bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic evolution of fingering patterns in a lifted Hele–Shaw cell
Authors: Nase Julia , Derks Didi , Lindner Anke
Published: December 2011

We present a study on pattern formation in a Newtonian liquid during lifting of a circular Hele–Shaw cell. When a confined layer of oil is subject to such a stretch flow, air penetrates into the liquid from the sides and a fingering instability, a variant of the classical Saffman–Taylor instability, evolves. This setting has the particularity that the finger growth takes place in a conserved volume of liquid and that the dimensionless surface tension, the control parameter which governs the Saffman–Taylor instability, is changing with time. This leads to a constantly evolving pattern, which we investigate with regard to number of fingers and finger amplitude. We distinguish in the pattern at each instant growing fingers and stagnant fingers. Systematically varying the properties of the viscous oil and the geometry of the Hele–Shaw cell, we show that the number of growing fingers is at each moment well described by a simple approach based on linear stability analysis and depends only on the dimensionless surface tension. In contrast, the finger amplitude and consequently the total number of fingers (growing and stagnant fingers) depend also on the cell confinement. We demonstrate that the finger amplitude has a distinct influence on the debonding force. Higher finger amplitude and number of fingers lead to lower forces.
Horizontal structures of velocity and temperature boundary layers in two-dimensional numerical turbulent Rayleigh-Bénard convection
Authors: Zhou Quan , Sugiyama Kazuyasu , Stevens Richard J. A. M. , Grossmann Siegfried , Lohse Detlef , Xia Ke-Qing
Published: December 2011

We investigate the structures of the near-plate velocity and temperature profiles at different horizontal positions along the conducting bottom (and top) plate of a Rayleigh-Bénard convection cell, using two-dimensional (2D) numerical data obtained at the Rayleigh number Ra = 108 and the Prandtl number Pr = 4.4 of an Oberbeck-Boussinesq flow with constant material parameters. The results show that most of the time, and for both velocity and temperature, the instantaneous profiles scaled by the dynamical frame method [Q. Zhou and K.-Q. Xia, “Measured instantaneous viscous boundary layer in turbulent Rayleigh-Bénard convection,” Phys. Rev. Lett. 104, 104301 (2010)] agree well with the classical Prandtl-Blasius laminar boundary layer (BL) profiles. Therefore, when averaging in the dynamical reference frames, which fluctuate with the respective instantaneous kinematic and thermal BL thicknesses, the obtained mean velocity and temperature profiles are also of Prandtl-Blasius type for nearly all horizontal positions. We further show that in certain situations the traditional definitions based on the time-averaged profiles can lead to unphysical BL thicknesses, while the dynamical method also in such cases can provide a well-defined BL thickness for both the kinematic and the thermal BLs.
Description of rank four entangled states of two qutrits having positive partial transpose
Authors: Chen Lin , Đoković Dragomir Ž
Published: December 2011

It is known that some two-qutrit entangled states of rank 4 with positive partial transpose can be built from the unextendible product bases (UPB) [C. H. Bennett, D. P. DiVincenzo, T. Mor, P. W. Shor, J. A. Smolin, and B. M. Terhal, Phys. Rev. Lett. 82, 5385 (1999)]. We show that this fact is indeed universal, namely, all such states can be constructed from UPB as conjectured recently by Leinaas, Myrheim, and Sollid. We also classify the five-dimensional subspaces of two qutrits which contain only finitely many product states (up to scalar multiple), and in particular those spanned by an UPB.
A comparison of the growth modes of (100)- and (110)-oriented CrO2 films through the calculation of surface and interface energies
Authors: Chetry K. B. , Sims H. , Butler W. H. , Gupta A.
Published: December 2011

The mechanism leading to different growth modes of (100)- and (110)-oriented CrO2 films on a TiO2 substrate has been investigated by using first-principles calculations based on density functional theory (DFT). The surface energies of (100)- and (110)-oriented CrO2 and TiO2 structures were calculated within a three-dimensional slab model. The convergence of the surface energy was studied with respect to the interslab vacuum distance and the thickness of the slab. A sandwich geometry was used to study the interface energy between CrO2 and TiO2. These results shed light on published experimental results on the growth of epitaxially grown CrO2 on (100)- and (110)-oriented TiO2 substrates.
Screened field enhancement factor for the floating sphere model of a carbon nanotube array
Authors: Zhbanov A. I. , Pogorelov E. G. , Chang Yia-Chung , Lee Yong-Gu
Published: December 2011

The screened field enhancement factor for a carbon nanotube (CNT) placed in a CNT array (which is reduced due to the screening effect) is derived based on the “floating sphere” model. We obtain an expression for the field enhancement factor for a CNT in the array as γ=3+2(1+η)/{(2+η)[2πα(2+η)δ2+η]}, where ρ is the radius of sphere, h is the distance from cathode to the center of sphere, and D is the distance between the nearest spheres, η=ρ/h, δ=ρ/D, and α=1 for square or 2/3 for hexagonal lattice made of CNTs. Explicit algebraic formulas for optimizing the distance between tubes, areal density of emitters, and the anode current are also obtained.
Temperature stability of Bloch surface wave biosensors
Authors: Michelotti Francesco , Descrovi Emiliano
Published: December 2011

