text:
aps placed in reserves yielded more (4.81 trap-1) and larger (7.03 mm CL) legal-sized lobsters than traps placed outside. Multiple linear regression revealed that 2.43 more legal lobsters per trap were captured for every 1 km moved from borders towards reserve centers. Additionally, lobsters tagged and released immediately inside reserve borders were recaptured in areas open to fishing at a higher rate than lobsters tagged and released farther inside reserves. These results suggest that abundance gradients inside reserve borders were caused by net emigration of lobsters (spillover). Sublegal lobsters were more abundant inside reserves and nearer to reserve centers, but these increases were much smaller in magnitude than for legal-sized lobsters. Our results indicate that the differences we observed for legal-sized lobsters were driven primarily by reserve effects but were partially influenced by habitat heterogeneity.},
  journal = {Marine Ecology Progress Series},
  doi = {10.3354/meps09592},
  author = {Kay, Matthew C. and Lenihan, Hunter S. and Kotchen, Matthew J. and Miller, Christopher J.},
  month = apr,
  year = {2012},
  pages = {137-150}
}

@article{costello2012,
  title = {Status and {{Solutions}} for the {{World}}'s {{Unassessed Fisheries}}},
  volume = {338},
  copyright = {All rights reserved},
  issn = {0036-8075, 1095-9203},
  abstract = {Recent reports suggest that many well-assessed fisheries in developed countries are moving toward sustainability. We examined whether the same conclusion holds for fisheries lacking formal assessment, which comprise {$>$}80\% of global catch. We developed a method using species' life-history, catch, and fishery development data to estimate the status of thousands of unassessed fisheries worldwide. We found that small unassessed fisheries are in substantially worse condition than assessed fisheries, but that large unassessed fisheries may be performing nearly as well as their assessed counterparts. Both small and large stocks, however, continue to decline; 64\% of unassessed stocks could provide increased sustainable harvest if rebuilt. Our results suggest that global fishery recovery would simultaneously create increases in abundance (56\%) and fishery yields (8 to 40\%).},
  language = {en},
  number = {6106},
  journal = {Science},
  doi = {10.1126/science.1223389},
  author = {Costello, Christopher and Ovando, Daniel and Hilborn, Ray and Gaines, Steven D. and Deschenes, Olivier and Lester, Sarah E.},
  month = oct,
  year = {2012},
  pages = {517-520},
  pmid = {23019613}
}

@article{babcock2011,
  title = {How Useful Is the Ratio of Fish Density Outside versus inside No-Take Marine Reserves as a Metric for Fishery Management Control Rules?},
  volume = {68},
  number = {2},
  journal = {Canadian journal of fisheries and aquatic sciences},
  author = {Babcock, Elizabeth A. and MacCall, Alec D.},
  year = {2011},
  pages = {343--359}
}

@article{gell2003,
  title = {Benefits beyond Boundaries: The Fishery Effects of Marine Reserves},
  volume = {18},
  issn = {0169-5347},
  shorttitle = {Benefits beyond Boundaries},
  abstract = {Marine reserves are areas of the sea where fishing is not allowed. They provide refuges where populations of exploited species can recover and habitats modified by fishing can regenerate. In some places, closed areas have been used for fisheries management for centuries [1] and, until recently, natural refugia also existed, inaccessible through depth, distance or adverse conditions. Developments in technology have left few areas of fishing interest beyond our reach. Recently, the idea of marine reserves as fisheries management tools has re-emerged with developing interest in ecosystem-based management, and observations of incidental fisheries benefits from reserves established for conservation. In light of new evidence, we argue that, by integrating large-scale networks of marine reserves into fishery management, we could reverse global fishery declines and provide urgently needed protection for marine species and their habitats.},
  number = {9},
  journal = {Trends in Ecology \& Evolution},
  doi = {10.1016/S0169-5347(03)00189-7},
  author = {Gell, Fiona R. and Roberts, Callum M.},
  month = sep,
  year = {2003},
  pages = {448-455}
}

@article{hilborn2004,
  title = {When Can Marine Reserves Improve Fisheries Management?},
  volume = {47},
  issn = {0964-5691},
  abstract = {Marine reserves are a promising tool for fisheries management and conservation of biodiversity, but they are not a panacea for fisheries management problems. For fisheries that target highly mobile single species with little or no by-catch or habitat impact, marine reserves provide few benefits compared to conventional fishery management tools. For fisheries that are multi-species or on more sedentary stocks, or for which broader ecological impacts of fishing are an issue, marine reserves have some potential advantages. Their successful use requires a case-by-case understanding of the spatial structure of impacted fisheries, ecosystems and human communities. Marine reserves, together with other fishery management tools, can help achieve broad fishery and biodiversity objectives, but their use will require careful planning and evaluation. Mistakes will be made, and without planning, monitoring and evaluation, we will not learn what worked, what did not, and why. If marine reserves are implemented without case by case evaluation and appropriate monitoring programs, there is a risk of unfulfilled expectations, the creation of disincentives, and a loss of credibility of what potentially is a valuable management tool.},
  number = {3\textendash{}4},
  journal = {Ocean \& Coastal Management},
  doi = {10.1016/j.ocecoaman.2004.04.001},
  author = {Hilborn, Ray and Stokes, Kevin and Maguire, Jean-Jacques and Smith, Tony and Botsford, Louis W and Mangel, Marc and Orensanz, Jos{\'e} and Parma, Ana and Rice, Jake and Bell, Johann and Cochrane, Kevern L and Garcia, Serge and Hall, Stephen J and Kirkwood, G.P and Sainsbury, Keith and Stefansson, Gunnar and Walters, Carl},
  year = {2004},
  pages = {197-205}
}

@article{gerber2005,
  title = {The Role of Dispersal and Demography in Determining the Efficacy of Marine Reserves},
  volume = {62},
  issn = {0706-652X},
  abstract = {Marine reserves are rapidly becoming an important tool for protection and recovery of depleted marine populations. However, the relative value of reserves to particular species is strongly dependent on its life history and behavior. We present a general conceptual framework for considering dispersal in simple demographic models. This framework includes transition matrices that consist of two age-structured models connected by transition probabilities for general migration, ontogenetic shifts, and recruitment in both a reserve and an unprotected area. We show that life history characteristics and perturbation analysis can be used to predict changes in growth rate due to a decrease in adult mortality resulting from a marine reserve for different levels and types of dispersal. Reserves enhanced growth rate for all species irrespective of net dispersal between the reserve and surrounding matrix habitat, but the efficacy of reserves relative to catch reduction depended significantly on the magnitude and sign o..., Les r{\'e}serves marines sont vite en train de devenir des outils importants pour la protection et la r{\'e}cup{\'e}ration des populations marines d{\'e}cim{\'e}es. Cependant, la valeur relative des r{\'e}serves pour une esp{\`e}ce en particulier d{\'e}pend de son cycle biologique et de son comportement. Nous pr{\'e}sentons un cadre conceptuel g{\'e}n{\'e}ral pour examiner la dispersion dans des mod{\`e}les d{\'e}mographiques simples. Ce cadre comprend des matrices de transition qui consistent en deux mod{\`e}les structur{\'e}s d'apr{\`e}s l'{\^a}ge reli{\'e}s par des probabilit{\'e}s de transition pour la migration g{\'e}n{\'e}rale, les changements ontog{\'e}niques et le recrutement dans une zone de r{\'e}serve et dans une zone sans protection. Nous montrons que les caract{\'e}ristiques d{\'e}mographiques et l'analyse de perturbation peuvent servir {\`a} pr{\'e}dire les changements du taux de croissance caus{\'e}s par un d{\'e}clin de la mortalit{\'e} des adultes associ{\'e} {\`a} la pr{\'e}sence d'une r{\'e}serve marine pour divers degr{\'e}s et types de dispersion. Les r{\'e}serves font augmenter le taux de croissance chez toutes les esp{\`e}ces, ...},
  number = {4},
  journal = {Canadian Journal of Fisheries and Aquatic Sciences},
  doi = {10.1139/f05-046},
  author = {Gerber, Leah R and Heppell, Selina S and Ballantyne, Ford and Sala, Enric},
  month = apr,
  year = {2005},
  pages = {863-871}
}

@article{sala2002,
  title = {A {{General Model}} for {{Designing Networks}} of {{Marine Reserves}}},
  volume = {298},
  issn = {0036-8075, 1095-9203},
  abstract = {There is debate concerning the most effective conservation of marine biodiversity, especially regarding the appropriate location, size, and connectivity of marine reserves. We describe a means of establishing marine reserve networks by using optimization algorithms and multiple levels of information on biodiversity, ecological processes (spawning, recruitment, and larval connectivity), and socioeconomic factors in the Gulf of California. A network covering 40\% of rocky reef habitat can fulfill many conservation goals while reducing social conflict. This quantitative approach provides a powerful tool for decision-makers tasked with siting marine reserves.},
  language = {en},
  number = {5600},
  journal = {Science},
  doi = {10.1126/science.1075284},
  author = {Sala, Enric and {Aburto-Oropeza}, Octavio and Paredes, Gustavo and Parra, Ivan and Barrera, Juan C. and Dayton, Paul K.},
  month = jun,
  year = {2002},
  pages = {1991-1993},
  pmid = {12471258}
}

@article{rassweiler2012,
  title = {Marine Protected Areas and the Value of Spatially Optimized Fishery Management},
  volume = {109},
  issn = {0027-8424, 1091-6490},
  abstract = {There is a growing focus around the world on marine spatial planning, including spatial fisheries management. Some spatial management approaches are quite blunt, as when marine protected areas (MPAs) are established to restrict fishing in specific locations. Other management tools, such as zoning or spatial user rights, will affect the distribution of fishing effort in a more nuanced manner. Considerable research has focused on the ability of MPAs to increase fishery returns, but the potential for the broader class of spatial management approaches to outperform MPAs has received far less attention. We use bioeconomic models of seven nearshore fisheries in Southern California to explore the value of optimized spatial management in which the distribution of fishing is chosen to maximize profits. We show that fully optimized spatial management can substantially increase fishery profits relative to optimal nonspatial management but that the magnitude of this increase depends on characteristics of the fishing fleet and target species. Strategically placed MPAs can also increase profits substantially compared with nonspatial management, particularly if fishing costs are low, although profit increases available through optimal MPA-based management are roughly half those from fully optimized spatial management. However, if the same total area is protected by randomly placing MPAs, starkly contrasting results emerge: most random MPA designs reduce expected profits. The high value of spatial management estimated here supports continued interest in spatially explicit fisheries regulations but emphasizes that predicted increases in profits can only be achieved if the fishery is well understood and the regulations are strategically designed.},
  language = {en},
  number = {29},
  journal = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1116193109},
  author = {Rassweiler, Andrew and Costello, Christopher and Siegel, David A.},
  month = jul,
  year = {2012},
  keywords = {reserve network design,spatial ecology,ecological modeling},
  pages = {11884-11889},
  pmid = {22753469}
}

