular cognitive impairment, and fatigue) have high incidence rates and significant impact on the lives of people who have had a stroke, impede recovery, and result in worse long-term outcomes. Significant practice variations and gaps in the research evidence have been reported for initial screening and in-depth assessment of stroke patients for these conditions. Also of concern, an increased number of family members and informal caregivers may also experience depressive symptoms in the poststroke recovery phase which further impact patient recovery. These factors emphasize the need for a system of care that ensures screening occurs as a standard and consistent component of clinical practice across settings as stroke patients transition from acute care to active rehabilitation and reintegration into their community. Additionally, building system capacity to ensure access to appropriate specialists for treatment and ongoing management of stroke survivors with these conditions is another great challenge.

Reduced visual function and its association with physical functioning in the Finnish adult population : Prevalence, causes, and need for eye care services

The purpose of this study was to estimate the prevalence and distribution of reduced visual acuity, major chronic eye diseases, and subsequent need for eye care services in the Finnish adult population comprising persons aged 30 years and older. In addition, we analyzed the effect of decreased vision on functioning and need for assistance using the World Health Organization’s (WHO) International Classification of Functioning, Disability, and Health (ICF) as a framework. The study was based on the Health 2000 health examination survey, a nationally representative population-based comprehensive survey of health and functional capacity carried out in 2000 to 2001 in Finland. The study sample representing the Finnish population aged 30 years and older was drawn by a two-stage stratified cluster sampling. The Health 2000 survey included a home interview and a comprehensive health examination conducted at a nearby screening center. If the invited participants did not attend, an abridged examination was conducted at home or in an institution. Based on our finding in participants, the great majority (96%) of Finnish adults had at least moderate visual acuity (VA ≥ 0.5) with current refraction correction, if any. However, in the age group 75–84 years the prevalence decreased to 81%, and after 85 years to 46%. In the population aged 30 years and older, the prevalence of habitual visual impairment (VA ≤ 0.25) was 1.6%, and 0.5% were blind (VA < 0.1). The prevalence of visual impairment increased significantly with age (p < 0.001), and after the age of 65 years the increase was sharp. Visual impairment was equally common for both sexes (OR 1.20, 95% CI 0.82 – 1.74). Based on self-reported and/or register-based data, the estimated total prevalences of cataract, glaucoma, age-related maculopathy (ARM), and diabetic retinopathy (DR) in the study population were 10%, 5%, 4%, and 1%, respectively. The prevalence of all of these chronic eye diseases increased with age (p < 0.001). Cataract and glaucoma were more common in women than in men (OR 1.55, 95% CI 1.26 – 1.91 and OR 1.57, 95% CI 1.24 – 1.98, respectively). The most prevalent eye diseases in people with visual impairment (VA ≤ 0.25) were ARM (37%), unoperated cataract (27%), glaucoma (22%), and DR (7%). One-half (58%) of visually impaired people had had a vision examination during the past five years, and 79% had received some vision rehabilitation services, mainly in the form of spectacles (70%). Only one-third (31%) had received formal low vision rehabilitation (i.e., fitting of low vision aids, receiving patient education, training for orientation and mobility, training for activities of daily living (ADL), or consultation with a social worker). People with low vision (VA 0.1 – 0.25) were less likely to have received formal low vision rehabilitation, magnifying glasses, or other low vision aids than blind people (VA < 0.1). Furthermore, low cognitive capacity and living in an institution were associated with limited use of vision rehabilitation services. Of the visually impaired living in the community, 71% reported a need for assistance and 24% had an unmet need for assistance in everyday activities. Prevalence of ADL, instrumental activities of daily living (IADL), and mobility increased with decreasing VA (p < 0.001). Visually impaired persons (VA ≤ 0.25) were four times more likely to have ADL disabilities than those with good VA (VA ≥ 0.8) after adjustment for sociodemographic and behavioral factors and chronic conditions (OR 4.36, 95% CI 2.44 – 7.78). Limitations in IADL and measured mobility were five times as likely (OR 4.82, 95% CI 2.38 – 9.76 and OR 5.37, 95% CI 2.44 – 7.78, respectively) and self-reported mobility limitations were three times as likely (OR 3.07, 95% CI 1.67 – 9.63) as in persons with good VA. The high prevalence of age-related eye diseases and subsequent visual impairment in the fastest growing segment of the population will result in a substantial increase in the demand for eye care services in the future. Many of the visually impaired, especially older persons with decreased cognitive capacity or living in an institution, have not had a recent vision examination and lack adequate low vision rehabilitation. This highlights the need for regular evaluation of visual function in the elderly and an active dissemination of information about rehabilitation services. Decreased VA is strongly associated with functional limitations, and even a slight decrease in VA was found to be associated with limited functioning. Thus, continuous efforts are needed to identify and treat eye diseases to maintain patients’ quality of life and to alleviate the social and economic burden of serious eye diseases.

