bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electronic tags and genetics explore variation in migrating steelhead kelts (Oncorhynchus mykiss), Ninilchik River, Alaska
Authors: Nielsen Jennifer L. , Turner Sara M. , Zimmerman Christian E. 
Published: February 2011

Acoustic and archival tags examined freshwater and marine migrations of postspawn steelhead kelts ( Oncorhynchus mykiss ) in the Ninilchik River, Alaska, USA. Postspawn steelhead were captured at a weir in 2002–2005. Scale analysis indicated multiple migratory life histories and spawning behaviors. Acoustic tags were implanted in 99 kelts (2002–2003), and an array of acoustic receivers calculated the average speed of outmigration, timing of saltwater entry, and duration of residency in the vicinity of the river mouth. Ocean migration data were recovered from two archival tags implanted in kelts in 2004 (one male and one female). Archival tags documented seasonal differences in maximum depth and behavior with both fish spending 97% of time at sea <6 m depth (day and night). All study fish were double tagged with passive integrated transponder (PIT) tags implanted in the body cavity. Less than 4% of PIT tags were retained in postspawn steelhead. Molecular genetics demonstrated no significant differences in genetic population structure across years or among spawning life history types, suggesting a genetically panmictic population with highly diverse life history characteristics in the Ninilchik River.
Estimating larval production of a broadcast spawner: the influence of density, aggregation, and the fertilization Allee effect
Authors: Lundquist Carolyn J. , Botsford Louis W. 
Published: February 2011

The effect of fishing on reproduction is typically quantified by computing the effects of changes in the species abundance and age structure on egg production. For broadcast spawners, reproduction also depends on the local spatial distribution of individuals. Broadcast spawners exhibit an Allee effect at low density: a decline in the fertilization of eggs, owing to increased distance between spawners. We present a method for assessing the likely impact of a fishery on broadcast spawners, based on gamete dispersion dynamics and individual spatial distributions. We use an individual-based model to simulate larval production over a range of uncertainties in dispersion characteristics. We illustrate our method for the red sea urchin, Strongylocentrotus franciscanus , fishery in northern California, USA. The density of red sea urchins varied over space (0.1–1.6·m–2), and indices of aggregation were highest at low densities. As gamete dispersion distances increased, larval production exhibited a more linear relationship with density. Average larval production in 1996–1998 was 33.8% of production near the inception of the fishery. After accounting for decreases in mean density, the fertilization Allee effect accounted for 21.7 ± 4.1% of the decrease in larval production, and 45.2 ± 21.7% if sea urchins were not aggregated.
Minimum viable population size for lake sturgeon (Acipenser fulvescens) using an individual-based model of demographics and genetics
Authors: Schueller Amy M. , Hayes Daniel B. 
Published: February 2011

Population viability analysis is a useful tool to explore the relationship between extinction risk and population size, but often does not include genetic factors. Our objectives were to determine minimum viable population size (MVP) for lake sturgeon ( Acipenser fulvescens ) and examine how inbreeding depression may affect MVP. Our individual-based model incorporated inbreeding depression in two ways: individuals with inbreeding coefficients above a threshold experienced inbreeding depression (threshold), and individuals experienced inbreeding depression at a rate related to their inbreeding coefficient (gradual). Three mechanisms relating inbreeding to fitness were explored (young-of-the-year (YOY) viability, post-YOY viability, number of progeny). The criterion we used to determine MVP was a 5% chance of extinction over 250 years. The estimated MVP without inbreeding effects was 80 individuals. For some scenarios incorporating inbreeding, MVP did not change, but for others, MVP was substantially higher, reaching values up to 1800. Results demonstrate that extinction risk and MVP can be influenced by both demographic stochasticity and inbreeding depression. This research should inform management by determining MVP and how inbreeding, which is expected to accrue in remnant populations because of generations of low abundance, may affect MVP.
Isolation or metapopulation: whence and whither the Smith Sound cod?
Authors: Rose George A. , Nelson R. John , Mello Luiz G.S. 
Published: February 2011