We report on the experimental characterization of the thermal sensitivity of biosensors based on the coupling of Bloch surface waves (BSW) on amorphous silicon nitride/silicon one dimensional photonic crystals (1DPC). The results show that the silicon alloys compensate the thermo-optic effect taking place in the external medium and indicate that a class of temperature insensitive biosensors can be fabricated by properly designing the layout of the 1DPC. The experimental results are in very good agreement with numerical simulations based on a transfer matrix approach. Moreover, the BSW biosensors show a resolution of 0.03 °C for the measurement of temperature.
Birth cohort changes in Chinese adolescents’ mental health
Authors: Xin Ziqiang , Niu Jianghe , Chi Liping
Published: December 2011

In China, rapid economic growth and increasing social problems constitute two basic characteristics of contemporary social change. During the process of dramatic social change, an emerging question is how adolescents’ mental health has changed across birth cohorts. The present paper reviews four studies of crosstemporal meta‐analysis conducted by us. By meta‐analysis of previous literature, we examined changes in mean scores on mental health measures over time (from the early 1990s to the mid‐2000s). It was found that since the early 1990s, Chinese adolescents’ mental health deteriorated across birth cohorts, shown in increased scores on the negative indicators of mental health (e.g. mental problems, anxiety, and depression), whereas self‐esteem as a positive trait decreased. The dropping trend in Chinese adolescents’ mental health could be attributed to social change, especially increasing social problems. Therefore, adequate attention must be paid to potential influences of social change on individuals’ psychological development.
Short-Term Response of Subadult White Sturgeon to Hopper Dredge Disposal Operations
Authors: Parsley Michael J. , Popoff Nicholas D. , Romine Jason G.
Published: December 2011

The effect of dredged-material disposal operations on the behavior of seven white sturgeon Acipenser transmontanus (50–101 cm fork length) was examined by analysis of the movements and depth use of these fish before, during, and after a series of hopper dredge disposal operations in the lower Columbia River. Analyses of fish locations showed that 12 flow-lane disposal operations within a 24-h period had minimal effect on subadult white sturgeon behavior; six of the seven fish showed slight attraction to the disposal area during disposals, and one fish increased its distance from the disposal area. The core area for all fish combined shifted toward the disposal area during disposals. In the 24 h after completion of the disposal operations the fish core areas shifted back toward those areas occupied before the disposals. The rates of movement, depths used, and diel movement patterns of the white sturgeon showed little change over all periods, suggesting that natural behaviors were not altered during and immediately after hopper dredge disposal operations.

Received June 9, 2010; accepted October 19, 2010
Do Alternative Leaders Affect Fish Catch in Pound Nets at the Mouth of Chesapeake Bay?
Authors: Schaffler Jason J. , Barco Susan G. , D’Eri Linda R. , Mark Swingle W. , Jones Cynthia M.
Published: December 2011

More than 60 stranded bottlenose dolphins Tursiops truncatus exhibiting marks consistent with interactions with pound nets have been documented in the lower Chesapeake Bay since 1997. Given this high rate of bycatch, action is needed to mitigate bottlenose dolphin mortality. However, for any such modification to the pound net to be acceptable to fishers, a clear demonstration of no reduction in the targeted finfish catch will be required. Working with fishers, we evaluated the effect of an experimental pound net leader on finfish catch. The experimental leader entailed similar or greater catches of finfish than did the traditional leader. Further, catches of Batoidea (cownose ray Rhinoptera bonasus, bullnose ray Myliobatis freminvillei, southern stingray Dasyatis americana and Atlantic stingray D. sabina) and clearnose skates Raja eglanteria were reduced with the experimental leader. This example demonstrates that working with fishers to devise alternative harvest strategies can result in the implementation of conservation measures. Although finfish catch was maintained with the experimental leader design, we must continue to monitor bottlenose dolphin bycatch to confirm that the use of the experimental leader reduces the bottlenose dolphin mortality associated with pound nets.