@article{costello2010,
  title = {The Value of Spatial Information in {{MPA}} Network Design},
  volume = {107},
  issn = {0027-8424, 1091-6490},
  abstract = {The science of spatial fisheries management, which combines ecology, oceanography, and economics, has matured significantly. As a result, there have been recent advances in exploiting spatially explicit data to develop spatially explicit management policies, such as networks of marine protected areas (MPAs). However, when data are sparse, spatially explicit policies become less viable, and we must instead rely on blunt policies such as total allowable catches or imprecisely configured networks of MPAs. Therefore, spatial information has the potential to change management approaches and thus has value. We develop a general framework within which to analyze the value of information for spatial fisheries management and apply that framework to several US Pacific coast fisheries. We find that improved spatial information can increase fishery value significantly ({$>$}10\% in our simulations), and that it changes dramatically the efficient management approach\textemdash{}switching from diffuse effort everywhere to a strategy where fishing is spatially targeted, with some areas under intensive harvest and others closed to fishing. Using all available information, even when incomplete, is essential to management success and may as much as double fishery value relative to using (admittedly incorrect) assumptions commonly invoked.},
  language = {en},
  number = {43},
  journal = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.0908057107},
  author = {Costello, Christopher and Rassweiler, Andrew and Siegel, David and Leo, Giulio De and Micheli, Fiorenza and Rosenberg, Andrew},
  month = oct,
  year = {2010},
  keywords = {fisheries management,dispersal kernel,value of information},
  pages = {18294-18299},
  pmid = {20176962}
}

@article{gerber2003,
  title = {Population {{Models For Marine Reserve Design}}: {{A Retrospective And Prospective Synthesis}}},
  volume = {13},
  issn = {1051-0761},
  shorttitle = {{{POPULATION MODELS FOR MARINE RESERVE DESIGN}}},
  abstract = {We synthesize results from existing models of marine reserves to identify key theoretical issues that appear to be well understood, as well as issues in need of further exploration. Models of marine reserves are relatively new in the scientific literature; 32 of the 34 theoretical papers we reviewed were published after 1990. These models have focused primarily on questions concerning fishery management at the expense of other objectives such as conservation, scientific understanding, recreation, education, and tourism. Roughly one-third of the models analyze effects on cohorts while the remaining models have some form of complete population dynamics. Few models explicitly include larval dispersal. In a fisheries context, the primary conclusion drawn by many of the complete population models is that reserves increase yield when populations would otherwise be overfished. A second conclusion, resulting primarily from single-cohort models, is that reserves will provide fewer benefits for species with greater adult rates of movement. Although some models are beginning to yield information on the spatial configurations of reserves required for populations with specific dispersal distances to persist, it remains an aspect of reserve design in need of further analysis. Other outstanding issues include the effects of (1) particular forms of density dependence, (2) multispecies interactions, (3) fisher behavior, and (4) effects of concentrated fishing on habitat. Model results indicate that marine reserves could play a beneficial role in the protection of marine systems against overfishing. Additional modeling and analysis will greatly improve prospects for a better understanding of the potential of marine reserves for conserving biodiversity.},
  number = {sp1},
  journal = {Ecological Applications},
  doi = {10.1890/1051-0761(2003)013[0047:PMFMRD]2.0.CO;2},
  author = {Gerber, Leah R. and Botsford, Louis W. and Hastings, Alan and Possingham, Hugh P. and Gaines, Steven D. and Palumbi, Stephen R. and Andelman, Sandy},
  month = feb,
  year = {2003},
  keywords = {marine protected area,conservation,biodiversity,population model,density dependence,larval pool,migration,spatial harvest,stochasticity,yield per recruit},
  pages = {47-64}
}

@article{ricker1954,
  title = {Stock and {{Recruitment}}},
  volume = {11},
  issn = {0015-296X},
  abstract = {Plotting net reproduction (reproductive potential of the adults obtained) against the density of stock which produced them, for a number of fish and invertebrate populations, gives a domed curve whose apex lies above the line representing replacement reproduction. At stock densities beyond the apex, reproduction declines either gradually or abruptly. This decline gives a population a tendency to oscillate in numbers; however, the oscillations are damped, not permanent, unless reproduction decreases quite rapidly and there is not too much mixing of generations in the breeding population. Removal of part of the adult stock reduces the amplitude of oscillations that may be in progress and, up to a point, increases reproduction., non disponible},
  number = {5},
  journal = {Journal of the Fisheries Research Board of Canada},
  doi = {10.1139/f54-039},
  author = {Ricker, W. E.},
  month = may,
  year = {1954},
  pages = {559-623}
}

@book{beverton1956,
  title = {On the {{Dynamics}} of {{Exploited Fish Populations}}},
  isbn = {978-0-412-54960-1},
  abstract = {This classic book reprint has become the most widely cited fisheries book ever published. Still containing current information, this book should appear on the shelves of all fisheries scientists throughout the world.},
  language = {en},
  publisher = {{Springer}},
  author = {Beverton, Raymond J. H. and Holt, Sidney J.},
  year = {1956},
  keywords = {Science / Life Sciences / Ecology,Nature / Ecosystems \& Habitats / Lakes; Ponds \& Swamps,Science / Environmental Science,Science / Life Sciences / Evolution,Technology \& Engineering / Environmental / General}
}

@article{clark2002,
  title = {F 35\% {{Revisited Ten Years Later}}},
  volume = {22},
  issn = {0275-5947},
  abstract = {This paper reviews the original derivation of the F 35\% (later F 40\%) harvest strategy, which consists of fishing at a rate that reduces spawning biomass per recruit to 35\% (or 40\%) of the unfished value, and investigates its applicability to long-lived stocks with low resiliency, such as some of the Pacific Coast rockfishes Sebastes spp. The life history parameters are unimportant (at least in deterministic calculations), but the possibility of extremely low levels of resiliency\textemdash{}well below the bounds of the original analysis\textemdash{}does render the strategy unworkable in the sense that there is no harvest rate that will obtain a large fraction of the maximum sustainable yield (MSY) across the entire range of possibilities. At low but still workable levels of resiliency, the F 40\% strategy results in undesirably low levels of biomass and recruitment by present-day standards. That can be cured by adopting a higher target for spawning biomass per recruit, though at some cost in yield. A purely biomass-based strategy and a modified F MSY strategy are discussed as alternatives for cases where adequate historical data are available.},
  number = {1},
  journal = {North American Journal of Fisheries Management},
  doi = {10.1577/1548-8675(2002)022<0251:FRTYL>2.0.CO;2},
  author = {Clark, William G.},
  month = feb,
  year = {2002},
  pages = {251-257}
}

@article{starr2015,
  title = {Variation in {{Responses}} of {{Fishes}} across {{Multiple Reserves}} within a {{Network}} of {{Marine Protected Areas}} in {{Temperate Waters}}},
  volume = {10},
  abstract = {Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic regime, and time since the reserve was implemented. We conducted collaborative, fishery-independent surveys of fishes for seven years in and near newly created marine protected areas (MPAs) in central California, USA. Results showed that initially most MPAs contained more and larger fishes than associated reference sites, likely due to differences in habitat quality. The differences between MPAs and reference sites did not greatly change over the seven years of our study, indicating that reserve benefits will be slow to accumulate in California's temperate eastern boundary current. Fishes in an older reserve that has been closed to fishing since 1973, however, were significantly more abundant and larger than those in associated reference sites. This indicates that reserve benefits are likely to accrue in the California Current ecosystem, but that 20 years or more may be needed to detect significant changes in response variables that are due to MPA implementation. Because of the high spatial and temporal variability of fish recruitment patterns, long-term monitoring is needed to identify positive responses of fishes to protection in the diverse set of habitats in a dynamic eastern boundary current. Qualitative estimates of response variables, such as would be obtained from an expert opinion process, are unlikely to provide an accurate description of MPA performance. Similarly, using one species or one MPA as an indicator is unlikely to provide sufficient resolution to accurately describe the performance of multiple MPAs.},
  number = {3},
  journal = {PLoS ONE},
  doi = {10.1371/journal.pone.0118502},
  author = {Starr, Richard M. and Wendt, Dean E. and Barnes, Cheryl L. and Marks, Corina I. and Malone, Dan and Waltz, Grant and Schmidt, Katherine T. and Chiu, Jennifer and Launer, Andrea L. and Hall, Nathan C. and Yochum, No{\"e}lle},
  month = mar,
  year = {2015},
  pages = {e0118502}
}

@article{fletcher2014,
  title = {Large-Scale Expansion of No-Take Closures within the {{Great Barrier Reef}} Has Not Enhanced Fishery Production.},
  issn = {1051-0761},
  abstract = {A rare opportunity to test hypotheses about potential fishery benefits of large-scale closures was initiated in July 2004 when an additional 28.4\% of the 348,000 km2 Great Barrier Reef (GBR) region of Queensland, Australia was closed to all fishing.  Advice to the Australian and Queensland governments that supported this initiative predicted these additional closures would generate minimal (10\%) initial reductions in both catch and landed value within the GBR area with recovery of catches becoming apparent after three years.  To test these predictions, commercial fisheries data from the GBR area and from the two adjacent (non-GBR) areas of Queensland were compared for the periods immediately prior to, and after the closures were implemented. The observed means for total annual catch and value within the GBR declined from pre-closure (2000-2003) levels of 12,780t and \$160 million, to initial post-closure (2005-2008) levels of 8,143t and \$102 million; decreases of 35\% and 36\% respectively.  Because the reference areas in the non-GBR had minimal changes in catch and value, the beyond-BACI analyses estimated initial net-reductions within the GBR of 35\% for both total catch and value.  There was no evidence of recovery in total catch levels or any comparative improvement in catch-rates within the GBR nine years after implementation.  These results are not consistent with the advice to governments that the closures would have minimal initial impacts and rapidly generate benefits to fisheries in the GBR through increased juvenile recruitment and adult 'spillovers'.  Instead, the absence of evidence of recovery in catches or catch-rates to date currently support an alternative hypothesis that where there is already effective fisheries management, the closing of areas to all fishing will generate reductions in overall catches similar to the percentage of the fished area that is closed.},
  journal = {Ecological Applications},
  doi = {10.1890/14-1427.1},
  author = {Fletcher, Warrick Jeffrey and Kearney, Robert E. and Wise, Brent S. and Nash, Warwick J.},
  month = dec,
  year = {2014}
}

@article{caselle2015,
  title = {Recovery Trajectories of Kelp Forest Animals Are Rapid yet Spatially Variable across a Network of Temperate Marine Protected Areas.},
  volume = {5},
  journal = {Scientific reports},
  author = {Caselle, Jennifer E. and Rassweiler, Andrew and Hamilton, Scott L. and Warner, Robert R.},
  year = {2015},
  pages = {14102}
}