In April 1995, a spawning aggregation of “northern” Atlantic cod ( Gadus morhua ) (10 000 t) appeared in Smith Sound, Newfoundland, growing to 26 000 t by year 2000. The origin of the founder year classes (primarily the 1990 and 1992 year classes) and potential for expansion remains controversial, with genetic isolation used to justify reopenings of coastal fisheries. We investigated the origin using historical, demographic, and genetic data. History provided no evidence of large aggregations before 1995. Demographics in the early 1990s suggested few spawners in Smith Sound, but many in the adjacent Bonavista Corridor. The strong 1990 year class was not evident until 1995 and the strong 1992 year class until 1997 (both age 5 and first maturity). Genetic study of six microsatellite loci from 791 cod from overwintering aggregations in Smith Sound and offshore regions indicated little to no differentiation (FST) among southern groups (Smith Sound, Bonavista Corridor, Halibut Channel). These results provide a perspective that these groups comprise a metapopulation and that the Smith Sound aggregation arose not from self-recruitment but immigration. By 2009, the aggregation had dispersed, with large concurrent increases in the Bonavista Corridor.
Sea lice (Lepeophtheirus salmonis) infestations and the productivity of pink salmon (Oncorhynchus gorbuscha) in the Broughton Archipelago, British Columbia, Canada
Authors: Krkošek Martin , Hilborn Ray 
Published: February 2011

The spread of salmon lice ( Lepeophtheirus salmonis ) from salmon farms may threaten some wild salmon populations. Infestations of wild juvenile pink salmon ( Oncorhynchus gorbuscha ) have been associated with high mortality and population decline. Using stock–recruit data for pink salmon from the central coast of British Columbia, we analyzed how fishing mortality and spatial covariation combine with louse infestation to affect pink salmon population dynamics. The results indicate substantial coherence in survival at nested spatial scales — large-scale regional covariation and smaller scale covariation within management areas. Populations exposed to salmon farms (those from the Broughton Archipelago) show a sharp decline in productivity during sea lice infestations relative to pre-infestation years. Unexposed populations (comprising four management areas) did not experience a change in productivity during infestation years and had similar productivity to exposed populations before infestations. Our results suggest that sea lice infestations may result in declines of pink salmon populations and that management and policy of salmon farms should consider protecting wild juvenile salmon from exposure to sea lice.
Rapid growth in the early marine period improves the marine survival of Chinook salmon (Oncorhynchus tshawytscha) in Puget Sound, Washington
Authors: Duffy Elisabeth J , Beauchamp David A 
Published: February 2011

We examined the effect of early marine entry timing and body size on the marine (smolt-to-adult) survival of Puget Sound Chinook salmon ( Oncorhynchus tshawytscha ). We used data from coded wire tag release groups of hatchery Chinook salmon to test whether hatchery release date, release size, and size in offshore waters in July and September influenced marine survival. Marine survival was most strongly related to the average body size in July, with larger sizes associated with higher survivals. This relationship was consistent over multiple years (1997–2002), suggesting that mortality after July is strongly size-dependent. Release size and date only slightly improved this relationship, whereas size in September showed little relationship to marine survival. Specifically, fish that experienced the highest marine survivals were released before 25 May and were larger than 17 g (or 120 mm fork length) by July. Our findings highlight the importance of local conditions in Puget Sound (Washington, USA) during the spring and summer, and suggest that declines in marine survival since the 1980s may have been caused by reductions in the quality of feeding and growing conditions during early marine life.
Population differences in otolith chemistry have a genetic basis in Menidia menidia
Authors: Clarke Lora M. , Thorrold Simon R. , Conover David O. 
Published: February 2011

