text:
{1994},
	pages = {2094--2100}
}

@article{murray_species_2014,
	title = {Species that share traits do not necessarily form distinct and universally applicable functional effect groups},
	volume = {516},
	url = {http://www.int-res.com/abstracts/meps/v516/p23-34/},
	doi = {10.3354/meps11020},
	journal = {Marine Ecology Progress Series},
	author = {Murray, F and Douglas, A and Solan, M},
	month = dec,
	year = {2014},
	keywords = {ecology, functional groups},
	pages = {23--34}
}

@article{chang_variables_2013,
	title = {Variables affecting sediment sulfide concentrations in regulatory monitoring at salmon farms in the {Bay} of {Fundy}, {Canada}},
	volume = {4},
	issn = {1869-215X},
	url = {http://www.int-res.com/abstracts/aei/v4/n1/p67-79/},
	doi = {10.3354/aei00074},
	number = {1},
	journal = {Aquaculture Environment Interactions},
	author = {Chang, BD and Page, FH and Losier, RJ},
	month = jun,
	year = {2013},
	keywords = {Environmental monitoring, Benthic impact, Management, Salmon farming, Southwestern New Brunswick},
	pages = {67--79}
}

@book{joye_nitrogen_2008-1,
	title = {Nitrogen {Cycling} in {Coastal} {Sediments}},
	isbn = {978-0-12-372522-6},
	abstract = {This chapter reviews the factors regulating sediment N-cycling, both in the bulk sediment environment and on a process level. N availability is frequently cited as the factor limiting primary production in marine systems over annual time scales though phosphorus (P), silica (Si) limitation or colimitation by N, P, and/or Si sometimes occur on seasonal time scales. In offshore waters, the presence of bioavailable iron can also regulate primary productivity, particularly that by diatoms. Sediment N pools reflect a balance between inputs (external or internal) and outputs (sedimentation, denitrification (DNF), long-term burial, or export), and this balance is affected by a variety of environmental and physiological factors. Within the sediment, N is cycled primarily by microbially mediated redox reactions between more highly oxidized forms (nitrate, NO3-, or nitrite, NO2-) and more reduced forms (ammonium, NH4-, amino acids, or organic nitrogen compounds). Gaseous products of these redox reactions may include dinitrogen, N2, nitric oxide, NO, and nitrous oxide, N2O. One characteristic of the sediment N-cycle is the coupling between aerobic and anaerobic processes. Another characteristic is that for a given species, for example, NO3-, several competing pathways and potential fates may exist. ?? 2008 Copyright ?? 2008 Elsevier Inc. All rights reserved..},
	author = {Joye, Samantha B. and Anderson, Iris C.},
	year = {2008},
	doi = {10.1016/B978-0-12-372522-6.00019-0}
}

@article{cranford_influence_2007,
	title = {Influence of mussel aquaculture on nitrogen dynamics in a nutrient enriched coastal embayment},
	volume = {347},
	doi = {10.3354/meps06997},
	abstract = {The combined influences of intensive mussel aquaculture and watershed nutrient inputs on nitrogen dynamics in Tracadie Bay, Prince Edward Island, Canada, were examined using a nitrogen budget and an ecosystem model. Budget calculations, and inputs and parameters for the model were based on extensive field data. Both approaches showed that mussel aquaculture has a dominant influence on all aspects of the nitrogen cycle and dramatically alters pathways by which nitrogen reaches the phytoplankton and benthos. A large proportion of phytoplankton production is supported by land-derived nitrogen and this anthropogenic input is important for sustaining existing levels of mussel production. The amount of nitrogen removed in the mussel harvest is small compared with agricultural nitrogen inputs and the amounts of excreted and biodeposited on the seabed. Mussel biodeposition greatly increases the flux of nitrogen to the benthos, with potentially serious eutrophication impacts. Results from the observation-based nitrogen budget and dynamic model were compared and both support the above conclusions. However, the ability of the model to test different scenarios and to provide additional information (e.g. fluxes) over a finer spatial scale led to insights unattainable with a nitrogen budget. For example, food appears to be less available to mussels at the head of the Bay than at the mouth, despite the lower density of grow-out sites in the former location. The number of fundamental ecosystem processes influenced by the mussels and the complexity of their interactions make it difficult to predict the effects of mussels on many ecosystem properties without resorting to a model.},
	journal = {Marine Ecology Progress Series},
	author = {Cranford, Peter J. and Strain, Peter M. and Dowd, Michael and Hargrave, Barry T. and Grant, Jonathan and Archambault, Marie-Claude},
	year = {2007},
	pages = {61--78}
}

@article{hartnett_role_2003,
	title = {Role of a strong oxygen-deficient zone in the preservation and degradation of organic matter: a carbon budget for the continental margins of northwest {Mexico} and {Washington} {State}},
	volume = {67},
	issn = {00167037},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0016703702010761},
	doi = {10.1016/S0016-7037(02)01076-1},
	number = {2},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Hartnett, Hilairy E and Devol, Allan H},
	month = jan,
	year = {2003},
	pages = {247--264}
}

@article{thibodeau_benthic_2010,
	title = {Benthic nutrient fluxes along the {Laurentian} {Channel}: {Impacts} on the {N} budget of the {St}. {Lawrence} marine system},
	volume = {90},
	issn = {02727714},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0272771410003203},
	doi = {10.1016/j.ecss.2010.08.015},
	number = {4},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Thibodeau, Benoît and Lehmann, Moritz F. and Kowarzyk, Jacqueline and Mucci, Alfonso and Gélinas, Yves and Gilbert, Denis and Maranger, Roxane and Alkhatib, Mohammad},
	month = dec,
	year = {2010},
	pages = {195--205}
}