Received December 11, 2009; accepted December 10, 2010
Accuracy and Precision of Visual Estimates and Photogrammetric Measurements of the Length of a Small-bodied Fish
Authors: Bower Michael R. , Gaines Daniel B. , Wilson Kevin P. , Wullschleger John G. , Dzul Maria C. , Quist Michael C. , Dinsmore Stephen J.
Published: December 2011

We assessed the accuracy and precision of visual estimates from two divers and photogrammetric measurements from a diver-operated stereo-video camera system for determining the length of Saratoga Springs pupfish Cyprinodon nevadensis nevadensis (12–36 mm total length) under controlled conditions. Visual estimates by two divers differed significantly from true fish length (P < 0.001) but were not significantly different from each other (P = 0.42). Levels of accuracy and precision were similar to those previously reported for visual estimates by divers. On average, the two divers underestimated fish length by 2.74 mm (11%) and 2.93 mm (12%). The magnitude of underestimation error increased with fish length. Photogrammetric measurements from a stereo-video camera system were more accurate and precise than diver estimates of fish length. Little to no bias was evident (mean error = 0.05 mm), and the level of precision (coefficient of variation of the difference between observed length and true length) was 4.5% for the photogrammetric measurements compared with 10% and 11% for the two divers’ estimates. In comparison with underwater visual surveys, surveys that use a stereo-video camera system may increase the consistency of long-term data sets and improve resolution to detect important length differences in small-bodied fishes. Managers must remain careful to avoid or correct sampling biases, which can affect underwater visual surveys and stereo-video surveys alike.

Received August 5, 2010; accepted December 6, 2010
Maximum Output of Peak Power for Two Backpack Electrofishers Operated at Various Pulsed Direct Current Duty Cycles and Water Conductivity Levels
Authors: Dean Jan C. , Temple Alan J.
Published: December 2011

The objectives of this research were to (1) determine the maximum output of peak power for two backpack electrofishers (Smith-Root Model LR-24; ETS Electrofishing Model ABP-3) at various pulsed DC (PDC) duty cycles and over a wide range of resistance levels and (2) use those results to develop a generalized model for predicting the maximum output of peak power available from backpack electrofishers for various water conductivity levels and duty cycles. The electrofishers were operated to maximum capacity under controlled conditions for water conductivities of 19, 155, and 610 μS/cm and for PDC duty cycles of 15, 25, and 50%. The results agreed closely with those expected based upon the manufacturer ratings for these backpack electrofishers and provided a graphical and analytical methodology for predicting backpack electrofisher capabilities over a range of water conductivity levels when operated at duty cycles recommended for electrofishing. Both electrofishers produced square wave PDC at low water conductivities. At higher water conductivities, the waveforms for both electrofishing units deviated from square pulses as they approached shutoff loading, but the response varied between electrofishers.

Received April 12, 2010; accepted February 9, 2011
Landscape Models of Brook Trout Abundance and Distribution in Lotic Habitat with Field Validation
Authors: McKenna James E. , Johnson James H.
Published: December 2011

Brook trout Salvelinus fontinalis are native fish in decline owing to environmental changes. Predictions of their potential distribution and a better understanding of their relationship to habitat conditions would enhance the management and conservation of this valuable species. We used over 7,800 brook trout observations throughout New York State and georeferenced, multiscale landscape condition data to develop four regionally specific artificial neural network models to predict brook trout abundance in rivers and streams. Land cover data provided a general signature of human activity, but other habitat variables were resistant to anthropogenic changes (i.e., changing on a geological time scale). The resulting models predict the potential for any stream to support brook trout. The models were validated by holding 20% of the data out as a test set and by comparison with additional field collections from a variety of habitat types. The models performed well, explaining more than 90% of data variability. Errors were often associated with small spatial displacements of predicted values. When compared with the additional field collections (39 sites), 92% of the predictions were off by only a single class from the field‐observed abundances. Among “least‐disturbed” field collection sites, all predictions were correct or off by a single abundance class, except for one where brown trout Salmo trutta were present. Other degrading factors were evident at most sites where brook trout were absent or less abundant than predicted. The most important habitat variables included landscape slope, stream and drainage network sizes, water temperature, and extent of forest cover. Predicted brook trout abundances were applied to all New York streams, providing a synoptic map of the distribution of brook trout habitat potential. These fish models set benchmarks of best potential for streams to support brook trout under broad‐scale human influences and can assist with planning and identification of protection or rehabilitation sites.

Received August 24, 2010; accepted March 1, 2011
Validation of Morphological Characteristics Used for Field Identification of Bull Trout × Brook Trout Hybrids
Authors: Popowich Ryan C. , Venturelli Paul A. , Stelfox Jim D. , Taylor Eric B.
Published: December 2011

Bull trout Salvelinus confluentus are of conservation concern throughout much of their range, in part because of displacement by and hybridization with nonnative brook trout S. fontinalis. Hybridization between these species can complicate efforts to control brook trout because hybrids are often difficult to distinguish from parental species. Here, we assess the reliability of five morphological characteristics that were used to identify bull trout × brook trout hybrids among 106 fish collected from Quirk Creek, Alberta. Genetic analysis of up to three microsatellite loci suggested that hybrids were correctly identified 95% of the time and that no bull trout were mistaken for hybrids. Visual inspection of photographs of hybrids suggested that dorsal fin markings were the most reliable morphological characteristic for identifying hybrids. Based on these results, we recommend that field identification of bull trout × brook trout hybrids be based solely on dorsal fin markings.