@article{thorson2012,
  title = {Spawning Biomass Reference Points for Exploited Marine Fishes, Incorporating Taxonomic and Body Size Information},
  volume = {69},
  issn = {0706-652X},
  abstract = {Surplus production represents the processes that affect sustainable fishery harvest and is central to the ecology and management of marine fishes. Taxonomy and life history influence the ratio of spawning biomass at maximum sustainable yield to average unfished spawning biomass (SBMSY/SB0), and estimating this ratio for individual stocks is notoriously difficult. We use a database of published landings data and stock assessment biomass estimates and determine that process errors predominate in this data set by fitting a state\textendash{}space model to data from each stock individually. We then fit multispecies process-error models while treating SBMSY/SB0 as a random effect that varies by taxonomic order and maximum length. The estimated SBMSY/SB0~= 0.40 for all 147 stocks is intermediate between the values assumed by the Fox and the Schaefer models, although Clupeiformes and Perciformes have lower and Gadiformes and Scorpaeniformes have higher SBMSY/SB0 values. Model selection supports the hypothesis that large-bod..., La production exc{\'e}dentaire repr{\'e}sente les processus qui ont une incidence sur la r{\'e}colte de poissons durable et est un {\'e}l{\'e}ment cl{\'e} de l'{\'e}cologie et de la gestion des poissons marins. La taxonomie et le cycle biologique influencent le rapport entre la biomasse f{\'e}conde correspondant au rendement maximum durable et la biomasse f{\'e}conde non exploit{\'e}e moyenne (SBMSY/SB0), l'estimation de ce rapport pour des stocks donn{\'e}s {\'e}tant particuli{\`e}rement difficile. Nous utilisons une base de donn{\'e}es sur les d{\'e}barquements publi{\'e}es et des estimations de la biomasse reposant sur des {\'e}valuations des stocks et d{\'e}terminons, en ajustant un mod{\`e}le d'espace d'{\'e}tats aux donn{\'e}es pour chaque stock pris individuellement, que les erreurs de traitement dominent dans cette base de donn{\'e}es. Nous ajustons ensuite des mod{\`e}les multi-esp{\`e}ces d'erreur de traitement en traitant le rapport SBMSY/SB0 comme s'il s'agissait d'un effet al{\'e}atoire qui varie selon l'ordre taxonomique et la longueur maximum. La valeur de SBMSY/SB0~= 0,40 estim{\'e}e pour le...},
  number = {9},
  journal = {Canadian Journal of Fisheries and Aquatic Sciences},
  doi = {10.1139/f2012-077},
  author = {Thorson, James T. and Cope, Jason M. and Branch, Trevor A. and Jensen, Olaf P.},
  month = aug,
  year = {2012},
  pages = {1556-1568}
}

@article{halpern2003,
  title = {The Impact of Marine Reserves: Do Reserves Work and Does Reserve Size Matter?},
  volume = {13},
  issn = {1051-0761},
  shorttitle = {{{THE IMPACT OF MARINE RESERVES}}},
  abstract = {Marine reserves are quickly gaining popularity as a management option for marine conservation, fisheries, and other human uses of the oceans. Despite the popularity of marine reserves as a management tool, few reserves appear to have been created or designed with an understanding of how reserves affect biological factors or how reserves can be designed to meet biological goals more effectively (e.g., attaining sustainable fish populations). This shortcoming occurs in part because the many studies that have examined the impacts of reserves on marine organisms remain isolated examples or anecdotes; the results of these many studies have not yet been synthesized. Here, I review the empirical work and discuss the theoretical literature to assess the impacts of marine reserves on several biological measures (density, biomass, size of organisms, and diversity), paying particular attention to the role reserve size has in determining those impacts. The results of 89 separate studies show that, on average, with the exception of invertebrate biomass and size, values for all four biological measures are significantly higher inside reserves compared to outside (or after reserve establishment vs. before) when evaluated for both the overall communities and by each functional group within these communities (carnivorous fishes, herbivorous fishes, planktivorous fishes/invertebrate eaters, and invertebrates). Surprisingly, results also show that the relative impacts of reserves, such as the proportional differences in density or biomass, are independent of reserve size, suggesting that the effects of marine reserves increase directly rather than proportionally with the size of a reserve. However, equal relative differences in biological measures between small and large reserves nearly always translate into greater absolute differences for larger reserves, and so larger reserves may be necessary to meet the goals set for marine reserves. The quality of the data in the reviewed studies varied greatly. To improve data quality in the future, whenever possible, studies should take measurements before and after the creation of a reserve, replicate sampling, and include a suite of representative species. Despite the variable quality of the data, the results from this review suggest that nearly any marine habitat can benefit from the implementation of a reserve. Success of a marine reserve, however, will always be judged against the expectations for that reserve, and so we must keep in mind the goals of a reserve in its design, management, and evaluation.},
  number = {sp1},
  journal = {Ecological Applications},
  doi = {10.1890/1051-0761(2003)013[0117:TIOMRD]2.0.CO;2},
  author = {Halpern, Benjamin S.},
  month = feb,
  year = {2003},
  keywords = {Marine reserves,reserve design,trophic cascades,reserve effect,reserve size},
  pages = {117-137}
}

@article{hilborn2014,
  title = {Reflections on the Success of Traditional Fisheries Management},
  volume = {71},
  copyright = {All rights reserved},
  issn = {1054-3139, 1095-9289},
  abstract = {The argument persists that the continued overexploitation by many fisheries around the world is evidence that current approaches to fisheries management are failing, and that more precautionary management approaches are needed. We review the available estimates of the status of fish stocks from three sources: the FAO's ``State of Marine Resources'', a database on scientific stock assessments, and recent estimates from statistical models designed to determine the status of unassessed fish stocks. The two key results are (i) that stocks that are scientifically assessed are in better shape and indeed are not typically declining but rebuilding, and (ii) that large stocks appear to be in better shape than small stocks. These results support the view that stocks that are managed are improving, while stocks that are not managed are not. Large stocks receive far more management attention than small stocks in jurisdictions that have active fisheries management systems, and most unassessed stocks are simply not managed. We assert that fisheries management as currently practised can (and often does) lead to sustainable fisheries, and what is needed is to actively manage the unassessed fisheries of the world. More precautionary management is not necessarily needed to ensure the sustainability of managed fisheries.},
  language = {en},
  number = {5},
  journal = {ICES Journal of Marine Science: Journal du Conseil},
  doi = {10.1093/icesjms/fsu034},
  author = {Hilborn, Ray and Ovando, Daniel},
  month = jan,
  year = {2014},
  keywords = {overfishing,fisheries management,stock status,precautionary management,sustainable fishing},
  pages = {1040-1046}
}

@book{hilborn1992,
  title = {Quantitative {{Fisheries Stock Assessment}}: {{Choice}}, {{Dynamics}} and {{Uncertainty}}},
  isbn = {978-1-4615-3598-0},
  shorttitle = {Quantitative {{Fisheries Stock Assessment}}},
  abstract = {This book really began in 1980 with our first microcomputer, an Apple II +. The great value of the Apple II + was that we could take the computer programs we had been building on mainframe and mini-computers, and make them available to the many fisheries biologists who also had Apple II + 's. About 6 months after we got our first Apple, John Glaister came through Vancouver and saw what we were doing and realized that his agency (New South Wales State Fisheries) had the same equipment and could run the same programs. John organized a training course in Australia where we showed about 25 Australian fisheries biologists how to use microcomputers to do many standard fisheries analyses. In the process of organizing this and sub sequent courses we developed a series of lecture notes. Over the last 10 years these notes have evolved into the chapters of this book.},
  language = {en},
  publisher = {{Springer Science \& Business Media}},
  author = {Hilborn, R. and Walters, C. J.},
  year = {1992},
  keywords = {Science / Life Sciences / Ecology,Mathematics / Probability \& Statistics / General,Science / Life Sciences / Zoology / General,Technology \& Engineering / Food Science}
}

@article{szuwalski2015,
  title = {Environment Drives Forage Fish Productivity},
  issn = {0027-8424, 1091-6490},
  abstract = {Extract
Understanding the interaction between fishing and natural variations in productivity is a central question in fisheries management. Essington et al. (1) advance the discussion on drivers of forage fish dynamics by highlighting the role of natural decreases in biomass collapses. A key conclusion of their work is that fishing increases the magnitude and frequency of collapse in biomass. More intense fishing necessarily results in fewer fish; however, the higher exploitation rates commonly seen as forage fish biomass declines do not always mean that fishing precipitated collapses in productivity.},
  language = {en},
  journal = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1507990112},
  author = {Szuwalski, Cody S. and Hilborn, Ray},
  month = jun,
  year = {2015},
  pages = {201507990},
  pmid = {26048908}
}

@article{grafton2000,
  title = {Private {{Property}} and {{Economic Efficiency}}: {{A Study}} of a {{Common}}-{{Pool Resource}}},
  volume = {43},
  issn = {0022-2186},
  shorttitle = {Private {{Property}} and {{Economic Efficiency}}},
  abstract = {Abstract The British Columbia halibut fishery provides a natural experiment of the effects of ``privatizing the commons.'' Using firm-level data from the fishery 2 years before private harvesting rights were introduced, the year they were implemented, and 3 years afterward, a stochastic frontier is estimated to test for changes in technical, allocative, and economic efficiency. The study indicates that (1) the short-run efficiency gains from privatization may take several years to materialize and can be compromised by restrictions on transferability, duration, and divisibility of the property right; (2) substantial long-run gains in efficiency can be jeopardized by preexisting regulations and the bundling of the property right to the capital stock; and (3) the gains from privatization are not just in terms of cost efficiency but include important benefits in revenue and product form.},
  number = {2},
  journal = {The Journal of Law \& Economics},
  doi = {10.1086/467469},
  author = {Grafton, R. Quentin and Squires, Dale and Fox, Kevin J.},
  year = {2000},
  pages = {679-714}
}

@article{froese2004,
  title = {Keep It Simple: Three Indicators to Deal with Overfishing},
  volume = {5},
  issn = {1467-2979},
  shorttitle = {Keep It Simple},
  abstract = {Three simple fisheries indicators are presented: (i) percentage of mature fish in catch, with 100\% as target; (ii) percent of specimens with optimum length in catch, with 100\% as target; and (iii) percentage of `mega-spawners` in catch, with 0\% as target, and 30\textendash{}40\% as representative of reasonable stock structure if no upper size limit exists. Application of these indicators to stocks of Gadus morhua, Sardinella aurita and Epinephelus aeneus demonstrate their usefulness. It is argued that such simple indicators have the potential to allow more stakeholders such as fishers, fish dealers, supermarket managers, consumers and politicians to participate in fisheries management and eventually hold and reverse the global pattern of convenience overfishing, which is defined here as deliberate overfishing sanctioned by official bodies who find it more convenient to risk eventual collapse of fish stocks than to risk social and political conflicts.},
  language = {en},
  number = {1},
  journal = {Fish and Fisheries},
  doi = {10.1111/j.1467-2979.2004.00144.x},
  author = {Froese, Rainer},
  month = mar,
  year = {2004},
  keywords = {overfishing,sustainable fishing,fisheries indicators,length at first maturity,longevity,optimum length},
  pages = {86-91}
}