Homeostasis of functional maps in active dendrites emerges in the absence of individual channelostasis

The maintenance of ion channel homeostasis, or channelostasis, is a complex puzzle in neurons with extensive dendritic arborization, encompassing a combinatorial diversity of proteins that encode these channels and their auxiliary subunits, their localization profiles, and associated signaling machinery. Despite this, neurons exhibit amazingly stereotypic, topographically continuous maps of several functional properties along their active dendritic arbor. Here, we asked whether the membrane composition of neurons, at the level of individual ion channels, is constrained by this structural requirement of sustaining several functional maps along the same topograph. We performed global sensitivity analysis on morphologically realistic conductance-based models of hippocampal pyramidal neurons that coexpressed six well-characterized functional maps along their trunk. We generated randomized models by varying 32 underlying parameters and constrained these models with quantitative experimental measurements from the soma and dendrites of hippocampal pyramidal neurons. Analyzing valid models that satisfied experimental constraints on all six functional maps, we found topographically analogous functional maps to emerge from disparate model parameters with weak pairwise correlations between parameters. Finally, we derived a methodology to assess the contribution of individual channel conductances to the various functional measurements, using virtual knockout simulations on the valid model population. We found that the virtual knockout of individual channels resulted in variable, measurement and location-specific impacts across the population. Our results suggest collective channelostasis as a mechanism behind the robust emergence of analogous functional maps and have significant ramifications for the localization and targeting of ion channels and enzymes that regulate neural coding and homeostasis.

Geomorphology reveals active decollement geometry in the central Himalayan seismic gap

The similar to 700-km-long ``central seismic gap'' is the most prominent segment of the Himalayan front not to have ruptured in a major earthquake during the last 200-500 yr. This prolonged seismic quiescence has led to the proposition that this region, with a population >10 million, is overdue for a great earthquake. Despite the region's recognized seismic risk, the geometry of faults likely to host large earthquakes remains poorly understood. Here, we place new constraints on the spatial distribution of rock uplift within the western similar to 400 km of the central seismic gap using topographic and river profile analyses together with basinwide erosion rate estimates from cosmogenic Be-10. The data sets show a distinctive physiographic transition at the base of the high Himalaya in the state of Uttarakhand, India, characterized by abrupt strike-normal increases in channel steepness and a tenfold increase in erosion rates. When combined with previously published geophysical imaging and seismicity data sets, we interpret the observed spatial distribution of erosion rates and channel steepness to reflect the landscape response to spatially variable rock uplift due to a structurally coherent ramp-flat system of the Main Himalayan Thrust. Although it remains unresolved whether the kinematics of the Main Himalayan Thrust ramp involve an emergent fault or duplex, the landscape and erosion rate patterns suggest that the decollement beneath the state of Uttarakhand provides a sufficiently large and coherent fault segment capable of hosting a great earthquake.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

A modelling approach to the development of an active management strategy for the Queen Elizabeth II reservoir

