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As part of the National Collegiate Honors Council's (2024) collection of essays honoring the life and work of Dr. Ada Long (1945-2024), the author reflects on the personal and professional impact she has made in the honors experience. [ABSTRACT FROM AUTHOR]

Laser threshold magnetometry using the negatively charged nitrogen-vacancy (NV−) centre in diamond as a gain medium has been proposed as a technique to dramatically enhance the sensitivity of room-temperature magnetometry. We experimentally explore a diamond-loaded open tunable fibre-cavity system as a potential contender for the realisation of lasing with NV− centres. We observe amplification of the transmission of a cavity-resonant seed laser at 721 nm when the cavity is pumped at 532 nm and attribute this to stimulated emission. Changes in the intensity of spontaneously emitted photons accompany the amplification, and a qualitative model including stimulated emission and ionisation dynamics of the NV− centre captures the dynamics in the experiment very well. These results highlight important considerations in the realisation of an NV− laser in diamond.

The article presents the literary criticism of the creations including the book "In the Blood," by Suzan-Lori Parks, and the play "Shakin' the Mess Outta Misery," by Shay Youngblood. It analyzes the language and the approach of the authors. Also being discussed is the work "The Scarlet Letter" by Nathaniel Hawthorne.

The ST1 center is a point defect in diamond with bright fluorescence and a mechanism for optical spin initialization and readout. The center has impressive potential for applications in diamond quantum computing as a quantum bus to a register of nuclear spins. This is because it has an exceptionally high readout contrast, and unlike the well-known nitrogen-vacancy center, it does not have a ground state electronic spin that decoheres the nuclear spins. However, its chemical structure is unknown, and there are large gaps in our understanding of its properties. We present the discovery of ST1 centers in natural diamond. Our experiments identify interesting power dependence of the center’s optical dynamics and reveal new electronic structure. We also present a theory of its electron-phonon interactions, which we combine with previous experiments, to shortlist likely candidates for its chemical structure.

Abstract Older adults and special populations (living with disability and/or chronic illness that may limit mobility and/or physical endurance) can benefit from practicing a more physically active lifestyle, typically by increasing ambulatory activity. Step counting devices (accelerometers and pedometers) offer an opportunity to monitor daily ambulatory activity; however, an appropriate translation of public health guidelines in terms of steps/day is unknown. Therefore this review was conducted to translate public health recommendations in terms of steps/day. Normative data indicates that 1) healthy older adults average 2,000-9,000 steps/day, and 2) special populations average 1,200-8,800 steps/day. Pedometer-based interventions in older adults and special populations elicit a weighted increase of approximately 775 steps/day (or an effect size of 0.26) and 2,215 steps/day (or an effect size of 0.67), respectively. There is no evidence to inform a moderate intensity cadence (i.e., steps/minute) in older adults at this time. However, using the adult cadence of 100 steps/minute to demark the lower end of an absolutely-defined moderate intensity (i.e., 3 METs), and multiplying this by 30 minutes produces a reasonable heuristic (i.e., guiding) value of 3,000 steps. However, this cadence may be unattainable in some frail/diseased populations. Regardless, to truly translate public health guidelines, these steps should be taken over and above activities performed in the course of daily living, be of at least moderate intensity accumulated in minimally 10 minute bouts, and add up to at least 150 minutes over the week. Considering a daily background of 5,000 steps/day (which may actually be too high for some older adults and/or special populations), a computed translation approximates 8,000 steps on days that include a target of achieving 30 minutes of moderate-to-vigorous physical activity (MVPA), and approximately 7,100 steps/day if averaged over a week. Measured directly and including these background activities, the evidence suggests that 30 minutes of daily MVPA accumulated in addition to habitual daily activities in healthy older adults is equivalent to taking approximately 7,000-10,000 steps/day. Those living with disability and/or chronic illness (that limits mobility and or/physical endurance) display lower levels of background daily activity, and this will affect whole-day estimates of recommended physical activity.

Abstract Background A better understanding of how prostate cancer survivors differ from men without prostate cancer and whether these potential differences vary across demographic subgroups will help to focus and prioritize future public health interventions for improving the health and well-being of prostate cancer survivors. Therefore, our study aims were to compare lifestyle behaviors, body mass index (BMI), and perceived health in men with and without a diagnosis of prostate cancer in a national, population-based sample and to explore whether these comparisons differ for demographic subgroups. Methods In a cross-sectional study, men aged ≥ 40 were identified from the Behavioral Risk Factor Surveillance System (BRFSS) 2002 data (n = 63,662). Respondents reporting history of prostate cancer (n = 2,524) were compared with non prostate cancer controls (n = 61,138) with regard to daily fruit and vegetable servings (FVPD), smoking, alcohol, sedentary behavior, BMI, and perceived health. Multivariable logistic regression calculated adjusted odds ratios (OR) and 95% confidence intervals (CI) for the entire sample and for age, race, education, and urbanicity subgroups. Results Men with prostate cancer did not differ from men without prostate cancer with regard to smoking, alcohol, sedentary behavior, and obesity but were more likely to consume ≥ 5 FVPD (OR, 95% CI: 1.30, 1.09–1.56) and report poor or fair health (OR, 95% CI: 1.62, 1.33–1.97). Subgroup analyses demonstrated attenuation of the higher likelihood of ≥ 5 FVPD among prostate cancer survivors in rural respondents (OR, 95% CI: 0.98, 0.72–1.33). Poorer perceived health was greatest if ≤ 65 years of age (OR, 95% CI: 2.54, 1.79–3.60) and nonsignificant if black (OR, 95% CI: 1.41, 0.70–2.82). Smoking and alcohol which were not significant for the sample as a whole, demonstrated significant associations in certain subgroups. Conclusion Although efforts to enhance perceived health and healthy lifestyle behaviors among prostate cancer survivors are warranted, demographic subgroups such as prostate cancer survivors ≤ 65 and rural populations may require more aggressive interventions.