@article{little2011,
  title = {Development and Evaluation of a Cpue-Based Harvest Control Rule for the Southern and Eastern Scalefish and Shark Fishery of {{Australia}}},
  issn = {1054-3139, 1095-9289},
  abstract = {Little, L. R., Wayte, S. E., Tuck, G. N., Smith, A. D. M., Klaer, N., Haddon, M., Punt, A. E., Thomson, R., Day, J., and Fuller, M. Development and evaluation of a cpue-based harvest control rule for the southern and eastern scalefish and shark fishery of Australia. \textendash{} ICES Journal of Marine Science, doi:10.1093/icesjms/fsr019 Many fishery management agencies are adopting harvest control rules (HCRs) to achieve harvest policies and management objectives. HCRs, however, often require data-intensive stock assessments to facilitate the harvest prescription. An HCR based on catch and catch per unit effort (cpue) was developed for the southern and eastern scalefish and shark fishery of Australia, for stocks that lack the data needed to conduct a full statistical catch-at-age assessment. The HCR produces a recommended biological catch and is characterized by two parameters, target cpue and target catch, both derived from historical data. Simulation tests showed that the HCR could guide the stock to the desired state from different initial levels of depletion. However, the selection of parameter values for the HCR was critical. Achieving fishery objectives was difficult when the target catch was a function of recent catch, rather than data from a predefined historical reference period. Problems may also arise when specifying the reference period on which the HCR parameters are determined. The cpue-based HCR is a valuable tool for managing fisheries where monitoring and assessment activities are relatively expensive, or in general, where data are scarce.},
  language = {en},
  journal = {ICES Journal of Marine Science: Journal du Conseil},
  doi = {10.1093/icesjms/fsr019},
  author = {Little, L. Richard and Wayte, Sally E. and Tuck, Geoffrey N. and Smith, Anthony D. M. and Klaer, Neil and Haddon, Malcolm and Punt, Andr{\'e} E. and Thomson, Robin and Day, Jemery and Fuller, Mike},
  month = mar,
  year = {2011},
  keywords = {Management strategy evaluation,Harvest control rule,cpue,Simulation,Australia},
  pages = {fsr019}
}

@article{airame2003,
  title = {Applying {{Ecological Criteria}} to {{Marine Reserve Design}}: {{A Case Study}} from the {{California Channel Islands}}},
  volume = {13},
  issn = {1939-5582},
  shorttitle = {Applying {{Ecological Criteria}} to {{Marine Reserve Design}}},
  abstract = {Using ecological criteria as a theoretical framework, we describe the steps involved in designing a network of marine reserves for conservation and fisheries management. Although we describe the case study of the Channel Islands, the approach to marine reserve design may be effective in other regions where traditional management alone does not sustain marine resources. A group of agencies, organizations, and individuals established clear goals for marine reserves in the Channel Islands, including conservation of ecosystem biodiversity, sustainable fisheries, economic viability, natural and cultural heritage, and education. Given the constraints of risk management, experimental design, monitoring, and enforcement, scientists recommended at least one, but no more than four, reserves in each biogeographic region. In general, the percentage of an area to be included in a reserve network depends on the goals. In the Channel Islands, after consideration of both conservation goals and the risk from human threats and natural catastrophes, scientists recommended reserving an area of 30\textendash{}50\% of all representative habitats in each biogeographic region. For most species of concern, except pinnipeds and seabirds, information about distributions, dispersal, and population growth was limited. As an alternative to species distribution information, suitable habitats for species of concern were used to locate potential reserve sites. We used a simulated annealing algorithm to identify potential reserve network scenarios that would represent all habitats within the smallest area possible. The analysis produced an array of potential reserve network scenarios that all met the established goals.},
  language = {en},
  number = {sp1},
  journal = {Ecological Applications},
  doi = {10.1890/1051-0761(2003)013[0170:AECTMR]2.0.CO;2},
  author = {Airam{\'e}, Satie and Dugan, Jenifer E. and Lafferty, Kevin D. and Leslie, Heather and McArdle, Deborah A. and Warner, Robert R.},
  month = feb,
  year = {2003},
  keywords = {habitat,fisheries management,Marine reserves,simulated annealing,Connectivity,MPA,biogeography,reserve size,Channel Islands,ecological linkages},
  pages = {170-184}
}

@article{gordon1954,
  title = {The Economic Theory of a Common-Property Resource: {{The}} Fishery},
  volume = {62},
  shorttitle = {{{THE ECONOMIC THEORY OF A COMMON}}-{{PROPERTY RESOURCE}}},
  number = {2},
  journal = {The Journal of Political Economy},
  author = {Gordon, H. Scott},
  year = {1954},
  pages = {124--142}
}

@article{costello2008,
  title = {Can {{Catch Shares Prevent Fisheries Collapse}}?},
  volume = {321},
  issn = {0036-8075, 1095-9203},
  abstract = {Recent reports suggest that most of the world's commercial fisheries could collapse within decades. Although poor fisheries governance is often implicated, evaluation of solutions remains rare. Bioeconomic theory and case studies suggest that rights-based catch shares can provide individual incentives for sustainable harvest that is less prone to collapse. To test whether catch-share fishery reforms achieve these hypothetical benefits, we have compiled a global database of fisheries institutions and catch statistics in 11,135 fisheries from 1950 to 2003. Implementation of catch shares halts, and even reverses, the global trend toward widespread collapse. Institutional change has the potential for greatly altering the future of global fisheries.},
  language = {en},
  number = {5896},
  journal = {Science},
  doi = {10.1126/science.1159478},
  author = {Costello, Christopher and Gaines, Steven D. and Lynham, John},
  month = sep,
  year = {2008},
  pages = {1678-1681},
  pmid = {18801999}
}

@article{melnychuk2016,
  title = {Reconstruction of Global Ex-Vessel Prices of Fished Species},
  issn = {1054-3139, 1095-9289},
  abstract = {Economic dimensions of global fishery analyses are often limited by unavailable or inconsistent ex-vessel price data from the world's fishing nations. We describe a novel method for estimating ex-vessel price time series for individual species by converting export prices of fishery commodities into ex-vessel prices and pairing these with species. The method relies exclusively on global, publicly-available data from the Food and Agricultural Organization of the United Nations (FAO). National datasets of ex-vessel prices are not used as inputs for the method, but comparisons of reconstructed ex-vessel prices with actual prices from national datasets showed strong correspondence. Correlation coefficients for paired reconstructed prices and actual prices of the same species were typically between 0.60 and 0.75 annually in the past two decades. There was a tendency for reconstructed prices to be less variable than actual prices, over-estimating actual prices at low values of actual prices and under-estimating actual prices at high values, likely the result of incomplete price transmission or assigning a given price time series to multiple species. However, there was no evidence of overall bias between reconstructed prices and actual prices, and correlations were strongest for comparisons involving multiple taxonomic groups. The method described carries advantages of global comprehensiveness and consistency across countries in reconstructed ex-vessel prices, reflecting the comprehensiveness and consistency of export price information. The method described links to species from the global FAO landings database, but can be modified to pair with other species lists or to focus on specific regions or countries. Data tables and source code are publicly available and ex-vessel price estimates can be updated annually following annual releases of the FAO fishery commodities database.},
  language = {en},
  journal = {ICES Journal of Marine Science: Journal du Conseil},
  doi = {10.1093/icesjms/fsw169},
  author = {Melnychuk, Michael C. and Clavelle, Tyler and Owashi, Brandon and Strauss, Kent},
  month = oct,
  year = {2016},
  keywords = {Environmental Economics,fish markets,fisheries revenue,landed value,price transmission,seafood trade.},
  pages = {fsw169}
}

@incollection{dowling2016,
  title = {{{FishPath}}: {{A Decision Support System}} for {{Assessing}} and {{Managing Data}}- and {{Capacity}}- {{Limited Fisheries}}},
  copyright = {All rights reserved},
  shorttitle = {{{FishPath}}},
  booktitle = {Assessing and {{Managing Data}}-{{Limited Fish Stocks}}},
  publisher = {{Alaska Sea Grant, University of Alaska Fairbansk}},
  author = {Dowling, Na and Wilson, Jr and Rudd, Mb and Babcock, Ea and Caillaux, M and Cope, J and Dougherty, D and Fujita, R and Gedamke, T and Gleason, M and Guttierrez, M and Hordyk, A and Maina, Gw and Mous, Pj and Ovando, D and Parma, Am and Prince, J and Revenga, C and Rude, J and Szuwalski, C and Valencia, S and Victor, S},
  editor = {Quinn II, Tj and Armstrong, Jl and Baker, Mr and Heifetz, J and Witherell, D},
  month = jun,
  year = {2016}
}

@article{costello2016,
  title = {Global Fishery Prospects under Contrasting Management Regimes},
  volume = {113},
  copyright = {All rights reserved},
  issn = {0027-8424, 1091-6490},
  abstract = {Data from 4,713 fisheries worldwide, representing 78\% of global reported fish catch, are analyzed to estimate the status, trends, and benefits of alternative approaches to recovering depleted fisheries. For each fishery, we estimate current biological status and forecast the impacts of contrasting management regimes on catch, profit, and biomass of fish in the sea. We estimate unique recovery targets and trajectories for each fishery, calculate the year-by-year effects of alternative recovery approaches, and model how alternative institutional reforms affect recovery outcomes. Current status is highly heterogeneous\textemdash{}the median fishery is in poor health (overfished, with further overfishing occurring), although 32\% of fisheries are in good biological, although not necessarily economic, condition. Our business-as-usual scenario projects further divergence and continued collapse for many of the world's fisheries. Applying sound management reforms to global fisheries in our dataset could generate annual increases exceeding 16 million metric tons (MMT) in catch, \$53 billion in profit, and 619 MMT in biomass relative to business as usual. We also find that, with appropriate reforms, recovery can happen quickly, with the median fishery taking under 10 y to reach recovery targets. Our results show that commonsense reforms to fishery management would dramatically improve overall fish abundance while increasing food security and profits.},
  language = {en},
  number = {18},
  journal = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1520420113},
  author = {Costello, Christopher and Ovando, Daniel and Clavelle, Tyler and Strauss, C. Kent and Hilborn, Ray and Melnychuk, Michael C. and Branch, Trevor A. and Gaines, Steven D. and Szuwalski, Cody S. and Cabral, Reniel B. and Rader, Douglas N. and Leland, Amanda},
  month = mar,
  year = {2016},
  keywords = {bioeconomic model,Rights-based fishery management,fishery recovery,fishery reform},
  pages = {5125-5129},
  pmid = {27035953}
}

@article{ovando2013,
  title = {Conservation Incentives and Collective Choices in Cooperative Fisheries},
  volume = {37},
  copyright = {All rights reserved},
  issn = {0308-597X},
  shorttitle = {Social and Cultural Impacts of Marine Fisheries},
  abstract = {Cooperatives are increasingly proposed as solutions for sustainable fisheries management. While individual case studies and economic theory suggest that cooperatives may manage fisheries effectively under some conditions, there is little empirical evidence comparing the actions of cooperative fisheries across a diverse set of environments. This study applies a standardized survey method to collect data from a set of cooperatively managed fisheries from around the globe, documenting their social, economic, and ecological settings as well as the cooperative behaviors in which they engage and the role they play in conservation. The resulting database covers 67 cooperatives from the major oceanic regions of the world, providing a unique overview of the global diversity of fishery cooperatives. It enables empirical analysis of the links between the characteristics and contexts of fisheries, such as the development status of the host nation, fisheries management practices, and species characteristics, and the collective actions taken by fishery cooperatives. The evidence shows that cooperatives form in a variety of development and governance contexts, and in diverse kinds of fisheries. Fishery cooperatives often take actions directed toward coordinating harvest activities, adopting and enforcing restrictions on fishing methods and effort, and taking direct conservation actions such as establishment of private marine protected areas.},
  number = {0},
  journal = {Marine Policy},
  doi = {10.1016/j.marpol.2012.03.012},
  author = {Ovando, Daniel A. and Deacon, Robert T. and Lester, Sarah E. and Costello, Christopher and Van Leuvan, Tonya and McIlwain, Karlynn and Strauss, Kent C. and Arbuckle, Michael and Fujita, Rod and Gelcich, Stefan and Uchida, Hirotsugu},
  month = jan,
  year = {2013},
  keywords = {fisheries management,conservation,Marine protected areas,Catch shares,Common pool resources,Cooperatives},
  pages = {132-140}
}