This article outlines the outcome of work that set out to provide one of the specified integral contributions to the overarching objectives of the EU- sponsored LIFE98 project described in this volume. Among others, these included a requirement to marry automatic monitoring and dynamic modelling approaches in the interests of securing better management of water quality in lakes and reservoirs. The particular task given to us was to devise the elements of an active management strategy for the Queen Elizabeth II Reservoir. This is one of the larger reservoirs supplying the population of the London area: after purification and disinfection, its water goes directly to the distribution network and to the consumers. The quality of the water in the reservoir is of primary concern, for the greater is the content of biogenic materials, including phytoplankton, then the more prolonged is the purification and the more expensive is the treatment. Whatever good that phytoplankton may do by way of oxygenation and oxidative purification, it is eventually relegated to an impurity that has to be removed from the final product. Indeed, it has been estimated that the cost of removing algae and microorganisms from water represents about one quarter of its price at the tap. In chemically fertile waters, such as those typifying the resources of the Thames Valley, there is thus a powerful and ongoing incentive to be able to minimise plankton growth in storage reservoirs. Indeed, the Thames Water company and its predecessor undertakings, have a long and impressive history of confronting and quantifying the fundamentals of phytoplankton growth in their reservoirs and of developing strategies for operation and design to combat them. The work to be described here follows in this tradition. However, the use of the model PROTECH-D to investigate present phytoplankton growth patterns in the Queen Elizabeth II Reservoir questioned the interpretation of some of the recent observations. On the other hand, it has reinforced the theories underpinning the original design of this and those Thames-Valley storage reservoirs constructed subsequently. The authors recount these experiences as an example of how simulation models can hone the theoretical base and its application to the practical problems of supplying water of good quality at economic cost, before the engineering is initiated.

Otolith morphometrics and population structure of Pacific sardine (Sardinops sagax) along the west coast of North America

The broad distribution of Pacific sardine (Sardinops sagax) along the Pacif ic coast of North America makes it difficult for fisheries managers to identify regional stocks of this dominant small pelagic species. An investigation of morphometric characteristics of otoliths of Pacific sardine across most of their range revealed regional differences in populations. In a survey of over 2000 otoliths, all ages (with an emphasis on age-1 recruits) were compared. Principal components analysis, multivariate analysis of variance, and a novel method derived from regression and residuals calculations, termed perimeter-weight profiles (PWPs), revealed otolith similarities and differences. The results of the different approaches to statistical comparisons did not always agree. Sardine otoliths from Mexican waters were generally lighter and more lobate than those from U.S. and Canadian populations. Age-1 otoliths from northern California in 2006–07 tended to be heavier and smoother than those from other areas, including year-class cohorts from southern California. Comparisons of age-groups and year-classes of northern California otoliths with the use of the PWP models indicated signif icant trends in year-to-year patterns. In conjunction with other established indices of population structure, otolith PWPs are a useful tool for identifying local and regional stocks of Pacific sardine and may help distinguish populations of other fish species as well.

The vulnerability of reproductively active squaretail coralgrouper (Plectropomus areolatus) to fishing

Squaretail coralgrouper (Plectropomus areolatus) were captured and tagged at a fish spawning aggregation (FSA) site with conventional and acoustic tags to assess their vulnerability to fishing and spatial dynamics during reproductive periods. Males outnumbered females in catch and, on average, were larger than females. Findings revealed a high vulnerability to fishing, particularly during reproductive periods, and most fish were recaptured within the 5-month spawning season and within 10−12 km of the aggregation site. Individual and sex-specific variability in movement to, and residency times at, the FSA site indicates that individual monthly spawning aggregations represent subsets of the total reproductive population. Some individuals appeared to move along a common migratory corridor to reach the FSA site. Sex-specific behavioral differences, particularly longer residency times, appear to increase the vulnerability of reproductively active males to fishing, particularly within a FSA, which could reduce reproductive output. Both fishery-dependent and fishery-independent data indicate that only males were present within the first month of aggregation. The combined results indicate that reproductively active P. areolatus are highly vulnerable to fishing and that FSAs and migratory corridors of reproductively active fish should be incorporated into marine protected areas. The capture of P. areolatus during reproductive periods should be restricted as part of a comprehensive management strateg