Received November 20, 2010; accepted March 21, 2011
Evaluating Two Observational Sampling Techniques for Determining the Distribution and Detection Probability of Age-0 Smallmouth Bass in Clear, Warmwater Streams
Authors: Brewer Shannon K. , Ellersieck Mark R.
Published: December 2011

Accurate determination of the distribution and abundance of age-0 sport fish, such as smallmouth bass Micropterus dolomieu, is an important aspect of successful species management (e.g., characterizing nursery habitats for protection or enhancement; identifying reproductive dynamics and influences of environmental variables). Two observational techniques—snorkeling and above-water (AW) observation—were evaluated in several Missouri Ozark streams to determine (1) accuracy of identifying age-0 smallmouth bass with each technique, (2) detection probabilities under a variety of channel unit (CU) conditions (i.e., discrete morphological features such as riffles or pools) and the relations between detection probability and hydraulic variables, and (3) behavioral responses (fright response, return response, or no response) of fish to the observers using each technique. Identification of age-0 smallmouth bass was over 90% accurate when using AW observation in shallow water and when snorkeling in deep water. In both streams, detection probabilities differed depending on the CU sampled and the method used. In deep pools, detection probabilities when snorkeling were two to three times those obtained from AW observation; however, AW observation was more efficient for sampling most shallow-water (<0.5-m) CUs. Velocity had no significant relation to detection probability, whereas depth was significantly related to detection probability for both sampling methods (the relationship was positive for snorkeling and negative for AW observation). The percentage of age-0 smallmouth bass that exhibited a fright response was greatest for fish observed by snorkeling in shallow-water CUs. On average, approximately 20% of fish showed a fright response, but a large proportion of these fish exhibited a return response. Our results indicate that multiple sampling methods may be necessary to achieve high accuracy when sampling small fish in a variety of CUs, and snorkeling and AW observation may be viable methods for selecting CUs in many warmwater streams. Additional work is recommended to address knowledge gaps, especially those related to the influence of biotic and abiotic variables that were not measured in this study.

Received November 9, 2010; accepted May 12, 2011
Estimating the Hatchery Fraction of a Natural Population: A Bayesian Approach
Authors: Barber Jarrett J. , Gerow Kenneth G. , Connolly Patrick J. , Singh Sarabdeep
Published: December 2011

There is strong and growing interest in estimating the proportion of hatchery fish that are in a natural population (the hatchery fraction). In a sample of fish from the relevant population, some are observed to be marked, indicating their origin as hatchery fish. The observed proportion of marked fish is usually less than the actual hatchery fraction, since the observed proportion is determined by the proportion originally marked, differential survival (usually lower) of marked fish relative to unmarked hatchery fish, and rates of mark retention and detection. Bayesian methods can work well in a setting such as this, in which empirical data are limited but for which there may be considerable expert judgment regarding these values. We explored a Bayesian estimation of the hatchery fraction using Monte Carlo–Markov chain methods. Based on our findings, we created an interactive Excel tool to implement the algorithm, which we have made available for free.

Received March 30, 2011; accepted June 21, 2011
Largemouth Bass Nest Site Selection in Small, North Temperate Lakes Varying in Littoral Coarse Woody Habitat Abundances
Authors: Weis Jerome J. , Sass Greg G.
Published: December 2011

Coarse woody habitat (CWH) in the littoral zone is an important habitat feature in freshwater systems and has been suggested to influence nest density and nest site selection by black basses Micropterus spp. (e.g., largemouth bass M. salmoides and smallmouth bass M. dolomieu). To test for a relationship between nest site selection or nest density and the abundance of littoral CWH, we monitored largemouth bass nest site selection in the littoral zones of two small, northern Wisconsin lakes (comprising a total of three separated basins) for three consecutive spawning seasons. Our study sites varied in natural and manipulated abundances of CWH; spawning seasons before and after a whole-basin CWH reduction or a whole-basin CWH addition were examined. Within-basin analysis provided some evidence that local variation in CWH abundance influenced local nest density; however, this relationship was only significant for one basin in a single season. Among basins and across seasons, we observed a positive but nonsignificant effect of littoral CWH density on nest density and inconsistent responses to the CWH manipulations. Although littoral CWH is an important habitat feature influencing fish populations, communities, and life histories, our results suggest that CWH did not directly limit largemouth bass nest densities and was not a strong driver of nest site selection in these lakes. Nevertheless, policies allowing human-mediated removals of CWH from freshwater systems may still be detrimental to fish communities and other taxa that are dependent upon CWH.