The number of studies using otolith chemistry as a tool to reconstruct the environmental history of fishes and to detect population structure continues to rise, despite the fact that factors influencing otolith deposition are not fully understood. Many studies have examined the influence of environmental parameters on otolith composition, but none to date have tested the possible influence of intrinsic factors. Using lab broodstock populations, we examined the influence of genetics and temperature on Mg:Ca, Mn:Ca, Sr:Ca, and Ba:Ca concentrations and partition coefficients in the otoliths of juvenile Atlantic silversides, Menidia menidia . Fish from two populations, South Carolina, USA, and Nova Scotia, Canada, were reared in 15, 21, and 27 °C. We found significant (p < 0.05) differences in otolith Mg:Ca, Mn:Ca, and Ba:Ca ratios as well as in Mg, Mn, and Ba partition coefficients among populations. Such genetic influences on otolith elemental concentrations have important implications for understanding the physiological mechanisms underlying otolith deposition and enhance the utility of otolith chemistry as a marker of fish population structure in the wild.
Greenland halibut (Reinhardtius hippoglossoides) spawn annually but successive cohorts of oocytes develop over 2 years, complicating correct assessment of maturity
Authors: Kennedy James , Gundersen Agnes C. , Høines Åge S. , Kjesbu Olav S. 
Published: February 2011

Ovary development in Greenland halibut ( Reinhardtius hippoglossoides ) is complex, with several cohorts of developing oocytes present during vitellogenesis; this is unusual for a determinate spawner. There are also speculations that Greenland halibut are not capable of spawning every year. To investigate this possibility, ovaries from Greenland halibut caught throughout the year were examined histologically, and successive cohorts of oocytes were tracked through development. Results showed that the initial maturation of the ovaries from immature to spawning takes more than 1 year. The ovary initially develops as far as early vitellogenesis; however, the time scale for this is unclear. During the final year of development, the cohort of vitellogenic oocytes splits to form two cohorts; the larger cohort increases in size and is spawned in the coming spawning season. The smaller cohort also continues to develop, but at a much lower rate, in preparation for development for spawning in the following year. Within each month, there is a large range of oocyte sizes between fish; this leads to the extended spawning season that is known in many populations of this species. This complicates the assessment of maturity, and a more accurate microscopic maturity scale is proposed.
Evaluating otolith Sr/Ca as a tool for reconstructing estuarine habitat use
Authors: Phillis Corey C. , Ostrach David J. , Ingram B. Lynn , Weber Peter K. 
Published: February 2011

There is no standard method to determine the applicability of otolith Sr/Ca ratio to reconstructing estuary use. We have developed a novel method to determine the response of otolith Sr/Ca to changes in water Sr/Ca and salinity in San Francisco Estuary (California, USA). We perform correlated, spatially resolved Sr/Ca and Sr isotope measurements using otoliths from adult striped bass ( Morone saxatilis ) in the San Francisco Estuary to estimate the otolith–water Sr/Ca partition coefficient (DSr = 0.305 ± 0.009). DSr did not vary significantly with salinity, and therefore the salinity–otolith Sr/Ca model was constructed by substituting the partition coefficient into the nonlinear salinity–water Sr/Ca mixing model for the system. The model demonstrates that the primary factor controlling the response of Sr/Ca to salinity is the Ca concentration in the freshwater source flowing into the estuary. A concentration of 60 ppm Ca is an approximate threshold below which estuary Sr/Ca increases rapidly to near the marine Sr/Ca at low salinities (5‰–15‰), thereby providing sharp delineation of estuary entrance, but little to no discrimination among higher salinity habitats. Our approach provides a general framework for assessing the potential utility of Sr/Ca in estuarine systems and specifically for the San Francisco Estuary.
Analysis of anchor foundation with root caissons loaded in nonhomogeneous soils
Authors: Huang Maosong , Zhang Chenrong , Mu Linlong , Gong Weiming 
Published: February 2011

This paper presents a novel type of deep foundation — an anchor foundation with root caissons, which improve the soil–caisson interaction using penetrating roots. A simplified analytical procedure is proposed for calculating responses of the new anchor foundation subjected to combined vertical, horizontal, and moment loadings. Caisson–soil interaction is simulated by a Winkler subgrade reaction model, with an improved Winkler spring constant to consider the reinforcement effect of roots. The method incorporates limiting soil stress to investigate soil nonlinear behavior and a transfer matrix to represent nonhomogeneous soils, with a passive caisson model accounting for group effects. The effectiveness of the present approach is evaluated by comparison with full-scale field load tests and a finite element analysis on a small-scale anchor foundation to give a preliminary design guideline for the Ma’anshan Yangtze River Bridge in China.
A computational study of the fluctional behaviour of group 14 substituted ortho-semiquinone radicals
Authors: Ingold K. U. , DiLabio Gino A. 
Published: February 2011