@article{stobart2009,
  title = {Long-Term and Spillover Effects of a Marine Protected Area on an Exploited Fish Community},
  volume = {384},
  issn = {0171-8630, 1616-1599},
  language = {en},
  journal = {Marine Ecology Progress Series},
  doi = {10.3354/meps08007},
  author = {Stobart, B and Warwick, R and Gonz{\'a}lez, C and Mallol, S and D{\'i}az, D and Re{\~n}ones, O and Go{\~n}i, R},
  month = may,
  year = {2009},
  pages = {47-60}
}

@article{mcclanahan2000,
  title = {Spillover of {{Exploitable Fishes}} from a {{Marine Park}} and {{Its Effect}} on the {{Adjacent Fishery}}},
  volume = {10},
  issn = {1939-5582},
  abstract = {The role of a marine protected area in enhancing local fisheries, through the emigration or spillover of exploitable fishes, was studied in a coral reef park (Mombasa Marine Park, Kenya) and fishery over a seven-year period during a time when the park's border changed and pull seines were eliminated. We measured catches before and after the park's establishment and during the management changes and compared these catches with the unmanaged side of the park. Additionally, we placed baited traps on both sides of the park over a full tidal cycle which allowed us to measure the spillover from the park compared to the deeper, rougher, and less fished reef edge. The total wet mass of catches per trap, the mean size of the trapped fish, and the number of fish species caught per trap declined as a function of the distance away from the park edge on both the southern and northern sides. However, this relationship was truncated on the unmanaged side which also had smaller catches, smaller fish, and fewer species than the managed side. Trap fishers on the managed side adapted to the spillover by increasing the traps per fisher, which had the effect of reducing the catch per trap. Tides and reef morphology also appeared to interact and influenced catches, but we found no relationships between catches and benthic substratum cover, which was usually dominated by seagrass and sand. Spillover from the deeper reef edge was evident for the managed but not the unmanaged side of the park, but may be due to differences in reef morphology interacting with tidal patterns rather than management. On the managed side, the park significantly increased the catch per fisher and catch per area by {$>$}50\%, but even after the park's size was reduced, the total catch was reduced by {$\sim$}30\%. The reduced park was still {$\sim$}50\% of the total area. Consequently, the catch per area increase was insufficient to compensate for the lost area over this early period of the park's establishment. Spillover was greatest for the dominant fisheries species. These were moderately vagile species in the rabbitfish (Siganidae; herbivores), emperors (Lethrinidae; carnivores), and surgeonfish (Acanthuridae; herbivores) families, which had instantaneous emigration rates from the park to the reserve fishing ground of {$\sim$}0.5. Our field survey, combined with previous modeling studies, based on adult emigration rates from marine reserves, suggests that tropical fisheries dominated by rabbitfish, emperors, and surgeonfish should be enhanced by closed areas of {$\sim$}10\textendash{}15\% of the total area. The optimal protected area may increase if larval export is important, but the predicted response should not be measurable for {$>$}10 years, beyond the length of our study, as breeding stock develop inside protected areas.},
  language = {en},
  number = {6},
  journal = {Ecological Applications},
  doi = {10.1890/1051-0761(2000)010[1792:SOEFFA]2.0.CO;2},
  author = {McClanahan, T. R. and Mangi, S.},
  month = dec,
  year = {2000},
  keywords = {dispersal,Marine protected areas,Coral reefs,Adaptive management,Acanthuridae,emigration rates,integrated coastal area management,Lethrinidae,marine fisheries reserves,Siganidae,tropical fisheries},
  pages = {1792-1805}
}

@article{palumbi2014,
  title = {Mechanisms of Reef Coral Resistance to Future Climate Change},
  volume = {344},
  copyright = {Copyright \textcopyright{} 2014, American Association for the Advancement of Science},
  issn = {0036-8075, 1095-9203},
  abstract = {Reef corals are highly sensitive to heat, yet populations resistant to climate change have recently been identified. To determine the mechanisms of temperature tolerance, we reciprocally transplanted corals between reef sites experiencing distinct temperature regimes and tested subsequent physiological and gene expression profiles. Local acclimatization and fixed effects, such as adaptation, contributed about equally to heat tolerance and are reflected in patterns of gene expression. In less than 2 years, acclimatization achieves the same heat tolerance that we would expect from strong natural selection over many generations for these long-lived organisms. Our results show both short-term acclimatory and longer-term adaptive acquisition of climate resistance. Adding these adaptive abilities to ecosystem models is likely to slow predictions of demise for coral reef ecosystems.
Hot and bothered corals can cope
How well can corals adapt to temperature extremes? Better than anticipated, it turns out. Corals from reef pools with wide temperature fluctuations resist stress better than corals from less extreme pools. Nevertheless, corals transplanted into the hotter and more variable conditions soon acquired thermal tolerance. Palumbi et al. (see the Perspective by Eakin) found that the tougher specimens produced more of certain proteins, such as the tumor necrosis factor receptor superfamily, which protected them from the effects of heat. Ramping up heat shock and transport proteins yielded heat tolerance far more rapidly than mutation and adaptation. Hopefully, this ability will allow some mitigation of climate change on coral reefs.
Science, this issue p. 895; see also p. 798.
The coral Acropora hyacinthus is capable of rapid acclimation to high temperatures [Also see Perspective by Eakin]
The coral Acropora hyacinthus is capable of rapid acclimation to high temperatures [Also see Perspective by Eakin]},
  language = {en},
  number = {6186},
  journal = {Science},
  doi = {10.1126/science.1251336},
  author = {Palumbi, Stephen R. and Barshis, Daniel J. and {Traylor-Knowles}, Nikki and Bay, Rachael A.},
  month = may,
  year = {2014},
  pages = {895-898},
  pmid = {24762535}
}

@article{shanks2003,
  title = {Propagule {{Dispersal Distance}} and the {{Size}} and {{Spacing}} of {{Marine Reserves}}},
  volume = {13},
  issn = {1939-5582},
  abstract = {This study compiled available information on the dispersal distance of the propagules of benthic marine organisms and used this information in the development of criteria for the design of marine reserves. Many benthic marine organisms release propagules that spend time in the water column before settlement. During this period, ocean currents transport or disperse the propagules. When considering the size of a marine reserve and the spacing between reserves, one must consider the distance which propagules disperse. We could find estimates of dispersal distance for 32 taxa; for 25 of these, we were also able to find data on the time the propagules spent dispersing. Dispersal distance ranged from meters to thousands of kilometers, and time in the plankton ranged from minutes to months. A significant positive correlation was found between the log-transformed duration in the plankton and the log-transformed dispersal distance (r = 0.7776, r2 = 0.60, df = 1, 25, P = 0.000); the more time propagules spend in the water column the further they tend to be dispersed. The frequency distribution of the log-transformed dispersal distance is bimodal (kurtosis = -1.29, t = -4.062, P {$<$} 0.001) with a gap between 1 and 20 km. Propagules that dispersed {$<$}1 km spent less time in the plankton ({$<$}100 h), or if they remained in the plankton for a longer period, they tended to remain in the waters near the bottom. Propagules that dispersed {$>$}20 km spent more than 300 h in the plankton. The bimodal nature of the distribution suggests that evolutionary constraints may reduce the likelihood of evolving mid-range dispersal strategies (i.e., dispersal between 1 and 20 km) resulting in two evolutionarily stable dispersal strategies: dispersal {$<$}1 km or {$>\sim$}20 km. We suggest that reserves be designed large enough to contain the short-distance dispersing propagules and be spaced far enough apart that long-distance dispersing propagules released from one reserve can settle in adjacent reserves. A reserve 4\textendash{}6 km in diameter should be large enough to contain the larvae of short-distance dispersers, and reserves spaced 10\textendash{}20 km apart should be close enough to capture propagules released from adjacent reserves.},
  language = {en},
  number = {sp1},
  journal = {Ecological Applications},
  doi = {10.1890/1051-0761(2003)013[0159:PDDATS]2.0.CO;2},
  author = {Shanks, Alan L. and Grantham, Brian A. and Carr, Mark H.},
  month = feb,
  year = {2003},
  keywords = {recruitment,marine protected area,dispersal,marine reserve,larvae,introduced species,plankton,propagules},
  pages = {159-169}
}

@book{ostrom1990,
  title = {Governing the {{Commons}}: {{The Evolution}} of {{Institutions}} for {{Collective Action}}},
  isbn = {978-0-521-40599-7},
  shorttitle = {Governing the {{Commons}}},
  abstract = {Congratulations to Elinor Ostrom, Co-Winner of The Sveriges Riksbank Prize in Economic Sciences in Memory of Alfred Nobel 2009! The governance of natural resources used by many individuals in common is an issue of increasing concern to policy analysts. Both state control and privatization of resources have been advocated, but neither the state nor the market have been uniformly successful in solving common pool resource problems. After critiquing the foundations of policy analysis as applied to natural resources, Elinor Ostrom here provides a unique body of empirical data to explore conditions under which common pool resource problems have been satisfactorily or unsatisfactorily solved. Dr. Ostrom first describes three models most frequently used as the foundation for recommending state or market solutions. She then outlines theoretical and empirical alternatives to these models in order to illustrate the diversity of possible solutions. In the following chapters she uses institutional analysis to examine different ways--both successful and unsuccessful--of governing the commons. In contrast to the proposition of the tragedy of the commons argument, common pool problems sometimes are solved by voluntary organizations rather than by a coercive state. Among the cases considered are communal tenure in meadows and forests, irrigation communities and other water rights, and fisheries.},
  language = {en},
  publisher = {{Cambridge University Press}},
  author = {Ostrom, Elinor},
  month = nov,
  year = {1990},
  keywords = {Political Science / General,Political Science / Public Policy / Economic Policy}
}

@article{allison1998,
  title = {Marine {{Reserves Are Necessary}} but {{Not Sufficient}} for {{Marine Conservation}}},
  volume = {8},
  issn = {1939-5582},
  abstract = {The intensity of human pressure on marine systems has led to a push for stronger marine conservation efforts. Recently, marine reserves have become one highly advocated form of marine conservation, and the number of newly designated reserves has increased dramatically. Reserves will be essential for conservation efforts because they can provide unique protection for critical areas, they can provide a spatial escape for intensely exploited species, and they can potentially act as buffers against some management miscalculations and unforeseen or unusual conditions. Reserve design and effectiveness can be dramatically improved by better use of existing scientific understanding. Reserves are insufficient protection alone, however, because they are not isolated from all critical impacts. Communities residing within marine reserves are strongly influenced by the highly variable conditions of the water masses that continuously flow through them. To a much greater degree than in terrestrial systems, the scales of fundamental processes, such as population replenishment, are often much larger than reserves can encompass. Further, they offer no protection from some important threats, such as contamination by chemicals. Therefore, without adequate protection of species and ecosystems outside reserves, effectiveness of reserves will be severely compromised. We outline conditions under which reserves are likely to be effective, provide some guidelines for increasing their conservation potential, and suggest some research priorities to fill critical information gaps. We strongly support vastly increasing the number and size of marine reserves; at the same time, strong conservation efforts outside reserves must complement this effort. To date, most reserve design and site selection have involved little scientific justification. They must begin to do so to increase the likelihood of attaining conservation objectives.},
  language = {en},
  number = {sp1},
  journal = {Ecological Applications},
  doi = {10.1890/1051-0761(1998)8[S79:MRANBN]2.0.CO;2},
  author = {Allison, Gary W. and Lubchenco, Jane and Carr, Mark H.},
  month = feb,
  year = {1998},
  keywords = {Marine protected areas,biodiversity,reserve design,harvest refugia,marine parks,open populations,population replenishment},
  pages = {S79-S92}
}