Census of Active Commercial Fishermen in Puerto Rico: 2008

The implementation of Puerto Rican Regulation No. 6768, which overhauled the existing fishery management framework, generated considerable hostility towards local managers. Among the controversial management measures adopted in 2004 were the assignment of fishing licenses based on fishing income, the establishment of closed seasons, and new minimum size restrictions for commercially valuable species. Though tensions have subsided, considerable opposition to these regulations remains. This paper provides a characterization of the current population of active small-scale fishermen, discusses their perceptions about the biological and socio-economic condition of the fishery, and describes their attitudes towards the new management framework. This study revealed that the number of active fishermen decreased from 1,731 in 1988 to 868 in 2008. Although a declining resource base was one of the main drivers behind these waning participation statistics, rising fuel costs and burdensome regulations exacerbated the rate of attrition. The majority of the fishermen were middleaged men (50 years) with moderate levels of formal education and high levels of fishing dependence which limited their employment opportunities outside the fishery. Most of the vessels were small (20 ft) and outfitted with a single outboard engine (80 hp). Hook and line and SCUBA were dominant gears because of their versatility and cost effectiveness. Fishermen suggested that their opposition to the regulations would continue unless they were afforded greater regulatory flexibility and provided with a larger role in the decision-making process. Fishermen were adamant about the need to reconsider the income reporting requirements to secure a fishing license because of the potential for losing public assistance benefits. They also objected to increasing the minimum size of many deepwater snapper (Lutjanidae) and grouper (Serranidae) species because it forced them to discard dead fish, a practice they consider wasteful since these species do not survive the ascent to the surface once hooked.

A Comparison of Two Stratification Schemes Used in Sampling Canadian Atlantic Cod, Gadus morhua

Sampling is a key element in the assessment of any fish stock. It is often one of the most expensive activities of the management process; thus, improved efficiency can result in significant cost savings. In most cases a two-phase sampling strategy is employed. Two commonly used versions of such stratified random schemes were simulated using a test population based on Atlantic cod, Gadus morhua. A 1 otolith per 1 cm length frequency currently used for many flatfish and some smaller gadoids and a 3 otolith per 3 cm length frequency currently used for many of the larger gadoids. No difference was detected in the age composition or mean length at age for either scheme; however, 10 percent fewer otoliths were collected in 1 for 1 sampling than 3 for 3. There was an improvement of between 30 and 60 percent in the coefficient of variation of the estimated catch numbers at age using the 1 for 1 compared with the 3 for 3 stratified sampling. For these reasons and other operational considerations, the 1 for 1 stratified random design of sampling appears to be superior.

Influence of a tilted cavity on quantum-dot optoelectronic active devices

Quantum-dot laser diodes (QD-LDs) with a Fabry-Perot cavity and quantum-dot semiconductor optical amplifiers (QD-SOAs) with 7° tilted cavity were fabricated. The influence of a tilted cavity on optoelectronic active devices was also investigated. For the QD-LD, high performance was observed at room temperature. The threshold current was below 30 mA and the slope efficiency was 0.36 W/A. In contrast, the threshold current of the QD-SOA approached 1000 mA, which indicated that low facet reflectivity was obtained due to the tilted cavity design.A much more inverted carrier population was found in the QD-SOA active region at high operating current, thus offering a large optical gain and preserving the advantages of quantum dots in optical amplification and processing applications. Due to the inhomogeneity and excited state transition of quantum dots, the full width at half maximum of the electroluminescence spectrum of the QD-SOA was 81.6 nm at the injection current of 120 mA, which was ideal for broad bandwidth application in a wavelength division multiplexing system. In addition, there was more than one lasing peak in the lasing spectra of both devices and the separation of these peak positions was 6-8 nm,which is approximately equal to the homogeneous broadening of quantum dots.