Received March 31, 2011; accepted July 13, 2011
Population Dynamics of Lake Ontario Lake Trout during 1985–2007
Authors: Brenden Travis O. , Bence James R. , Lantry Brian F. , Lantry Jana R. , Schaner Ted
Published: December 2011

Lake trout Salvelinus namaycush were extirpated from Lake Ontario circa 1950 owing to commercial and recreational fishing, predation by sea lampreys Petromyzon marinus, and habitat degradation. Since the 1970s, substantial efforts have been devoted to reestablishing a self-sustaining population through stocking, sea lamprey control, and harvest reduction. Although a stocking-supported population has been established, only limited natural reproduction has been detected. Since the 1990s, surveys have indicated a continuing decline in overall abundance despite fairly static stocking levels. We constructed a statistical catch-at-age model to describe the dynamics of Lake Ontario lake trout from 1985 to 2007 and explore what factor(s) could be causing the declines in abundance. Model estimates indicated that abundance had declined by approximately 76% since 1985. The factor that appeared most responsible for this was an increase in age-1 natural mortality rates from approximately 0.9 to 2.5 between 1985 and 2002. The largest source of mortality for age-2 and older fish was sea lamprey predation, followed by natural and recreational fishing mortality. Exploitation was low, harvest levels being uncertain and categorized by length rather than age. Accurate predictions of fishery harvest and survey catch per unit effort were obtained despite low harvest levels by using atypical data (e.g., numbers stocked as an absolute measure of recruitment) and a flexible modeling approach. Flexible approaches such as this might allow similar assessments for a wide range of lightly exploited stocks. The mechanisms responsible for declining age-1 lake trout survival are unknown, but the declines were coincident with an increase in the proportion of stocked fish that were of the Seneca strain and a decrease in the overall stocking rate. It is possible that earlier studies suggesting that Seneca strain lake trout would be successful in Lake Ontario are no longer applicable given the large ecosystem changes that have occurred subsequent to invasion by dreissenid mussels.

Received January 19, 2011; accepted July 6, 2011
Using Lindgren–Pitman Hook Timers to Understand the Dynamics of Trotline Catches in a Large River
Authors: Steffensen Kirk D. , Eder Brandon L. , Pegg Mark A.
Published: December 2011

Trotlines have historically been used by commercial fishers to target ictalurids and have recently been shown to be effective for collecting sturgeons Scaphirhynchus spp. However, little is known about the gear–fish interaction after trotlines are deployed. Therefore, the objectives of this study were to determine whether trotlines equipped with Lindgren-Pitman (LP) hook timers could withstand harsh riverine conditions and whether catch rates, retention rates of hooked fish, capture times of targeted species, and bycatch would be affected. Our results showed no difference between standardized trotlines and trotlines with hook timers and indicated that 31% of pulled hook timers resulted in no fish being collected. Hook timers were activated by 69% of all the fish collected. The majority of fish collected were shovelnose sturgeon S. platorynchus (77%), of which 70% activated the timer. The fork length of the shovelnose sturgeon that did activate the timer (571.0 ± 60.1 mm [mean ± SE]) did not differ from that of fish that did not (542.4 mm). Overall, 43% of the hook timers were activated within the first 2 h of deployment and an additional 19% in the next 2-h period; 54% of the fish were collected prior to sunset. Our study shows that hook timers can be a valuable tool that will aid in the interpretation of trotline catches.

Received March 16, 2011; accepted June 14, 2011
Estimating Habitat-Specific Abundances of PIT-Tagged Juvenile Salmonids Using Mobile Antennas: A Comparison with Standard Electrofishing Techniques in a Small Stream
Authors: Sloat Matthew R. , Baker Peter F. , Ligon Franklin K.
Published: December 2011

The use of passive integrated transponder (PIT) tags in ecological studies is increasingly common, but evaluations of their performance and range of application in the field are still emerging. Here, we compare habitat unit–scale abundance estimates of PIT-tagged juvenile coho salmon Oncorhynchus kisutch and steelhead O. mykiss derived from multiple-pass surveys with a submersible pole-mounted PIT antenna and backpack electrofishing in a small coastal California stream. We found high concordance of methods for coho salmon and age-0 steelhead and moderate concordance for age-1 and older steelhead. Regression analysis of PIT antenna estimates on electrofishing estimates indicated an approximately one-to-one relationship between methods. Regression intercepts for coho salmon and age-0 steelhead were significantly greater than zero, but the differences were small (with an effect equivalent to less than one fish). We found no evidence that pool area, cover area, or cover complexity influenced the relationship between methods for coho salmon and age-0 steelhead, but some evidence that electrofishing may be more effective than PIT antennas for estimating the abundance of age-1 and older steelhead in pools with high cover complexity. Our results demonstrate that surveys using submersible PIT antennas can provide habitat unit–scale estimates of juvenile salmonid abundance similar to those derived from electrofishing in small streams. An advantage of using PIT antennas is that they allow fish abundance estimation without fish recapture and frequent sampling can occur without subjecting study animals to excessive handling stress or mortality. This is a particularly important consideration in studies of small populations, sensitive species, or fish listed under the U.S. Endangered Species Act.