Marine heatwaves (MHWs) are often associated with physiological changes throughout biological communities but can also result in biomass declines that correspond with shifts in phenology. We examined the response of larval Pacific cod (Gadus macrocephalus) to MHWs in the Gulf of Alaska across seven years to evaluate the effects of MHWs on hatch phenology, size-at-age, and daily growth and identify potential regulatory mechanisms. Hatch dates were, on average, 19 days earlier since the onset of MHWs, shifting a mean of 15 days earlier per 1 ℃ increase. Size-at-capture was larger during & between MHWs but, contrary to expectations, larvae grew slower and were smaller in size-at-age. The larger size during & between MHWs can be entirely explained by older ages due to earlier hatching. Daily growth variation was well-explained by an interaction among age, temperature, and hatch date. Under cool conditions, early growth was fastest for the latest hatchers. However, this variation converged at warmer temperatures, due to faster growth of earlier hatchers. Stage-specific growth did not vary with temperature, remaining relatively similar from 4 to 8 ℃. Temperature-related demographic changes were more predictable based on phenological shifts rather than changes in growth, which could affect population productivity after MHWs., (© 2024. The Author(s).)

Empirical dynamic modelling (EDM) is becoming an increasingly popular method for understanding the dynamics of ecosystems. It has been applied to laboratory, terrestrial, freshwater and marine systems, used to forecast natural populations and has addressed fundamental ecological questions. Despite its increasing use, we have not found full explanations of EDM in the ecological literature, limiting understanding and reproducibility. Here we expand upon existing work by providing a detailed introduction to EDM. We use three progressively more complex approaches. A short verbal explanation of EDM is then explicitly demonstrated by graphically working through a simple example. We then introduce a full mathematical description of the steps involved. Conceptually, EDM translates a time series of data into a path through a multi-dimensional space, whose axes are lagged values of the time series. A time step is chosen from which to make a prediction. The state of the system at that time step corresponds to a 'focal point' in the multi-dimensional space. The set (called the library) of candidate nearest neighbours to the focal point is constructed, to determine the nearest neighbours that are then used to make the prediction. Our mathematical explanation explicitly documents which points in the multi-dimensional space should not be considered as focal points. We suggest a new option for excluding points from the library that may be useful for short-term time series that are often found in ecology. We focus on the core simplex and S-map algorithms of EDM. Our new R package, pbsEDM, enhances understanding (by outputting intermediate calculations), reproduces our results and can be applied to new data. Our work improves the clarity of the inner workings of EDM, a prerequisite for EDM to reach its full potential in ecology and have wide uptake in the provision of advice to managers of natural resources., (© 2024 His Majesty the King in Right of Canada. Ecology and Evolution published by John Wiley & Sons Ltd. Reproduced with the permission of the Minister of Fisheries and Oceans Canada.)

We studied how patient beliefs regarding the need for antibiotics, as measured by expectation scores, and antibiotic prescribing outcome affect patient satisfaction using data from 2,710 urgent-care visits. Satisfaction was affected by antibiotic prescribing among patients with medium-high expectation scores but not among patients with low expectation scores., Competing Interests: All authors report no conflicts of interest relevant to this article., (© The Author(s) 2023.)

Sustainability-maintaining catches within the historical range of socially and ecologically acceptable values-is key to fisheries success. Climate change may rapidly threaten sustainability, and recognizing these instances is important for effective climate adaptation. Here, we present one approach for evaluating changing sustainability under a changing climate. We use Bayesian regression models to compare fish population processes under historical climate norms and emerging anthropogenic extremes. To define anthropogenic extremes we use the Fraction of Attributable Risk (FAR), which estimates the proportion of risk for extreme ocean temperatures that can be attributed to human influence. We illustrate our approach with estimates of recruitment (production of young fish, a key determinant of sustainability) for two exploited fishes (Pacific cod Gadus macrocephalus and walleye pollock G. chalcogrammus) in a rapidly warming ecosystem, the Gulf of Alaska. We show that recruitment distributions for both species have shifted towards zero during anthropogenic climate extremes. Predictions based on the projected incidence of anthropogenic temperature extremes indicate that expected recruitment, and therefore fisheries sustainability, is markedly lower in the current climate than during recent decades. Using FAR to analyze changing population processes may help fisheries managers and stakeholders to recognize situations when historical sustainability expectations should be reevaluated., (© 2021. The Author(s).)

Some of the longest and most comprehensive marine ecosystem monitoring programs were established in the Gulf of Alaska following the environmental disaster of the Exxon Valdez oil spill over 30 years ago. These monitoring programs have been successful in assessing recovery from oil spill impacts, and their continuation decades later has now provided an unparalleled assessment of ecosystem responses to another newly emerging global threat, marine heatwaves. The 2014-2016 northeast Pacific marine heatwave (PMH) in the Gulf of Alaska was the longest lasting heatwave globally over the past decade, with some cooling, but also continued warm conditions through 2019. Our analysis of 187 time series from primary production to commercial fisheries and nearshore intertidal to offshore oceanic domains demonstrate abrupt changes across trophic levels, with many responses persisting up to at least 5 years after the onset of the heatwave. Furthermore, our suite of metrics showed novel community-level groupings relative to at least a decade prior to the heatwave. Given anticipated increases in marine heatwaves under current climate projections, it remains uncertain when or if the Gulf of Alaska ecosystem will return to a pre-PMH state.