The dynamics of the 1,4-migration of some O-substituted 3,5-di-tert-butyl-ortho-semiquinone radicals have been calculated by density-functional theory (DFT). There is very good agreement in the rate constant and Arrhenius parameters between these calculations and experimental values for migration of H, D, and the Me3Si group. For the Me3Sn group, the calculations indicate an incredibly fast migration (k293K = 2.0 × 1012 s–1), a result that is consistent with experimental data (k293K > 109 s–1). Other O-substituents examined by DFT and compared with experimental data were H3C and Me2ClSn.
Insights into the effect of ketylimine, aldimine, and vinylene group attachment and regiosubstitution on the fluorescence deactivation of fluorene
Authors: Dufresne Stéphane , Skalski Thomas , Skene W. G. 
Published: February 2011

The spectroscopic and electrochemical properties of a 9-substituted fluorene ketylimine (3) were investigated and compared with those of its vinylene analogue (4) to determine the origins of the quenched fluorescence of these compounds. The predominate mode of singlet excited state deactivation of the heteroatomic fluorene was found to be internal conversion involving bond rotation. Meanwhile, its carbon counterpart was found to undergo deactivation preferentially by intersystem crossing to form its triplet, which was confirmed by laser flash photolysis. Both 3 and 4 quenched the fluorescence of fluorene with diffusion-controlled rate constants, implying that the singlet excited states of 3 and 4 are also quenched by intramolecular photoinduced electron transfer (PET). This deactivation mode was found to be exergonically favorable (–90 kJ/mol for 3 and –81 kJ/mol for 4) according to the Rehm–Weller equation. The position of the heteroatomic bond on the fluorene moiety was further found to influence the singlet excited state deactivation pathway. The 2-substituted regioisomer decayed predominately by intramolecular PET and its fluorescence can be restored by acid protonation. Conversely, the PET mechanism is a minor deactivation mode for the 9-substituted fluorene derivative and its fluorescence can be enhanced by suppressing bond rotational modes, possible at low temperature and potentially in thin films.
Luminescence studies of copper(I)-containing [2]pseudorotaxanes
Authors: Briggs Breeze N. , Durola Fabien , McMillin David R. , Sauvage Jean-Pierre 
Published: February 2011

This report describes photoluminescence studies of copper-containing [2]pseudorotaxanes that mimic elements of functioning molecular machines. Excitation with visible light induces a formal oxidation of the metal center and simulates an actuation process. In all four [2]pseudorotaxanes studied, the ring ligand is the same, but the thread ligand is variable, namely 2,9-di(anisol-4-yl)-1,10-phenanthroline (dap), 6,6′-di(anisol-4-yl)-2,2′-bipyridine (o-dabipy), 5,5′-di(anisol-4-yl)-2,2′-bipyridine (m-dabipy), or 8,8′-di(anisol-4-yl)-3,3′-bi-isoquinoline (dabiiq). The absorbance bandshapes suggest that aryl substituents extending from the core ligands engage in stacking interactions and induce a partially flattened structure in the ground state. More severe flattening occurs in the excited state and precludes the observation of emission if inter-ligand steric forces do not limit the distortion. Thus, the [2]pseudorotaxanes containing dap or o-dabipy as the thread ligand exhibit uncorrected emission maxima at around 720 nm in room-temperature dichloromethane, while the less constrained analogues, containing dabiiq or m-dabipy, are not emissive in fluid solution and barely exhibit a signal in rigid media. In dichloromethane, the luminescence quantum yields of the dap- and o-dabipy-containing systems are 6 × 10−4 and 4 × 10−4, and the excited-state lifetimes are 98 ns and 90 ns, respectively.
Photochemistry of matrix-isolated 5-cyano-2H-pyran-2-one (δ-cyano-α-pyrone) and cyanocyclobuta-1,3-diene
Authors: Menke Jessica L. , McMahon Robert J. 
Published: February 2011