@techreport{costello2015,
  title = {Country-{{Level Costs}} vs. {{Benefits}} of {{Improved Fishery Management}}},
  author = {Costello, Christopher and Mangin, Tracey},
  year = {2015}
}

@article{wang2018,
  title = {Does More Fish Mean More Money? {{Evaluating}} Alternative Escapement Goals in the {{Bristol Bay}} Salmon Fishery},
  issn = {0706-652X},
  shorttitle = {Does More Fish Mean More Money?},
  abstract = {We develop an economically sophisticated management strategy evaluation for four sockeye salmon (Onchorhynchus nerka) fishing districts in Bristol Bay, Alaska, to evaluate whether proposed increases in escapement goals \textemdash{} the number of fish allowed up each river to spawn \textemdash{} could improve fishery outcomes for the industry and the region. Higher escapements increase average runs toward biological maximum sustainable yield, but this is driven by infrequent years of very abundant runs. Our economic model shows processors do not add capacity in response to infrequent abundant runs. Therefore, interannual variance in district-specific catch increases because years with little or no fishing become more frequent to meet higher escapement in low-run years, but industry cannot capture greater value in the high-run years. In abundant runs, processors shift available labor to focus on high-volume, lower-margin products; in very abundant years, insufficient processing capacity allows additional fish to escape. Mobile dr..., Nous d{\'e}veloppons une {\'e}valuation de strat{\'e}gies de gestion {\'e}conomiquement complexes pour quatre districts de p{\^e}che au saumon rouge (Onchorhynchus nerka) dans la baie de Bristol (Alaska) pour d{\'e}terminer si des augmentations propos{\'e}es des objectifs d'{\'e}chappement, soit le nombre de poissons qui peuvent remonter chaque cours d'eau pour frayer, pourraient am{\'e}liorer les r{\'e}sultats des p{\^e}ches pour l'industrie et la r{\'e}gion. Un plus grand {\'e}chappement accro{\^i}t les migrations moyennes qui contribuent au rendement {\'e}quilibr{\'e} maximal biologique, mais cela est principalement le fait d'ann{\'e}es peu fr{\'e}quentes de migrations tr{\`e}s abondantes. Notre mod{\`e}le {\'e}conomique montre que les transformateurs ne rehaussent pas leurs capacit{\'e}s en r{\'e}ponse {\`a} des migrations abondantes peu fr{\'e}quentes. La variance interannuelle des prises par district augmente donc parce que les ann{\'e}es o{\`u} il y a peu ou pas de p{\^e}che deviennent plus fr{\'e}quentes pour respecter les objectifs d'{\'e}chappement plus {\'e}lev{\'e}s durant les ann{\'e}es de faible migration, mais l'industr...},
  journal = {Canadian Journal of Fisheries and Aquatic Sciences},
  doi = {10.1139/cjfas-2017-0336},
  author = {Wang, Jocelyn Yun-Ling and Anderson, Christopher M. and Cunningham, Curry J. and Hilborn, Ray and Link, Michael R.},
  month = apr,
  year = {2018},
  pages = {1-15}
}

@article{dowling,
  title = {Generic Solutions for Data-Limited Fishery Assessments Are Not so Simple},
  volume = {0},
  copyright = {\textcopyright{} 2018 John Wiley \& Sons Ltd},
  issn = {1467-2979},
  abstract = {The majority of the world's fisheries, by number, are data-poor/limited, and there is a growing body of literature pertaining to approaches to estimate data-limited stock status. There are at least two drivers for assessing the status of data-limited fisheries. The first is to try to understand and report on the global or regional status of fisheries across many stocks. The second is to attempt to assess individual data-limited stocks, for status reporting and/or guiding management decisions. These drivers have led to attempts to find simple, generic, low-cost solutions, including the broad application of generically parameterised models, and the blanket application of a single, or limited number of possible, analytical approach(es). It is unclear that generic methods function as intended, especially when taken out of their original design context or used without care. If the intention is to resolve individual stock status for the purposes of management, there is concern with the indiscriminate application of a single method to a suite of stocks irrespective of the particular circumstances of each. We examine why caution needs to be exercised, and provide guidance on the appropriate application of data-limited assessment methods (DLMs). We recommend: (a) obtaining better data, (b) using care in acknowledging and interpreting uncertainties in the results of DLMs, (c) embedding DLMs in harvest strategies that are robust to the higher levels of uncertainty in the output of DLMs by including precautionary management measures or buffers and (d) selecting and applying DLMs appropriate to specific species' and fisheries' data and context.},
  language = {en},
  number = {0},
  journal = {Fish and Fisheries},
  doi = {10.1111/faf.12329},
  author = {Dowling, Natalie A. and Smith, Anthony D. M. and Smith, David C. and Parma, Ana M. and Dichmont, Catherine M. and Sainsbury, Keith and Wilson, Jono R. and Dougherty, Dawn T. and Cope, Jason M.},
  keywords = {stock status,data-limited stock assessment,data-poor}
}

@article{clements2018,
  title = {Predator in the {{Pool}}? {{A Quantitative Evaluation}} of {{Non}}-Indexed {{Open Access Journals}} in {{Aquaculture Research}}},
  volume = {5},
  issn = {2296-7745},
  shorttitle = {Predator in the {{Pool}}?},
  abstract = {Predatory open access (OA) journals can be defined as non-indexed journals that exploit the gold OA model for profit, often spamming academics with questionable e-mails promising rapid OA publication for a fee. In aquaculture \textendash{} a rapidly growing and highly scrutinized field \textendash{} the issue of such journals remains undocumented. We employed a quantitative approach to determine whether attributes of scientific quality and rigor differed between OA aquaculture journals not indexed in reputable databases and well-established, indexed journals. Using a Google search, we identified several non-indexed OA journals, gathered data on attributes of these journals and articles therein, and compared these data to well-established aquaculture journals indexed in quality-controlled bibliometric databases. We then used these data to determine if non-indexed journals were likely predatory OA journals and if they pose a potential threat to aquaculture research. On average, non-indexed OA journals published significantly fewer papers per year, had cheaper fees, and were more recently established than indexed journals. Articles in non-indexed journals were, on average, shorter, had fewer authors and references, and spent significantly less time in peer review than their indexed counterparts; the proportion of articles employing rigorous statistical analyses was also lower for non-indexed journals. Additionally, articles in non-indexed journals were more likely to be published by scientists from developing nations. Worryingly, non-indexed journals were more likely to be found using a Google search, and their articles superficially resembled those in indexed journals. These results suggest that the non-indexed aquaculture journals identified herein are likely predatory OA journals and pose a threat to aquaculture research and the public education and perception of aquaculture. There are several points of reference from this study that, in combination, may help scientists and the public more easily identify these possibly predatory journals typically were established after 2010, publishing {$<$}20 papers per year, had fees {$<\$$}1000, and published articles {$<$}80 days after submission. Subsequently checking reputable and quality-controlled databases such as the Directory of Open Access Journals, Web of Science, Scopus, and Thompson Reuters can aid in confirming the legitimacy of non-indexed OA journals and can facilitate avoidance of these aquaculture journals.},
  language = {English},
  journal = {Frontiers in Marine Science},
  doi = {10.3389/fmars.2018.00106},
  author = {Clements, Jeff C. and Daigle, R{\'e}mi M. and Froehlich, Halley E.},
  year = {2018},
  keywords = {Ethics,scientific publishing,Open access,journal selection,Peer Review,science communicaion}
}

@article{froehlich2018,
  title = {Comparative Terrestrial Feed and Land Use of an Aquaculture-Dominant World},
  copyright = {\textcopyright{} 2018 . Published under the PNAS license.},
  issn = {0027-8424, 1091-6490},
  abstract = {Reducing food production pressures on the environment while feeding an ever-growing human population is one of the grand challenges facing humanity. The magnitude of environmental impacts from food production, largely around land use, has motivated evaluation of the environmental and health benefits of shifting diets, typically away from meat toward other sources, including seafood. However, total global catch of wild seafood has remained relatively unchanged for the last two decades, suggesting increased demand for seafood will mostly have to rely on aquaculture (i.e., aquatic farming). Increasingly, cultivated aquatic species depend on feed inputs from agricultural sources, raising concerns around further straining crops and land use for feed. However, the relative impact and potential of aquaculture remains unclear. Here we simulate how different forms of aquaculture contribute and compare with feed and land use of terrestrial meat production and how spatial patterns might change by midcentury if diets move toward more cultured seafood and less meat. Using country-level aquatic and terrestrial data, we show that aquaculture requires less feed crops and land, even if over one-third of protein production comes from aquaculture by 2050. However, feed and land-sparing benefits are spatially heterogeneous, driven by differing patterns of production, trade, and feed composition. Ultimately, our study highlights the future potential and uncertainties of considering aquaculture in the portfolio of sustainability solutions around one of the largest anthropogenic impacts on the planet.},
  language = {en},
  journal = {Proceedings of the National Academy of Sciences},
  doi = {10.1073/pnas.1801692115},
  author = {Froehlich, Halley E. and Runge, Claire A. and Gentry, Rebecca R. and Gaines, Steven D. and Halpern, Benjamin S.},
  month = apr,
  year = {2018},
  keywords = {animal feed,aquatic farming,human diets,land use,livestock},
  pages = {201801692},
  pmid = {29712823}
}

@article{froehlich2018a,
  title = {Avoiding the Ecological Limits of Forage Fish for Fed Aquaculture},
  volume = {1},
  copyright = {2018 The Author(s)},
  issn = {2398-9629},
  abstract = {Aquaculture is surpassing wild-caught seafood, but we feed aquaculture with wild forage fish for key nutrients. This study finds removing such forage fish from diets of livestock and non-carnivorous aquaculture species and moderating its use in China will help sustain forage fish populations in the future.},
  language = {En},
  number = {6},
  journal = {Nature Sustainability},
  doi = {10.1038/s41893-018-0077-1},
  author = {Froehlich, Halley E. and Jacobsen, Nis Sand and Essington, Timothy E. and Clavelle, Tyler and Halpern, Benjamin S.},
  month = jun,
  year = {2018},
  pages = {298}
}