The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring ( Clupea pallasii ) across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular SYNE2 , which influences the development of retinal photoreceptors in vertebrates. SYNE2 is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring ( Clupea harengus ). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes.

The effects of climate warming on ecosystem dynamics are widespread throughout the world's oceans. In the Northeast Pacific, large-scale climate patterns such as the El Niño/Southern Oscillation and Pacific Decadal Oscillation, and recently unprecedented warm ocean conditions from 2014 to 2016, referred to as a marine heatwave (MHW), resulted in large-scale ecosystem changes. Larval fishes quickly respond to environmental variability and are sensitive indicators of ecosystem change. Categorizing ichthyoplankton dynamics across marine ecosystem in the Northeast Pacific can help elucidate the magnitude of assemblage shifts, and whether responses are synchronous or alternatively governed by local responses to regional oceanographic conditions. We analyzed time-series data of ichthyoplankton abundances from four ecoregions in the Northeast Pacific ranging from subarctic to subtropical: the Gulf of Alaska (1981-2017), British Columbia (2001-2017), Oregon (1998-2017), and the southern California Current (1981-2017). We assessed the impact of the recent (2014-2016) MHW and how ichthyoplankton assemblages responded to past major climate perturbations since 1981 in these ecosystems. Our results indicate that the MHW caused widespread changes in the ichthyoplankton fauna along the coast of the Northeast Pacific Ocean, but impacts differed between marine ecosystems. For example, abundances for most dominant taxa were at all-time lows since the beginning of sampling in the Gulf of Alaska and British Columbia, while in Oregon and the southern California Current species richness increased as did abundances of species associated with warmer waters. Lastly, species associated with cold waters also increased in abundances close to shore in southern California during the MHW, a pattern that was distinctly different from previous El Niño events. We also found several large-scale, synchronized ichthyoplankton assemblage composition shifts during past major climate events. Current climate projections suggest that MHWs will become more intense and thus our findings can help project future changes in larval dynamics, allowing for improved ecosystem management decisions., (© 2020 Her Majesty the Queen in Right of Canada. Reproduced with the permission of the Minister of Fisheries and Oceans Canada. This article has been contributed to by US Government employees and their work is in the public domain in the USA.)

Societies increasingly use multisector ocean planning as a tool to mitigate conflicts over space in the sea, but such plans can be highly sensitive to species redistribution driven by climate change or other factors. A key uncertainty is whether planning ahead for future species redistributions imposes high opportunity costs and sharp trade-offs against current ocean plans. Here, we use more than 10,000 projections for marine animals around North America to test the impact of climate-driven species redistributions on the ability of ocean plans to meet their goals. We show that planning for redistributions can substantially reduce exposure to risks from climate change with little additional area set aside and with few trade-offs against current ocean plan effectiveness. Networks of management areas are a key strategy. While climate change will severely disrupt many human activities, we find a strong benefit to proactively planning for long-term ocean change., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Shifts in phenology are a well-documented ecological response to changes in climate, which may or may not be adaptive for a species depending on the climate sensitivity of other ecosystem processes. Furthermore, phenology may be affected by factors in addition to climate, which may accentuate or dampen climate-driven phenological responses. In this study, we investigate how climate and population demographic structure jointly affect spawning phenology of a fish species of major commercial importance: walleye pollock (Gadus chalcogrammus). We use 32 years of data from ichthyoplankton surveys to reconstruct timing of pollock reproduction in the Gulf of Alaska and find that the mean date of spawning has varied by over 3 weeks throughout the last >3 decades. Climate clearly drives variation in spawn timing, with warmer temperatures leading to an earlier and more protracted spawning period, consistent with expectations of advanced spring phenology under warming. However, the effects of temperature were nonlinear, such that additional warming above a threshold value had no additional effect on phenology. Population demographics were equally as important as temperature: An older and more age-diverse spawning stock tended to spawn earlier and over a longer duration than a younger stock. Our models suggest that demographic shifts associated with sustainable harvest rates could shift the mean spawning date 7 days later and shorten the spawning season by 9 days relative to an unfished population, independent of thermal conditions. Projections under climate change suggest that spawn timing will become more stable for walleye pollock in the future, but it is unknown what the consequences of this stabilization will be for the synchrony of first-feeding larvae with production of zooplankton prey in spring. With ongoing warming in the world's oceans, knowledge of the mechanisms underlying reproductive phenology can improve our ability to monitor and manage species under changing climate conditions., (Published 2018. This article is a U.S. Government work and is in the public domain in the USA.)

The roles of dispersal and recruitment have long been a focal point in ecology and conservation. The adopted migrant hypothesis proposes a life history in which social learning transmits migratory knowledge between generations of iteroparous fish. Specifically, juveniles disperse from the parental spawning site, encounter and recruit to a local adult population, and learn migration routes between spawning and foraging habitats by following older, experienced fish. Although the adopted migrant life history may apply to many species of pelagic marine fishes, there is scant theoretical or empirical work on the consequent population dynamics. We developed and analyzed a mathematical model of this life history in which the recruitment of juveniles depends on the relative abundance of the local populations and recruitment overlap, which measures the ease with which juveniles are recruited by a nonparental population. We demonstrate that the adopted migrant life history can maintain spatial demographic structure among local populations, that it can also predispose local populations to collapse when a tipping point is crossed, and that recovery after collapse is impaired by reduced recruitment at small local population sizes.