Matrix-isolation photochemistry (λ > 299 nm; Ar, 10 K) of 5-cyano-2H-pyran-2-one (5, δ-cyano-α-pyrone) shows complete conversion to a mixture of several ring-opened ketene isomers (6) and a ring-closed Dewar lactone (7), as detected by infrared spectroscopy. Subsequent irradiation (λ > 200 nm) causes decarboxylation of the Dewar lactone (7) to produce cyanocyclobuta-1,3-diene (8). Continued irradiation (λ > 200 nm) results in the photodecomposition of cyanocyclobuta-1,3-diene (8) to cyanoacetylene and acetylene. 4-Cyanopyridine (10) was explored as an alternative photochemical precursor to cyanocyclobuta-1,3-diene (8). It was found, however, that 10 does not exhibit observable photochemistry under our irradiation conditions.
Dynamics of capsuleplex formed between octaacid and organic guest molecules — Photophysical techniques reveal the opening and closing of capsuleplex
Authors: Jayaraj Nithyanandhan , Jockusch Steffen , Kaanumalle Lakshmi S. , Turro N. J. , Ramamurthy V. 
Published: February 2011

This manuscript is concerned with the opening and closing of a capsuleplex made up of organic guest molecules and two cavitand molecules known as octaacid (OA). The capsuleplex is loosely held together in water through weak interactions. We have investigated the opening–closing of the OA capsuleplex by monitoring the quenching of excited singlet and (or) triplet states of nine different guest molecules encapsulated within a capsule by molecular oxygen that is dissolved in water surrounding the capsule. The rate constants for oxygen quenching of the excited guest molecules were estimated by monitoring the intensity of fluorescence/phosphorescence or lifetimes of excited states of guest molecules in the presence of different concentrations of oxygen in water. Guest molecules were chosen such that one could probe the opening–closing process during a time range of 0.05 to 922 µs. We believe that the oxygen quenching constant reflects the accessibility of oxygen to the guest enclosed within the OA capsuleplex, and this in turn depends on the capsule opening–closing rate constant. Based on the quenching studies, we conclude that guests whose lifetimes are shorter than 5 µs are inaccessible to oxygen. Results presented in this report suggest that the extent and time scale for opening depends on the guest.
Strain-promoted 1,3-dipolar cycloadditions of diazo compounds with cyclooctynes
Authors: Moran Joseph , McKay Craig S. , Pezacki John Paul 
Published: February 2011

Strain-promoted cycloadditions of diazo compounds with dibenzocyclooctyne proceed with second-order rate constants of >10 L mol–1 s–1 at 25 °C. These reactions display rate constants that are comparable or greater than those of the analogous reactions of nitrones or azides with cyclooctynes.
Distribution and reactivity of gallates toward galvinoxyl radicals in SDS micellar solutions — Effect of the alkyl chain length
Authors: Bridi Raquel , Aliaga Carolina , Aspée Alexis , Abuin Elsa , Lissi Eduardo 
Published: February 2011

In this work, we have evaluated the reactivity of methyl gallate, propyl gallate, and n-octyl gallate toward galvinoxyl radicals in homogeneous solution (ethanol) and sodium dodecyl sulfate micelles. In ethanol, the rate of galvinoxyl consumption was independent of the gallate’s alkyl chain length. On the other hand, reaction rates in micelles were dependent on the length of the gallate alkyl chain. Measurements of the rate of the reaction at different pH show that, even at pH 7.0, the reaction mainly involves the monodeprotonated anionic form of the gallates. Plots of reaction rates as a function of the surfactant concentration allowed us to evaluate the distribution of the gallates (KGH) and an apparent rate constant defined by the product between the intramicellar rate constant of the anion ([Formula: see text]) and its partition constant ([Formula: see text]). The values of the increment of the apparent rate constant per methylene group in the alkyl chain strongly suggest that intramicellar rate constant values are independent of the alkyl chain length. This points to a similar intramicellar localization of the phenolate moiety in the three gallates considered.