@article{froehlich2018b,
  title = {Global Change in Marine Aquaculture Production Potential under Climate Change},
  volume = {2},
  copyright = {2018 The Author(s), under exclusive licence to Springer Nature Limited},
  issn = {2397-334X},
  abstract = {Marine aquaculture is a rapidly growing global source of food, but is likely to be affected by climate change. Here, the effect of warming oceans on the production potential of 180 cultured finfish and bivalve species is mapped over the next century.},
  language = {En},
  number = {11},
  journal = {Nature Ecology \& Evolution},
  doi = {10.1038/s41559-018-0669-1},
  author = {Froehlich, Halley E. and Gentry, Rebecca R. and Halpern, Benjamin S.},
  month = nov,
  year = {2018},
  pages = {1745}
}

@article{stock,
  title = {The Utility of Spatial Model-Based Estimators of Unobserved Bycatch},
  abstract = {Abstract.  Quantifying effects of fishing on non-targeted (bycatch) species is an important management and conservation issue. Bycatch estimates are typically c},
  language = {en},
  journal = {ICES Journal of Marine Science},
  doi = {10.1093/icesjms/fsy153},
  author = {Stock, Brian C. and Ward, Eric J. and Thorson, James T. and Jannot, Jason E. and Semmens, Brice X.}
}

@article{myers_maximum_1999,
  title = {Maximum Reproductive Rate of Fish at Low Population Sizes},
  volume = {56},
  issn = {0706-652X},
  abstract = {We examine a database of over 700 spawner-recruitment series to search for parameters that are constant, or nearly so, at the level of a species or above. We find that the number of spawners produced per spawner each year at low populations, i.e., the maximum annual reproductive rate, is relatively constant within species and that there is relatively little variation among species. This quantity can be interpreted as a standardized slope at the origin of a spawner-recruitment function. We employ variance components models that assume that the log of the standardized slope at the origin is a normal random variable. This approach allows improved estimates of spawner-recruitment parameters, estimation of empirical prior distributions for Bayesian analysis, estimation of the biological limits of fishing, calculation of the maximum sustainable yield, and impact assessment of dams and pollution., Nous {\'e}tudions une base de donn{\'e}es comptant plus de 700 s{\'e}ries g{\'e}niteur-recrutement {\`a} la recherche de param{\`e}tres qui sont constants, ou presque, au niveau de l'esp{\`e}ce ou {\`a} un niveau hi{\'e}rarchique sup{\'e}rieur. Nous avons trouv{\'e} que le nombre de g{\'e}niteurs produits par g{\'e}niteur chaque ann{\'e}e dans des populations peu abondantes, c'est-{\`a}-dire le taux de reproduction annuel maximal, est relativement constant dans une esp{\`e}ce, et qu'il y a peu de variation d'une esp{\`e}ce {\`a} l'autre. Cette valeur peut {\^e}tre interpr{\'e}t{\'e}e comme une pente normalis{\'e}e {\`a} l'origine d'une fonction g{\'e}niteur-recrutement. Nous avons recours {\`a} des mod{\`e}les de composantes de la variance selon lesquels le log de la pente normalis{\'e}e {\`a} l'origine est une variable al{\'e}atoire normale. Cette approche permet d'obtenir de meilleures estimations des param{\`e}tres du rapport g{\'e}niteur-recrutement, une estimation des donn{\'e}es empiriques avant les r{\'e}partitions pour l'analyse bayesienne, une estimation des limites biologiques de la p{\^e}che, un calcul de la production maximale...},
  number = {12},
  journal = {Canadian Journal of Fisheries and Aquatic Sciences},
  doi = {10.1139/f99-201},
  author = {Myers, Ransom A and Bowen, Keith G and Barrowman, Nicholas J},
  month = dec,
  year = {1999},
  pages = {2404-2419}
}

@article{davis-stober2018,
  title = {Estimation Accuracy in the Psychological Sciences},
  volume = {13},
  issn = {1932-6203},
  abstract = {Sample means comparisons are a fundamental and ubiquitous approach to interpreting experimental psychological data. Yet, we argue that the sample and effect sizes in published psychological research are frequently so small that sample means are insufficiently accurate to determine whether treatment effects have occurred. Generally, an estimator should be more accurate than any benchmark that systematically ignores information about the relations among experimental conditions. We consider two such benchmark estimators: one that randomizes the relations among conditions and another that always assumes no treatment effects. We show conditions under which these benchmark estimators estimate the true parameters more accurately than sample means. This perverse situation can occur even when effects are statistically significant at traditional levels. Our argument motivates the need for regularized estimates, such as those used in lasso, ridge, and hierarchical Bayes techniques.},
  language = {en},
  number = {11},
  journal = {PLOS ONE},
  doi = {10.1371/journal.pone.0207239},
  author = {{Davis-Stober}, Clintin P. and Dana, Jason and Rouder, Jeffrey N.},
  month = nov,
  year = {2018},
  keywords = {Learning,Psychology,African American people,Equipment,Experimental psychology,Normal distribution,Psychologists,Scientists},
  pages = {e0207239}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

gha_license_id: MIT

extension: bib


text:
FILE(REMOVE_RECURSE
  "CMakeFiles/t3AlGloA1.dir/t3AlGloA1.cpp.o"
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  "../../../../bin/t3AlGloA1"
  "CMakeFiles/CMakeRelink.dir/t3AlGloA1.pdb"
  "CMakeFiles/CMakeRelink.dir/t3AlGloA1"
)

# Per-language clean rules from dependency scanning.
FOREACH(lang CXX)
  INCLUDE(CMakeFiles/t3AlGloA1.dir/cmake_clean_${lang}.cmake OPTIONAL)
ENDFOREACH(lang)

repository: bkahlert/seqan-research

repo_name: bkahlert/seqan-research

extension: cmake


text:
本科毕业论文（设计）参考文献式样

@article{ustc-bachelor:01,
  title = {网络时代经济发展战略特征},
  author = {刘文富 and 顾丽梅},
  year = {2000},
  journal = {学术研究},
  volume = {21},
  number = {4},
  pages = {35--40},
  url = {https://kns.cnki.net/kcms2/article/abstract?v=3uoqIhG8C44YLTlOAiTRKgchrJ08w1e79zTD32bjb4xSTlZqRyr7rTIf7ok1AFpatLUPx8UT1OWFBNkw65sK7Uwjbq66SQOt&uniplatform=NZKPT},
  langid = {chinese}
}

@book{ustc-bachelor:02,
  title = {知识时代的企业合作经营},
  author = {肖渡 and 沈群红 and 张芸 and 胡汉辉},
  year = {2000},
  pages = {67--69},
  publisher = {北京大学出版社},
  address = {北京},
  url = {https://book.douban.com/subject/1632549/},
  langid = {chinese}
}

@techreport{ustc-bachelor:03,
  title = {Technology for Economic Growth},
  author = {{The White House}},
  year = {1993},
  month = nov,
  address = {Washington},
  url = {https://clintonwhitehouse6.archives.gov/1993/11/1993-11-04-technology-for-economic-growth-table-of-contents.html},
  langid = {english}
}

@article{ustc-bachelor:04,
  title = {Vibrational Dependence of the Anisotropic Intermolecular Potential of Argon-Hydrogen Chloride},
  author = {Hutson, Jeremy M.},
  year = {1992},
  month = may,
  journal = {J. Phys. Chem.},
  volume = {96},
  number = {11},
  pages = {4237--4247},
  issn = {0022-3654},
  doi = {10.1021/j100190a026},
  url = {https://doi.org/10.1021/j100190a026},
  urldate = {2023-05-31},
  langid = {english}
}

repository: ustctug/ustcthesis

repo_name: ustctug/ustcthesis

gha_language: TeX


text:
@article{breaking-crypto-dl:prouff,
	author    = {Houssem Maghrebi and
	Thibault Portigliatti and
	Emmanuel Prouff},
	title     = {Breaking Cryptographic Implementations Using Deep Learning Techniques},
	journal   = {{IACR} Cryptology ePrint Archive},
	volume    = {2016},
	pages     = {921},
	year      = {2016},
	url       = {http://eprint.iacr.org/2016/921},
	timestamp = {Thu, 08 Jun 2017 14:26:37 +0200},
	biburl    = {http://dblp.uni-trier.de/rec/bib/journals/iacr/MaghrebiPP16},
	bibsource = {dblp computer science bibliography, http://dblp.org}
}
@techreport{first-sca:kocher,
	editor       = {{Paul C. Kocher}},
	TITLE        = {Timing Attacks on Implementations of Diffie-Hellman, RSA, DSS, and Other Systems},
	YEAR         = {1996},
	institution = {Cryptography Research, Inc.},
	address         = {607
	Market Street, 5th Floor, San Francisco, CA 94105, USA.}
}
@INPROCEEDINGS{nn-aes:gilmore,
	author={R. Gilmore and N. Hanley and M. O'Neill},
	booktitle={2015 IEEE International Symposium on Hardware Oriented Security and Trust (HOST)},
	title={Neural network based attack on a masked implementation of AES},
	year={2015},
	pages={106-111},
	keywords={cryptography;neural nets;pattern classification;principal component analysis;AES;Advanced Encryption Standard;DPA;PCA;cryptographic algorithms;differential power analysis contest data set;embedded cryptographic devices;machine learning;mask value identification;masked implementation;neural network based attack;principal component analysis;secret key value identification;side channel attacks;Artificial neural networks;Cryptography;Error analysis;Hardware;Power demand;Principal component analysis;Training;AES;SCA;machine learning;masking;neural network},
	doi={10.1109/HST.2015.7140247},
	month={May},}
@Inbook{sca-framework:standaert,
	author="Standaert, Fran{\c{c}}ois-Xavier
	and Malkin, Tal G.
	and Yung, Moti",
	editor="Joux, Antoine",
	title="A Unified Framework for the Analysis of Side-Channel Key Recovery Attacks",
	bookTitle="Advances in Cryptology - EUROCRYPT 2009: 28th Annual International Conference on the Theory and Applications of Cryptographic Techniques, Cologne, Germany, April 26-30, 2009. Proceedings",
	year="2009",
	publisher="Springer Berlin Heidelberg",
	address="Berlin, Heidelberg",
	pages="443--461",
	isbn="978-3-642-01001-9",
	doi="10.1007/978-3-642-01001-9_26",
	url="http://dx.doi.org/10.1007/978-3-642-01001-9_26"
}
@book{sca-design:mangard,
	title={Constructive Side-Channel Analysis and Secure Design: 6th International Workshop, COSADE 2015, Berlin, Germany, April 13-14, 2015. Revised Selected Papers},
	author={Mangard, S. and Poschmann, A.Y.},
	isbn={9783319214764},
	series={Lecture Notes in Computer Science},
	url={https://books.google.de/books?id=PFYwCgAAQBAJ},
	year={2015},
	publisher={Springer International Publishing}
}
@incollection{cnn-beats-svm:alex,
	title = {ImageNet Classification with Deep Convolutional Neural Networks},
	author = {Alex Krizhevsky and Sutskever, Ilya and Hinton, Geoffrey E},
	booktitle = {Advances in Neural Information Processing Systems 25},
	editor = {F. Pereira and C. J. C. Burges and L. Bottou and K. Q. Weinberger},
	pages = {1097--1105},
	year = {2012},
	publisher = {Curran Associates, Inc.},
	url = {http://papers.nips.cc/paper/4824-imagenet-classification-with-deep-convolutional-neural-networks.pdf}
}
@misc{aes:Rijndael_1999,
	author        = {Joan Daemen and Vincent Rijmen},
	howpublished  = {AES submission},
	title         = {AES Proposal: {{\sc Rijndael}}},
	note          = {\url{http://jda.noekeon.org/}},
	year          = {1999}
}
@misc{dpacv2:web,
	url = {http://www.dpacontest.org/v2/},
	year = {2009},
	author = {COMELEC, TELECOM ParisTech SEN research group},
}

repository: nimarb/deep-learning-sca-paper

repo_name: nimarb/deep-learning-sca-paper


text:
DESCRIPTION = "Simple helloworld scons application"
SECTION = "examples"
LICENSE = "MIT"
LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/MIT;md5=0835ade698e0bcf8506ecda2f7b4f302"