Genetic data are commonly used to estimate connectivity between putative populations, but translating them to demographic dispersal rates is complicated. Theoretical equations that infer a migration rate based on the genetic estimator F ST , such as Wright's equation, F ST ≈ 1/(4 N e m + 1), make assumptions that do not apply to most real populations. How complexities inherent to real populations affect migration was exemplified by Atlantic cod in the North Sea and Skagerrak and was examined within an age-structured model that incorporated genetic markers. Migration was determined under various scenarios by varying the number of simulated migrants until the mean simulated level of genetic differentiation matched a fixed level of genetic differentiation equal to empirical estimates. Parameters that decreased the N e / N t ratio (where N e is the effective and N t is the total population size), such as high fishing mortality and high fishing gear selectivity, increased the number of migrants required to achieve empirical levels of genetic differentiation. Higher maturity-at-age and lower selectivity increased N e / N t and decreased migration when genetic differentiation was fixed. Changes in natural mortality, fishing gear selectivity, and maturity-at-age within expected limits had a moderate effect on migration when genetic differentiation was held constant. Changes in population size had the greatest effect on the number of migrants to achieve fixed levels of F ST , particularly when genetic differentiation was low, F ST ≈ 10 -3 Highly variable migration patterns, compared with constant migration, resulted in higher variance in genetic differentiation and higher extreme values. Results are compared with and provide insight into the use of theoretical equations to estimate migration among real populations., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may have played a role in driving local dynamics. More generally, we demonstrated how state-space models can be used to test evidence for population spatial structure based on survey time-series data. Our study shows the importance of considering spatially structured dynamics, as the inferences from such an approach can lead to a different ecological understanding of the drivers of population declines, and fundamentally different management actions to restore populations., (© 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

The relationship between mercury (Hg) and selenium (Se) toxicity is complex, with coexposure reported to reduce, increase, and have no effect on toxicity. Different interactions may be related to chemical compound, but this has not been systematically examined. Our goal was to assess the interactive effects between the two elements on growth in the nematode Caenorhabditis elegans, focusing on inorganic and organic Hg (HgCl2 and MeHgCl) and Se (selenomethionine, sodium selenite, and sodium selenate) compounds. We utilized aqueous Hg/Se dosing molar ratios that were either above, below, or equal to 1 and measured the internal nematode total Hg and Se concentrations for the highest concentrations of each Se compound. Observed interactions were complicated, differed between Se and Hg compounds, and included greater-than-additive, additive, and less-than-additive growth impacts. Biologically significant interactions were only observed when the dosing Se solution concentration was 100-25,000 times greater than the dosing Hg concentration. Mitigation of growth impacts was not predictable on the basis of internal Hg/Se molar ratio; improved growth was observed at some internal Hg/Se molar ratios both above and below 1. These findings suggest that future assessments of the Hg and Se relationship should incorporate chemical compound into the evaluation.

Effective disease management can benefit from mathematical models that identify drivers of epidemiological change and guide decision-making. This is well illustrated in the host-parasite system of sea lice and salmon, which has been modelled extensively due to the economic costs associated with sea louse infections on salmon farms and the conservation concerns associated with sea louse infections on wild salmon. Consequently, a rich modelling literature devoted to sea louse and salmon epidemiology has been developed. We provide a synthesis of the mathematical and statistical models that have been used to study the epidemiology of sea lice and salmon. These studies span both conceptual and tactical models to quantify the effects of infections on host populations and communities, describe and predict patterns of transmission and dispersal, and guide evidence-based management of wild and farmed salmon. As aquaculture production continues to increase, advances made in modelling sea louse and salmon epidemiology should inform the sustainable management of marine resources., (© 2016 The Author(s).)

A persistent debate in population ecology concerns the relative importance of environmental stochasticity and density dependence in determining variability in adult year-class strength, which contributes to future reproduction as well as potential yield in exploited populations. Apart from the strength of the processes, the timing of density regulation may affect how stochastic variation, for instance through climate, translates into changes in adult abundance. In this study, we develop a life-cycle model for the population dynamics of a large marine fish population, Northeast Arctic cod, to disentangle the effects of density-independent and density-dependent processes on early life-stages, and to quantify the strength of compensatory density dependence in the population. The model incorporates information from scientific surveys and commercial harvest, and dynamically links multiple effects of intrinsic and extrinsic factors on all life-stages, from eggs to spawners. Using a state-space approach we account for observation error and stochasticity in the population dynamics. Our findings highlight the importance of density-dependent survival in juveniles, indicating that this period of the life cycle largely determines the compensatory capacity of the population. Density regulation at the juvenile life-stage dampens the impact of stochastic processes operating earlier in life such as environmental impacts on the production of eggs and climate-dependent survival of larvae. The timing of stochastic versus regulatory processes thus plays a crucial role in determining variability in adult abundance. Quantifying the contribution of environmental stochasticity and compensatory mechanisms in determining population abundance is essential for assessing population responses to climate change and exploitation by humans.

Most stars and their planets form in open clusters. Over 95 per cent of such clusters have stellar densities too low (less than a hundred stars per cubic parsec) to withstand internal and external dynamical stresses and fall apart within a few hundred million years. Older open clusters have survived by virtue of being richer and denser in stars (1,000 to 10,000 per cubic parsec) when they formed. Such clusters represent a stellar environment very different from the birthplace of the Sun and other planet-hosting field stars. So far more than 800 planets have been found around Sun-like stars in the field. The field planets are usually the size of Neptune or smaller. In contrast, only four planets have been found orbiting stars in open clusters, all with masses similar to or greater than that of Jupiter. Here we report observations of the transits of two Sun-like stars by planets smaller than Neptune in the billion-year-old open cluster NGC6811. This demonstrates that small planets can form and survive in a dense cluster environment, and implies that the frequency and properties of planets in open clusters are consistent with those of planets around field stars in the Galaxy.