Received July 30, 2010; accepted June 10, 2011
Applying Structured Decision Making to Recreational Fisheries Management
Authors: Irwin Brian J , Wilberg Michael J , Jones Michael L , Bence James R
Published: December 2011

Multiple objectives associated with recreational fishing, combined with multiple uncertainties, pose real challenges for management. We suggest that applying formal decision-making frameworks to partnership-based policy evaluations can prove beneficial to recreational fisheries management. We describe how a sequence of workshops can be used to engage scientists, managers, and other stakeholders and execute the steps of a structured decision-making process that centers on collaborative development of a quantitative forecasting model. This approach should aim to specify objectives and corresponding performance measures, identify critical uncertainties, and aid decision makers in making more informed choices among possible management options. An inclusive, participatory process can increase the transparency by which management decisions are made, provide an opportunity for tradeoffs to be discussed in a tangible way, and promote consensus building. Constructing and documenting a well-specified representation of the management process should also help reduce contention surrounding complex management decisions and promote proactive management.

Resumen

Toma Estructurada de Decisiones en el manejo de la pesca recreativa

Diversos objetivos relacionados con la pesca recreativa, combinados con múltiples incertidumbres, representan desafíos reales para el manejo. Se sugiere que al aplicar el enfoque de “toma formal de decisiones” a las evaluaciones de las políticas de participación, el manejo de la pesca recreativa puede beneficiarse. Se describe cómo una secuencia de talleres puede utilizarse tanto para concertar científicos, manejadores y otros participantes, así como también para llevar a cabo las etapas de un proceso estructurado de toma de decisiones, centrado en el desarrollo colaborativo de un modelo cuantitativo de predicción. Este enfoque debiera perseguir la postulación de objetivos precisos, el desarrollo de las correspondientes medidas de desempeño, identificación de las incertidumbres y asistencia a los administradores a tomar decisiones mejor informadas de entre diversas opciones de manejo. Un proceso incluyente y participativo puede incrementar la transparencia en las medidas de manejo, ofrece una oportunidad para que el espacio de negociación pueda discutirse de manera tangible y promueve el consenso. Crear y documentar una representación específica del proceso de manejo, también debiera ayudar a reducir los conflictos que rodean a las decisiones complejas de manejo y a promover un manejo proactivo.
Evolution of Catch Share Management: Lessons from Catch Share Management in the North Pacific
Authors: Fina Mark
Published: December 2011

Fishery managers, economists, industry advocates, and some environmental public interest groups are currently promoting catch shares (or the allocation of exclusive portions of the total allowable catch) as a means to address both environmental and economic fishery management problems. At the same time, a vocal opposition to catch share management has developed among some industry stakeholders, academics, and other public interest groups. Over the course of the last 20 years, while the debate has percolated, the North Pacific Fishery Management Council (known henceforth as the Council) has incrementally developed and overseen the implementation of five major catch share management programs for the fisheries it governs. This article draws on the experiences in the North Pacific fisheries to shed light on several facets of the debate over the efficacy of catch share management and suggests that catch share management is most effective and beneficial to stakeholders, when used in a measured manner, as part of a management program adapted specifically to a fishery and its stakeholders.
Red Snapper in the Gulf of Mexico and U.S. South Atlantic: Data, Doubt, and Debate
Authors: Cowan James H
Published: December 2011

Stock assessments provide fisheries managers with information that is used in the regulation of a fish stock. Assessments often rely upon a wide array of biological and fisheries data of varying quantity and quality, making the assessment process data hungry, complex, and uncertain. Assessment scientists face the difficulty of estimating numbers of individuals (among other biological benchmarks) of a population of widely distributed, often mobile, fishes for which direct measurement of almost everything is impossible. Consequently, stock assessment scientists are forced to use tools designed to assemble a variety of indirect measures into a statistical model capable of producing predictions to inform fisheries management about stock status and the consequences of past, current and future fishing practices. Despite large differences in estimates of the status of red snapper stocks in the Gulf of Mexico (U.S.) and south Atlantic Ocean (U.S.), and the management conclusions and decision drawn from these assessments, there are more similarities than differences in the basic data being used to inform assessment models, as well as in model outcomes concerning trends in biomass, catch-at-age and stock productivity. There are key differences in some of these data, and in how historical landings and uncertainty is handled in the assessment process, that result in large differences between the two management regions in beliefs about current and future productivity of red snapper stocks, and regulatory measures necessary for reaching management goals.
Eleven Ways to Improve Executive Management of Conflict
Authors: Fraidenburg Michael E
Published: December 2011