SRC_URI = "file://SConstruct \
           file://helloworld.c"

S = "${WORKDIR}"

inherit scons

EXTRA_OESCONS = ""

do_install() {
    install -d ${D}/${bindir}
    install -m 0755 helloworld ${D}${bindir}
}

extension: bb


text:
@article{Emori2015,
 abstract = {We present a simple technique using a cavity-based resonance spectrometer to quantify the anti-damping torque due to the spin Hall effect. Modification of ferromagnetic resonance is observed as a function of small DC current in sub-mm-wide strips of bilayers, consisting of magnetically soft FeGaB and strong spin-Hall metal Ta. From the detected current-induced linewidth change, we obtain an effective spin Hall angle of 0.08-0.09 independent of the magnetic layer thickness. Our results demonstrate that a sensitive resonance spectrometer can be a general tool to investigate spin Hall effects in various material systems, even those with vanishingly low conductivity and magnetoresistance.},
 author = {Emori, Satoru and Nan, Tianxiang and Oxholm, Trevor M. and Boone, Carl T. and Jones, John G. and Howe, Brandon M. and Brown, Gail J. and Budil, David E. and Sun, Nian X.},
 doi = {10.1063/1.4906062},
 file = {:Users/Tianxiang/Library/Application Support/Mendeley Desktop/Downloaded/Emori et al. - 2015 - Quantification of the spin-Hall anti-damping torque with a resonance spectrometer.pdf:pdf},
 issn = {00036951},
 journal = {Appl. Phys. Lett.},
 number = {2},
 pages = {022406},
 title = {Quantification of the spin-Hall anti-damping torque with a resonance spectrometer},
 url = {http://scitation.aip.org/content/aip/journal/apl/106/2/10.1063/1.4906062},
 volume = {106},
 year = {2015}
}


text:
@article{avl_tree,
  author       = {Adelson-Velskii, G. M. and Landis, E. M.},
  fjournal     = {Doklady Akademii Nauk SSSR},
  issn         = {0002-3264},
  journal = {Dokl. Akad. Nauk SSSR},
  mrclass      = {94.20},
  mrnumber     = {0156719},
  pages        = {263--266},
  title        = {An algorithm for organization of information},
  volume       = {146},
  year         = {1962},
}

@article{knott,
author = {Knott, G. D.},
doi = {10.1093/comjnl/18.3.265},
issn = {0010-4620},
journal = {The Computer Journal},
mendeley-groups = {Thesis},
number = {3},
pages = {265--278},
title = {{Hashing functions}},
url = {http://comjnl.oxfordjournals.org/content/18/3/265.short},
volume = {18},
year = {1975}
}

@book{cormen,
  author    = {Cormen, Thomas H. and Leiserson, Charles E. and Rivest, Ronald L. and Stein, Clifford},
  edition   = {3rd},
  isbn      = {9780262033848},
  publisher = {The MIT Press},
  title     = {Introduction to Algorithms, Third Edition},
  year      = {2009},
}

@book{knuth3,
 author = {Knuth, Donald E.},
 title = {The Art of Computer Programming,  Volume 3: (2Nd Ed.) Sorting and Searching},
 year = {1998},
 isbn = {0-201-89685-0},
 publisher = {Addison Wesley Longman Publishing Co., Inc.},
 address = {Redwood City, CA, USA},
}

@article{champ,
  author   = {Tamir, Orr and Morrison, Adam and Rinetzky, Noam},
  doi      = {10.4230/LIPIcs.OPODIS.2015.186},
  keywords = {4230,and phrases priority queues,changekey,concurrent data structures,digital object identifier 10,dijkstra,lipics,p,s,single-source shortest path algorithm,xxx,yyy},
  pages    = {1--16},
  title    = {{A Heap-Based Concurrent Priority Queue with Mutable Priorities for Faster Parallel Algorithms}},
  url      = {http://www.cs.tau.ac.il/~mad/publications/opodis2015-heap.pdf},
  volume   = {i},
  year = {1998},
  journal = {19th International Conference On Principles Of Distributed Systems}
}

@book{sedgewick,
  author    = {Sedgewick, Robert and Wayne, Kevin},
  edition   = {4},
  isbn      = {9780321573513},
  publisher = {Addison-Wesley},
  title     = {{Algorithms}},
  year      = {2011},
}

@misc{lfu,
  author = {Shah, Ketan and Mitra, Anirban and Matani, Dhruv},
  pages  = {1--8},
  title  = {{An (1) algorithm for implementing the LFU cache eviction scheme}},
  url    = {http://dhruvbird.com/lfu.pdf},
  year   = {2010},
  note   = {visited on 2017-05-03},
}

@article{concurrent_heap1,
  author       = {Hunt, Galen C. and Michael, Maged M. and Parthasarathy, Srinivasan and Scott, Michael L.},
  journal = {Information Processing Letters},
  pages        = {151--157},
  title        = {{An Efficient Algorithm for Concurrent Priority Queue Heaps}},
  url          = {http://www.research.ibm.com/people/m/michael/ipl-1996.pdf},
  volume       = {60},
  year         = {1996},
}

@misc{boost,
  author  = {Boost},
  title   = {{Boost C++ Libraries}},
  url     = {http://www.boost.org/},
  note    = {visited on 2017-05-03},
  year    = {2017},
}

@misc{cb_tree,
  author      = {Korenfeld, Boris},
  institution = {Tel Aviv University},
  title       = {CBTree: A practical concurrent self-adjusting search tree},
  url         = {http://link.springer.com/chapter/10.1007/978-3-642-33651-5\_1},
  year        = {2012},
  note        = {visited on 2017-05-03},
}

@misc{ccherish,
  author = {Mašat, Miroslav},
  title  = {{CCherish}},
  url    = {https://github.com/tyrhus/CCherish},
  year   = {2016},
  note   = {visited on 2017-05-03},
}

@misc{complete_bt,
  author    = {Black, Paul E.},
  booktitle = {Dictionary of Algorithms and Data Structures [online]},
  title     = {complete binary tree},
  url       = {https://xlinux.nist.gov/dads/HTML/completeBinaryTree.html},
  year      = {2016},
  note      = {visited on 2017-05-03},
}

@article{crtp,
  author       = {Coplien, J},
  isbn         = {0201533936},
  issn         = {1040-6042},
  journal      = {C++ Report},
  number       = {February},
  volume       = {1},
  pages        = {24--27},
  title        = {{Curiously Recurring Template Patterns}},
  year         = {1995},
}

@misc{std_hash,
  author  = {{Free Software Foundation}, Inc.},
  title   = {libstdc++: functional\_hash.h},
  url     = {https://gcc.gnu.org/onlinedocs/gcc-6.2.0/libstdc++/api/a01298\_source.html},
  note    = {visited on 2017-05-03},
}

@misc{murmurhash,
  author = {Appleby, Austin},
  title  = {{MurmurHash}},
  url    = {https://github.com/aappleby/smhasher},
  note   = {visited on 2017-05-03},
}

@misc{masat,
  author        = {Mašat, Miroslav},
  institution   = {Czech Technical University in Prague},
  title         = {{Numerical Database System}},
  url           = {https://dspace.cvut.cz/handle/10467/65871},
  note          = {Bachelor’s thesis. Czech Technical University in Prague, Faculty of Information Technology, 2016.},
}

@article{park94,
  author       = {Park, S. C. and Bahri, C. and Draayer, J. P. and Zheng, S. Q.},
  doi          = {10.1016/0010-4655(94)90172-4},
  issn         = {00104655},
  journal      = {Computer Physics Communications},
  keywords     = {avl tree,binary tree,heap,weighted search tree},
  number       = {2-3},
  pages        = {247--264},
  title        = {{Numerical database system based on a weighted search tree}},
  volume       = {82},
  year         = {1994},
}

@article{partial_splaying,
  author       = {Klostermeyer, William F},
  doi          = {10.1080/02522667.1992.10699094},
  issn         = {0252-2667},
  journal = {J. Information and Optimization Sciences},
  month        = {jan},
  number       = {1},
  pages        = {85--95},
  publisher    = {Taylor {\&} Francis Group},
  title        = {{Optimizing searching with self-adjusting trees}},
  url          = {http://www.tandfonline.com/doi/abs/10.1080/02522667.1992.10699094},
  volume       = {13},
  year         = {1992},
}

@misc{splay_overview,
  author = {Huus, Evan},
  pages  = {1--15},
  title  = {{Reduced Restructuring in Splay Trees}},
  year   = {2014},
  url    = {https://eapache.github.io/assets/Huus2014_SplayTrees.pdf},
  note   = {visited on 2017-05-03},
}

@article{splay_tree,
  author       = {Sleator, Daniel Dominic and Tarjan, Robert Endre},
  doi          = {10.1145/3828.3835},
  issn         = {0004-5411},
  journal      = {Journal of the ACM},
  number       = {3},
  pages        = {652--686},
  title        = {{Self-adjusting Binary Search Trees}},
  url          = {http://doi.acm.org/10.1145/3828.3835},
  volume       = {32},
  year         = {1985},
}

@misc{sizeof_empty,
  author  = {Stroustrup, Bjarne},
  title   = {{Stroustrup: C++ Style and Technique FAQ}},
  url     = {http://www.stroustrup.com/bs\_faq2.html\#sizeof-empty},
  note    = {visited on 2017-05-03},
  year    = {2013},
}

@article{ebo,
  author       = {Myers, Nathan C.},
  journal      = {Dr. Dobb's Journal},
  number       = {C++ Issue},
  volume       = {1},
  title        = {{The "Empty Member" C++ Optimization}},
  url          = {http://www.cantrip.org/emptyopt.html},
  note         = {visited on 2017-05-03},
  year         = {1997},
}

@article{park90,
  author       = {Park, S. C. and Draayer, J. P. and Zheng, S. Q.},
  journal = {Proc. Int. Computer Symposium},
  pages        = {333--338},
  title        = {{Time-Space Optimal Numerical Database for Large-Scale Scientific Applications}},
  note   = {visited on 2017-05-03},
  url          = {http://www.phys.lsu.edu/draayerpubs/Conference Proceedings/Time-Space Optimal Numerical Database for Large-Scale Scientific Applications.pdf},
  year         = {1990},
}

@misc{wstree,
  author = {Park, S. C. and Draayer, J. P. and Zheng, S. Q. and Bahri, C.},
  title  = {{WSTREE}},
  url    = {http://cpc.cs.qub.ac.uk/summaries/ACTZ\_v1\_0.html},
  note   = {visited on 2017-05-03},
  year   = {1994},
}