Observational data from the past century have highlighted the importance of interdecadal modes of variability in fish population dynamics, but how these patterns of variation fit into a broader temporal and spatial context remains largely unknown. We analyzed time series of stable nitrogen isotopes from the sediments of 20 sockeye salmon nursery lakes across western Alaska to characterize temporal and spatial patterns in salmon abundance over the past ∼500 y. Although some stocks varied on interdecadal time scales (30- to 80-y cycles), centennial-scale variation, undetectable in modern-day catch records and survey data, has dominated salmon population dynamics over the past 500 y. Before 1900, variation in abundance was clearly not synchronous among stocks, and the only temporal signal common to lake sediment records from this region was the onset of commercial fishing in the late 1800s. Thus, historical changes in climate did not synchronize stock dynamics over centennial time scales, emphasizing that ecosystem complexity can produce a diversity of ecological responses to regional climate forcing. Our results show that marine fish populations may alternate between naturally driven periods of high and low abundance over time scales of decades to centuries and suggest that management models that assume time-invariant productivity or carrying capacity parameters may be poor representations of the biological reality in these systems.

Conservation management of wild fish may include fish health management in sympatric populations of domesticated fish in aquaculture. We developed a mathematical model for the population dynamics of parasitic sea lice (Lepeophtheirus salmonis) on domesticated populations of Atlantic salmon (Salmo salar) in the Broughton Archipelago region of British Columbia. The model was fit to a seven-year dataset of monthly sea louse counts on farms in the area to estimate population growth rates in relation to abiotic factors (temperature and salinity), local host density (measured as cohort surface area), and the use of a parasiticide, emamectin benzoate, on farms. We then used the model to evaluate management scenarios in relation to policy guidelines that seek to keep motile louse abundance below an average three per farmed salmon during the March-June juvenile wild Pacific salmon (Oncorhynchus spp.) migration. Abiotic factors mediated the duration of effectiveness of parasiticide treatments, and results suggest treatment of farmed salmon conducted in January or early February minimized average louse abundance per farmed salmon during the juvenile wild salmon migration. Adapting the management of parasites on farmed salmon according to migrations of wild salmon may therefore provide a precautionary approach to conserving wild salmon populations in salmon farming regions.

In the solar system, the planets' compositions vary with orbital distance, with rocky planets in close orbits and lower-density gas giants in wider orbits. The detection of close-in giant planets around other stars was the first clue that this pattern is not universal and that planets' orbits can change substantially after their formation. Here, we report another violation of the orbit-composition pattern: two planets orbiting the same star with orbital distances differing by only 10% and densities differing by a factor of 8. One planet is likely a rocky "super-Earth," whereas the other is more akin to Neptune. These planets are 20 times more closely spaced and have a larger density contrast than any adjacent pair of planets in the solar system.

Since the discovery of the first extrasolar giant planets around Sun-like stars, evolving observational capabilities have brought us closer to the detection of true Earth analogues. The size of an exoplanet can be determined when it periodically passes in front of (transits) its parent star, causing a decrease in starlight proportional to its radius. The smallest exoplanet hitherto discovered has a radius 1.42 times that of the Earth's radius (R(⊕)), and hence has 2.9 times its volume. Here we report the discovery of two planets, one Earth-sized (1.03R(⊕)) and the other smaller than the Earth (0.87R(⊕)), orbiting the star Kepler-20, which is already known to host three other, larger, transiting planets. The gravitational pull of the new planets on the parent star is too small to measure with current instrumentation. We apply a statistical method to show that the likelihood of the planetary interpretation of the transit signals is more than three orders of magnitude larger than that of the alternative hypothesis that the signals result from an eclipsing binary star. Theoretical considerations imply that these planets are rocky, with a composition of iron and silicate. The outer planet could have developed a thick water vapour atmosphere.

Humans have more than doubled the amount of reactive nitrogen (Nr) added to the biosphere, yet most of what is known about its accumulation and ecological effects is derived from studies of heavily populated regions. Nitrogen (N) stable isotope ratios ((15)N:(14)N) in dated sediments from 25 remote Northern Hemisphere lakes show a coherent signal of an isotopically distinct source of N to ecosystems beginning in 1895 ± 10 years (±1 standard deviation). Initial shifts in N isotope composition recorded in lake sediments coincide with anthropogenic CO(2) emissions but accelerate with widespread industrial Nr production during the past half century. Although current atmospheric Nr deposition rates in remote regions are relatively low, anthropogenic N has probably influenced watershed N budgets across the Northern Hemisphere for over a century.

Understanding how populations respond to changes in climate requires long-term, high-quality datasets, which are rare for marine systems. We estimated the effects of climate warming on cod lengths and length variability using a unique 91-y time series of more than 100,000 individual juvenile cod lengths from surveys that began in 1919 along the Norwegian Skagerrak coast. Using linear mixed-effects models, we accounted for spatial population structure and the nested structure of the survey data to reveal opposite effects of spring and summer warming on juvenile cod lengths. Warm summer temperatures in the coastal Skagerrak have limited juvenile growth. In contrast, warmer springs have resulted in larger juvenile cod, with less variation in lengths within a cohort, possibly because of a temperature-driven contraction in the spring spawning period. A density-dependent reduction in length was evident only at the highest population densities in the time series, which have rarely been observed in the last decade. If temperatures rise because of global warming, nonlinearities in the opposing temperature effects suggest that negative effects of warmer summers will increasingly outweigh positive effects of warmer springs, and the coastal Skagerrak will become ill-suited for Atlantic cod.