Conflict comes with the job of managing the public's natural resources. When I ask, fish and wildlife executives tell me they want employees with excellent conflict management skills. When I next ash what they are doing to prepare their employees to become skilled conflict managers, I regularly get a blank stare. Professionals are usually on their own to acquire these skills, largely through unguided, trial-and-error learning. Eleven actions leaders can take to improve conflict management in their organizations fall into four categories: Conflict prevention through training, adding a “conflict resolution” dimension to employee performance evaluations, maintaining an early warning system to detect emerging conflict, and creating robust stakeholder involvement processes.Contingency planning through systematically assessing vulnerabilities, conducting “What if…” strategy analyses, and maintaining a rapid response capacity for when a conflict emerges.Crisis management through ensuring that the organization can effectively analyze a conflict situation and can efficiently stabilize a bad situation so relationships can be rebuilt.Encouraging completed staff work by using a planning tool that teaches employees to bring a finished situation analysis and remedial plan forward at the same time they bring a conflict to the executive's attention.
Comparative Susceptibility of Deschutes River, Oregon, Tubifex tubifex Populations to Myxobolus cerebralis
Authors: Zielinski Christopher M. , Lorz Harriet V. , Hallett Sascha L. , Xue Lan , Bartholomew Jerri L.
Published: December 2011

Dams along the Deschutes River (DR) in central Oregon have blocked fish migration for over 40 years. Reestablishment of anadromous fish runs above the dams as part of a fish passage plan may introduce fish pathogens, such as Myxobolus cerebralis, the myxozoan parasite that causes salmonid whirling disease. This parasite is carried by adult salmon that stray into the DR system during their return to enzootic areas of the upper Columbia River basin, and it is now known to be established in at least one lower DR tributary. The life cycle of M. cerebralis involves two obligate hosts: a salmonid and the oligochaete worm Tubifex tubifex. To determine the likelihood of parasite establishment above the DR dams, we conducted benthic sediment surveys between 1999 and 2007 and found that T. tubifex had a patchy distribution and low relative abundance. Mitochondrial 16S ribosomal DNA gene analysis indicated that two lineages of T. tubifex (III and VI) were present both above and below the dams. Laboratory susceptibility studies to characterize differences in infection prevalence and parasite production between nine T. tubifex populations revealed that production varied considerably among exposed groups and was proportional to the number of lineage III worms present. Our results suggest that M. cerebralis could become established above the dams if infected fish are allowed passage into the upper DR system, but not all areas of the DR basin can be classified as having the same likelihood for parasite establishment, and the potential impact will be location dependent.

Received July 2, 2010; accepted October 24, 2010
An Evaluation of the Influence of Stock Origin and Out-migration History on the Disease Susceptibility and Survival of Juvenile Chinook Salmon
Authors: Dietrich Joseph P. , Boylen Deborah A. , Thompson Donald E. , Loboschefsky Erik J. , Bravo Claudia F. , Spangenberg Dina K. , Ylitalo Gina M. , Collier Tracy K. , Fryer Derek S. , Arkoosh Mary R. , Loge Frank J.
Published: December 2011

Various methods have been developed to mitigate the adverse effects of the Federal Columbia River Power System on juvenile Pacific salmon out-migrating through the Columbia River basin. In this study, we found that hatchery-reared spring Chinook salmon Oncorhynchus tshawytscha in the river are in varying degrees of health, which may affect delayed mortality and the assessment of the effectiveness of management actions to recover listed stocks (e.g., barging fish downstream versus leaving fish in the river). A laboratory disease challenge with Listonella anguillarum was completed on fish from Rapid River Hatchery and Dworshak National Fish Hatchery (NFH) with different out-migration histories: (1) transported by barge, (2) removed from the river before barging, or (3) left to travel in-river. Barged fish from Rapid River Hatchery experienced less mortality than fish from Dworshak NFH. No statistical differences were found between the hatcheries with fish that had in-river out-migration histories. We suggest that the stressors and low survival associated with out-migration through the hydropower system eliminated any differences that could have been present. However, 18–25% of the fish that were barged or collected before barging died in the laboratory before the disease challenge, compared with less than 2% of those that traveled in-river. Owing to disproportionate prechallenge mortality, the disease-challenged populations may have been biased; thus, they were also considered together with the prechallenge mortalities. The synthesis of prechallenge and disease-challenged mortalities and health characteristics evaluated during out-migration indicated that the benefit of barging was not consistent between the hatcheries. This finding agrees with adult survival and delayed mortality estimates for the individual hatcheries determined from adult returns. The results suggest that the health status of fish and their history before entering the hydropower system (hatchery of origin and out-migration path) are critical variables affecting the conclusions drawn from studies that evaluate mitigation strategies.

Received November 18, 2009; accepted January 6, 2011
Uptake of Metronidazole in Artemia at Different Developmental Life Stages
Authors: Rodriguez Loretta , Livengood Elisa J. , Miles Richard D. , Chapman Frank A.
Published: December 2011

The purpose of this study was to examine the capacity of live brine shrimp Artemia spp. to accumulate metronidazole at different developmental life stages. Metronidazole is used in fish as an antiparasitic medication. An effective drug delivery method is to enrich the Artemia with metronidazole and offer them as live feed to the infected fish, usually ornamental species and other small fishes. Artemia cysts were hatched and then soaked in a metronidazole solution (0.05%) at instars 1–3 of larval development. Our findings indicated that Artemia were able to accumulate metronidazole at levels considered therapeutic to other animals and humans (25–100 mg/kg). However, the levels varied depending on the stage of larval development. Artemia accumulated the highest levels of metronidazole (137–143 mg/kg) when they started filter feeding (instar 2), whereas newly hatched Artemia (instar 1) contained the lowest level (85 mg/kg). Based on this study and a review of the literature, a new protocol recommended for enriching Artemia with metronidazole consists of soaking the Artemia in a 0.05% metronidazole solution for 3 h at room temperature. Because metronidazole is relatively insoluble in water, it must first be dissolved in warm water with continuous stirring.