One of the most pervasive themes in ecology is that biological diversity stabilizes ecosystem processes and the services they provide to society, a concept that has become a common argument for biodiversity conservation. Species-rich communities are thought to produce more temporally stable ecosystem services because of the complementary or independent dynamics among species that perform similar ecosystem functions. Such variance dampening within communities is referred to as a portfolio effect and is analogous to the effects of asset diversity on the stability of financial portfolios. In ecology, these arguments have focused on the effects of species diversity on ecosystem stability but have not considered the importance of biologically relevant diversity within individual species. Current rates of population extirpation are probably at least three orders of magnitude higher than species extinction rates, so there is a pressing need to clarify how population and life history diversity affect the performance of individual species in providing important ecosystem services. Here we use five decades of data from Oncorhynchus nerka (sockeye salmon) in Bristol Bay, Alaska, to provide the first quantification of portfolio effects that derive from population and life history diversity in an important and heavily exploited species. Variability in annual Bristol Bay salmon returns is 2.2 times lower than it would be if the system consisted of a single homogenous population rather than the several hundred discrete populations it currently consists of. Furthermore, if it were a single homogeneous population, such increased variability would lead to ten times more frequent fisheries closures. Portfolio effects are also evident in watershed food webs, where they stabilize and extend predator access to salmon resources. Our results demonstrate the critical importance of maintaining population diversity for stabilizing ecosystem services and securing the economies and livelihoods that depend on them. The reliability of ecosystem services will erode faster than indicated by species loss alone.

Molecular dynamics (MD) simulations of phosphatidylinositol (4,5)-bisphosphate (PIP2) and phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in 1-palmitoyl 2-oleoyl phosphatidylcholine (POPC) bilayers indicate that the inositol rings are tilted approximately 40 degrees with respect to the bilayer surface, as compared with 17 degrees for the P-N vector of POPC. Multiple minima were obtained for the ring twist (analogous to roll for an airplane). The phosphates at position 1 of PIP2 and PIP3 are within an Angström of the plane formed by the phosphates of POPC; lipids in the surrounding shell are depressed by 0.5-0.8 A, but otherwise the phosphoinositides do not substantially perturb the bilayer. Finite size artifacts for ion distributions are apparent for systems of approximately 26 waters/lipid, but, based on simulations with a fourfold increase of the aqueous phase, the phosphoinositide positions and orientations do not show significant size effects. Electrostatic potentials evaluated from Poisson-Boltzmann (PB) calculations show a strong dependence of potential height and ring orientation, with the maxima on the -25 mV surfaces (17.1 +/- 0.1 A for PIP2 and 19.4 +/- 0.3 A for PIP3) occurring near the most populated orientations from MD. These surfaces are well above the background height of 10 A estimated for negatively charged cell membranes, as would be expected for lipids involved in cellular signaling. PB calculations on microscopically flat bilayers yield similar maxima as the MD-based (microscopically rough) systems, but show less fine structure and do not clearly indicate the most probable regions. Electrostatic free energies of interaction with pentalysine are also similar for the rough and flat systems. These results support the utility of a rigid/flat bilayer model for PB-based studies of PIP2 and PIP3 as long as the orientations are judiciously chosen.

The Arabidopsis thaliana mutants de-etiolated3 (det3), pom-pom1 (pom1) and ectopic lignification1 (eli1) all deposit lignins in cells where these polymers would not normally be found. Comparison of these mutants provides an opportunity to determine if the shared mutant phenotype arose by perturbing a common regulatory mechanism in each of the mutants. The mutants were compared using a combination of genetics, histochemistry, chemical profiling, transcript profiling using both Northern blots and microarrays, and bioinformatics. The subset of cells that ectopically lignified was shared between all three mutants, but clear differences in cell wall chemistry were evident between the mutants. Northern blot analysis of lignin biosynthetic genes over diurnal and circadian cycles revealed that transcript abundance of several key genes was clearly altered in all three mutants. Microarray analysis suggests that changes in the expression of specific members of the R2R3-MYB and Dof transcription factor families may contribute to the ectopic lignification phenotypes. This comparative analysis provides a suite of hypotheses that can be tested to examine the control of lignin biosynthesis.

Experiments were undertaken to investigate some of the mechanisms that may function to regulate lignin biosynthesis (lignification) in Arabidopsis thaliana. Northern blot analyses revealed that several genes encoding enzymes involved in the synthesis of lignin monomers displayed significant changes in transcript abundance over a diurnal cycle. Northern blot analysis also suggested that some of the changes in diurnal transcript abundance were likely to be attributable to circadian regulation, whereas others were likely to be attributable to light perception. Comparison of circadian changes in transcript abundance of lignin biosynthetic genes between wild-type plants and the sex1 mutant, which is impaired in starch turnover, suggested that carbon availability related to starch turnover might determine the capacity to synthesize lignins. This hypothesis was supported by the observation that the sex1 mutant accumulated fewer lignins than wild-type plants. Consistent with the relationship between carbon availability and lignin accumulation, analysis of dark-grown wild-type A. thaliana seedlings uncovered a role for sugars in the regulation of lignin biosynthesis. Analysis of lignin accumulation, as determined by qualitative changes in phloroglucinol staining, suggested that metabolizable sugars positively influence the abundance of lignins. Transcriptome analysis supports the hypothesis that sugars are not merely a source of carbon skeletons for lignification, but they also function as a signal to enhance the capacity to synthesize lignins.

Lignins are complex, three-dimensional polymers embedded in the cell walls of specialised plant cells, where they play important roles in plant growth and development. Plants must possess mechanisms to coordinate lignin deposition so that its synthesis occurs at the appropriate time and place, in response to endogenous and exogenous cues. Here we consider the genetic basis of the control of lignin deposition. We focus on the transcriptional regulation of lignification, considering how the genes encoding the lignin biosynthetic pathway might be co-ordinately controlled, and the transcription factors that are likely to be involved. We also discuss the mechanisms regulating lignification that have been revealed by mutants with altered lignin deposition. We conclude that, while transcriptional regulation is a common feature in the control of lignification, there are many different regulators that may bring about this common mode of regulation. Contents Summary 17 I. Introduction 17 II. Transcriptional regulation of genes encoding lignin biosynthetic enzymes 19 III. Co-ordinate regulation of genes encoding lignin biosynthetic enzymes 21 IV. Mutants with altered spatial and temporal control of lignification 23 V. Conclusion 28 Acknowledgements 28 References 28.

A 2-year-old, purebred Holstein heifer with exercise intolerance and cardiovascular compromise was diagnosed at postmortem with tetralogy of Fallot, which typically results in death within a few months of life. Survival past the age of 2 was unexpected. The concurrent endocarditis of the pulmonic valve is discussed.

Since there is a preponderance of large bowel cancer in males, both in humans and in experimental models, and hormone replacement therapy is protective, a role for sex steroid hormones in the pathogenesis of this neoplasm seems likely. Evidence of functional oestrogen receptor has been looked for in large bowel mucosa and cancer. Expression of oestrogen receptor, and of the oestrogen-inducible receptor-associated genes pS2 and ERD5, was sought. Oestrogen receptor mRNA was detected in cancers and paired normal mucosae in equal amounts. In situ hybridization identified stromal cells above the muscularis mucosae that were positive for oestrogen receptor mRNA. pS2 mRNA was also detected, with a signal intensity significantly higher in normal mucosa compared with cancers, whereas the reverse was seen with ERD5 mRNA levels. pS2 and ERD5 were expressed in epithelium, with the former in a greater amount in distal colon and rectum than proximal colon. Although oestrogen-inducible and receptor-associated genes are expressed in large bowel mucosa, their expression does not correlate with oestrogen receptor.

In situ Hybridisation (ISH) to detect mRNA is widely applicable to studies of human pathology and experimental models including transgenic mice, where it can provide crucial information as to where a gene is expressed, that is not available in other ways. ISH was used to establish that relatively high levels of expression of E-cadherin mRNA were associated with long-term survival in colorectal cancer, before suitable antisera became available. There is increasing awareness that ISH can be used to help select between candidate disease genes found at a linked locus, and that ISH can help validate therapeutic targets. For instance, when several closely related receptor genes are expressed in a tissue, it may be possible to determine which combinations are expressed together in a single cell type. These diverse applications demand a robust method that works on a variety of clinical and experimental materials, and is easily interpreted. To date, the ICRF in situ Hybridisation Service has hybridised over 30,000 sections of principally formalin-fixed, paraffin-embedded tissues, with a high success rate. The practicalities of our preferred method are discussed and key steps for quality control highlighted.

In situ hybridisation methods to localise messenger ribonucleic acid (mRNA) targets in tissue sections or cell preparations using riboprobes can be successful with either isotopic or non-isotopic labelling. Investigators often wish to decide which labelling method provides the maximum specificity, sensitivity and resolution, with minimum nonspecific background. In this study we compared isotopic (35S) and non-isotopic (digoxigenin) labelling, using a variety of probes and paraffin-embedded tissues. The targets were human beta-actin and von Willebrand Factor mRNAs in archival human tissues; and mRNAs for two closely related trefoil factor family (TFF) peptides, TFF2 and TFF3, in rat duodenum. Patterns of localisation with both isotopic and non-isotopic probes were broadly similar for each target. The 35S labelling provided good contrast and sensitive detection under darkfield illumination, but the cellular or subcellular resolution of the target was less precise than that obtained with the digoxigenin-labelled probes in transmitted light. Digoxigenin labelling in individual cells was more clearly demonstrated, but occasionally the contrast of positive staining with background was poor. The sensitivity of each method appeared to be similar for these high-abundance targets, therefore the choice between isotopic and non-isotopic labels is dependent upon the aim of the study and the cellular resolution required.

Accuracy of diagnoses rendered using a live video telepathology network was assessed for permanent sections of surgical pathology specimens. To determine accuracy, telepathology diagnoses were compared with those obtained by directly viewing the glass slide using a standard microscope. A total of 294 cases were read via both telepathology and glass slide by attending pathologists at a tertiary care medical center. Overall accuracy was defined as exact concordance between diagnoses. Clinically insignificant differences in diagnoses were excluded to determine clinically significant accuracy. For the 285 cases with complete data, the overall accuracy for telepathology was 0.912 (95% confidence interval [CI], 0.872-0.941), whereas the overall accuracy for glass slide readings was 0.968 (95% CI, 0.939-0.985). This difference is statistically significant (p = 0.009). When focusing on clinically significant discrepancies, where the difference in diagnosis might affect therapeutic decisions, the video accuracy was only slightly less than the glass slide accuracy (0.965 [95% CI, 0.934-0.982] vs. 0.982 [95% CI, 0.957-0.994], respectively), but this difference is not statistically significant (p = 0.302). Most of the cases with clinically significant differences involved lesions with inherently high interobserver variation. Certainty of diagnosis did not differ between video and glass slide readings (p = 0.911), but there was an association between certainty of diagnosis and diagnostic accuracy for video (p = 0.003 for clinically significant accuracies). Based on these findings, we recommend when using this telepathology system that only preliminary diagnoses should be given in the following situations: for diagnostic areas with known high interobserver variability; when the consultant has any degree of uncertainty about the presence or absence of the lesion in question; and when there is insufficient experience using telepathology as a diagnostic medium.