Received December 5, 2010; accepted January 30, 2011
A Real-Time Polymerase Chain Reaction Assay for Quantification of Edwardsiella ictaluri in Catfish Pond Water and Genetic Homogeneity of Diagnostic Case Isolates from Mississippi
Authors: Griffin Matt J. , Mauel Michael J. , Greenway Terrence E. , Khoo Lester H. , Wise David J.
Published: December 2011

A quantitative polymerase chain reaction (qPCR) assay was developed for the detection and quantification of Edwardsiella ictaluri in channel catfish Ictalurus punctatus pond water using modifications to a published E. ictaluri–specific qPCR assay and previously established protocols for the molecular detection of myxozoan parasites in catfish ponds. Genomic DNA equivalents indicative of the number of bacteria in a sample were determined and standard curves correlating to bacterial numbers were established. The assay was found to be highly repeatable and reproducible, with a linear dynamic range of five orders of magnitude. There was no interference of the assay from the presence of large quantities of nontarget DNA. Known quantities of bacteria were added to sample volumes of 40 or 500 mL of pond water collected from several different ponds. The minimum level of detection was approximately 100 cell equivalents (CE) in 40 (2.5 CE/mL) or 500 mL of pond water (0.2 CE/mL). Sample volumes of 40 mL yielded the most consistent results, which were not significantly different from those obtained from broth culture alone. Cell equivalents determined by qPCR in 40-mL pond water samples spiked with known quantities of bacteria were within one order of magnitude of the actual number of cells added. Repetitive element-based polymerase chain reaction analysis of archived isolates demonstrated the genetic homogeneity of E. ictaluri, and consistent amplification of these isolates by qPCR analysis demonstrated the stability of the PCR target. The assay described here provides a reliable method for the detection and quantification of E. ictaluri in pond water and will be an invaluable tool in epidemiological studies. Additionally, the assay provides a way to evaluate the effects that vaccination, antibiotic treatments, and restricted feeding practices have on E. ictaluri populations during an outbreak. Information obtained with these tools will aid in optimizing disease management practices designed to maximize productivity while minimizing losses.

Received October 20, 2010; accepted June 13, 2011
Epidermal growth factor induction of front–rear polarity and migration in keratinocytes is mediated by integrin-linked kinase and ELMO2
Authors: Ho Ernest , Dagnino Lina
Published: December 2011

Epidermal growth factor (EGF) is a potent chemotactic and mitogenic factor for epidermal keratinocytes, and these properties are central for normal epidermal regeneration after injury. The involvement of mitogen-activated protein kinases as mediators of the proliferative effects of EGF is well established. However, the molecular mechanisms that mediate motogenic responses to this growth factor are not clearly understood. An obligatory step for forward cell migration is the development of front–rear polarity and formation of lamellipodia at the leading edge. We show that stimulation of epidermal keratinocytes with EGF, but not with other growth factors, induces development of front–rear polarity and directional migration through a pathway that requires integrin-linked kinase (ILK), Engulfment and Cell Motility-2 (ELMO2), integrin β1, and Rac1. Furthermore, EGF induction of front–rear polarity and chemotaxis require the tyrosine kinase activity of the EGF receptor and are mediated by complexes containing active RhoG, ELMO2, and ILK. Our findings reveal a novel link between EGF receptor stimulation, ILK-containing complexes, and activation of small Rho GTPases necessary for acquisition of front–rear polarity and forward movement.
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
Authors: Xi Yuanxin , Bock Christoph , Müller Fabian , Sun Deqiang , Meissner Alexander , Li Wei
Published: December 2011

Summary: Reduced representation bisulfite sequencing (RRBS) is a powerful yet cost-efficient method for studying DNA methylation on a genomic scale. RRBS involves restriction-enzyme digestion, bisulfite conversion and size selection, resulting in DNA sequencing data that require special bioinformatic handling. Here, we describe RRBSMAP, a short-read alignment tool that is designed for handling RRBS data in a user-friendly and scalable way. RRBSMAP uses wildcard alignment, and avoids the need for any preprocessing or post-processing steps. We benchmarked RRBSMAP against a well-validated MAQ-based pipeline for RRBS read alignment and observed similar accuracy but much improved runtime performance, easier handling and better scaling to large sample sets. In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS.

Availability:  http://rrbsmap.computational-epigenetics.org/  http://code.google.com/p/bsmap/

Contact:  wl1@bcm.tmc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.