The six-cysteine P-domain motif forms the basic repeat unit of a growing family of mucin-associated peptides. A precursor for a human secretory polypeptide has been discovered by molecular cloning and deduced to have a single P-domain, termed hP1.B. The pre-pro-peptide has 67% amino acid identity with rat intestinal trefoil factor. We find, using the techniques of RNA analysis and in situ hybridization, that this P-domain peptide is expressed in the human gastrointestinal tract, where a number of pathological conditions affect its expression, and surprisingly find it is expressed in the uterus also. In the intestine, hP1.B is expressed by goblet cells, but in Crohn disease this peptide is synthesized and secreted additionally by the ulcer-associated cell lineage that is known to secrete two other trefoil peptides, pS2 and spasmolytic polypeptide (hSP). In the stomach, hP1.B mRNA is relatively scarce but is more abundant in foci of intestinal metaplasia and near to ulceration. Mucin-rich epithelial cells in hyperplastic polyps of the colon also express this peptide. The discovery of this P-domain peptide and its expression in association with mucins support the hypothesis that P-domains with mucins may subserve related functions in the maintenance and repair of mucosal function.

The cytologic features of fine-needle aspiration specimens from 16 breast carcinomas that closely simulated benign lesions were analyzed and compared to smears from fibroadenomas and fibrocystic change. No combination of features was found that accurately separated all benign and malignant cases. Many nuclei with discernible small nucleoli in smears with many single bipolar nuclei indicated a benign lesion, whereas nuclear hyperchromasia indicated a malignant one.

A cDNA encoding rat intestinal trefoil factor (rITF) was prepared by reverse transcription and PCR amplification. The sequence obtained was well conserved with that of other trefoil peptides. An antisense riboprobe produced from the clone was used to localize the sites of ITF expression in the rat gastrointestinal tract using hybridization in situ. We found rITF mRNA in goblet cells in the small intestine and colon; a gradient of signal strength greatest near the crypt base was sometimes present. We found no evidence for rITF expression in Brunner's glands, the pancreas, or most regions of the gastric mucosa. Surprisingly, strong signals for rITF mRNA were detected in a region of stomach at the junction of the squamous fore-stomach with the glandular gastric mucosa. This region, which may correspond to the cardiac region, formed part of a larger area of cells staining positive for acid mucins. We hypothesize that concerted expression occurs of particular trefoil peptides with specific mucins, and that this organization reflects a functional relationship between mucins and trefoil peptides.

The timing, pathways, and number of migrations involved in the early peopling of the New World are examined from a variety of perspectives. Ultimately, the occupation of the Western Hemisphere was a direct result of boreal cultural adaptations in the Old World. Here, we discuss (1) the dates of appearance of these boreal cultural adaptations and their relevance to the peopling of America, (2) archeological and linguistic evidence bearing on the earliest peopling of the New World, (3) ecological and linguistic evidence on two alternative routes into the New World, and (4) the assumptions present in various migration models. The relative strengths of opposing hypotheses are analyzed by observing whether different approaches point to the same answers.

To determine whether cytolytic T lymphocyte activity is associated with a particular lymphokine profile, lymphokine synthesis was analyzed in a large panel of primary clones derived from single murine CD8+ lymph node T cells. The clones were generated at high efficiency (60-70%), under conditions that had been optimized for the induction of specific cytolytic activity, by culture with phorbol 12-myristate 13-acetate, ionomycin, IL-2, and IFN-gamma for 6 days and then with IL-2 and IL-6 for a further 2 days. When the clones were restimulated for 24 hr with IL-2 and immobilized antibodies to CD3, CD8, and LFA-1, most secreted IL-3 and IFN-gamma and about a third secreted TNF. Although levels of production of IL-3 and IFN-gamma were positively correlated with each other (r = 0.85) and weakly correlated with cytolytic activity (r = 0.68 and 0.55, respectively). TNF titers were unrelated to any other function measured. None of the clones tested secreted detectable IL-4 or IL-6. Similarly, analysis of several clones for lymphokine mRNA expression following cDNA amplification by the polymerase chain reaction revealed the presence of IL-2, IL-3, IFN-gamma, TNF-alpha, and GM-CSF but not IL-4 or IL-6 transcripts. Cytolytic CD8+ T cell clones generated in this high efficiency, accessory cell-independent cloning system therefore expressed a restricted lymphokine profile characterized by the synthesis of IL-3 and IFN-gamma, with variable production of TNF.

Constitutive lymphokine production by cells isolated from mice injected with keyhole limpet haemocyanin (KLH) or from mice undergoing an acute graft vs host reaction (GVHR) was very low, but could be markedly increased by T cell receptor (TCR) ligation. This suggested that in vivo levels of lymphokine production are much lower than those induced by in vitro stimulation. Serum lymphokine titres were consistent with this possibility, and analysis of lymphokine mRNA levels using S1-nuclease protection demonstrated that in vitro-stimulated cells from normal, KLH and GVHR mice all had markedly increased levels of lymphokine transcripts relative to levels found in vivo. A novel method combining limiting dilution analysis with polymerase chain reaction amplification of cDNA was developed that showed that these differences in levels of lymphokine production were due at least in part to differences in the frequencies of lymphokine mRNA-containing cells. Studies of the means by which differential lymphokine production is achieved demonstrated that CD4+, CD8+ and cytotoxic T lymphocyte (CTL) clones all express a common, restricted set of lymphokines in response to a defined in vitro stimulus, but that individual in vivo primed cells can express at least seven distinct patterns of lymphokine production.