@phdthesis{behrendt_competition_2014,
	type = {{PhD} {Thesis}},
	title = {Competition between dissimilatory nitrate reduction to ammonium and denitrification in marine sediments},
	school = {Universität Bremen},
	author = {Behrendt, A.},
	year = {2014}
}

@article{neubacher_potential_2013,
	title = {The potential effect of sustained hypoxia on nitrogen cycling in sediment from the southern {North} {Sea}: {A} mesocosm experiment},
	volume = {113},
	issn = {01682563},
	url = {http://link.springer.com/10.1007/s10533-012-9749-5},
	doi = {10.1007/s10533-012-9749-5},
	abstract = {The potential effect of sustained hypoxia (up to 70 days) on the production of N-2 gas through denitrification and anammox, as well as sediment-water exchange of nitrite, nitrate and ammonia, oxygen consumption and penetration, were measured in mesocosms using sediment collected from the southern North Sea (north of Dogger Bank). As expected, both the penetration of oxygen into, and consumption of oxygen by, the sediment decreased by 42 and 46 \%, respectively, once hypoxia was established. Importantly, the oxygen regime did not change significantly (P {\textbackslash}textgreater 0.05) during the experiment, suggesting that organic carbon was not depleted. During the first 10 days, the exchange of NO3 (-), NO2 (-) and NH4 (+) between the sediment and water was erratic but once a steady state was established the sediment acted as either a sink for fixed nitrogen under hypoxia or as a source in the controls. Over the course of the mesocosm experiment the rate of both anammox and denitrification increased, with anammox increasing disproportionately under hypoxia relative to the controls, whereas the rate of increase in denitrification was the same for both. Under sustained hypoxia the production of N-2 gas increased by 72 \% relative to the controls, with this increase in N-2 production remaining constant regardless of the duration of hypoxia. Longer periods of stratification and oxygen depletion are predicted to occur more regularly in the bottom waters of shallow coastal seas as one manifestation of climate change. Under sustained hypoxia the potential for nitrogen removal by the production of N-2 gas in this region of the southern North Sea was estimated to increase from 2.1 kt N 150 days(-1) to 3.6 kt 150 days(-1), while the efflux of dissolved inorganic nitrogen ceased altogether; both of which could down regulate the productivity of this region as a whole.},
	number = {1-3},
	journal = {Biogeochemistry},
	author = {Neubacher, Elke C and Parker, Ruth E and Trimmer, Mark},
	month = may,
	year = {2013},
	keywords = {Denitrification, Anammox, Hypoxia, Sediment, Nitrogen removal},
	pages = {69--84}
}

@article{mccarthy_bottom-water_2008,
	title = {Bottom-water {Hypoxia} {Effects} on {Sediment}–{Water} {Interface} {Nitrogen} {Transformations} in a {Seasonally} {Hypoxic}, {Shallow} {Bay} ({Corpus} {Christi} {Bay}, {TX}, {USA})},
	volume = {31},
	issn = {1559-2723},
	url = {http://link.springer.com/10.1007/s12237-008-9041-z},
	doi = {10.1007/s12237-008-9041-z},
	number = {3},
	journal = {Estuaries and Coasts},
	author = {McCarthy, Mark J. and McNeal, Karen S. and Morse, John W. and Gardner, Wayne S.},
	month = jul,
	year = {2008},
	pages = {521--531}
}

@article{donald_comparative_2011,
	title = {Comparative effects of urea, ammonium, and nitrate on phytoplankton abundance, community composition, and toxicity in hypereutrophic freshwaters},
	volume = {56},
	issn = {00243590},
	url = {http://doi.wiley.com/10.4319/lo.2011.56.6.2161},
	doi = {10.4319/lo.2011.56.6.2161},
	abstract = {Dissolved nitrogen (N) as urea ([NH2](2)CO), nitrate (NO3-), and ammonium (NH4+) was added to naturally phosphorus (P)-rich lake water (up to 175 mu g P L-1) to test the hypotheses that pollution of hypereutrophic lakes with N increases total algal abundance, alters community composition, and favors toxic cyanobacteria that do not fix atmospheric N-2. Monthly experiments were conducted in triplicate in polymictic Wascana Lake, Saskatchewan, Canada, during July, August, and September 2008 using large ({\textbackslash}textgreater 3140 liters) enclosures. Addition of all forms of N added at 6 mg N L-1 increased total algal abundance (as chlorophyll a) by up to 350\% relative to controls during August and September, when soluble reactive P (SRP) was {\textbackslash}textgreater 50 mu g P L-1 and dissolved N: P was {\textbackslash}textless 20 : 1 by mass. In particular, NH4+ and urea favored non-heterocystous cyanobacteria and chlorophytes and NO3-, urea promoted chlorophytes, some cyanobacteria, and transient blooms of siliceous algae, whereas N-2-fixing cyanobacteria and dinoflagellates exhibited little response to added N. Added N also increased microcystin production by up to 13-fold in August and September, although the magnitude of response varied with N species and predominant algal taxon (Planktothrix agardhii, Microcystis spp.). These findings demonstrate that pollution with N intensifies eutrophication and algal toxicity in lakes with elevated concentrations of SRP and low N: P, and that the magnitude of these effects depends on the chemical form, and hence source, of N.},
	number = {6},
	journal = {Limnology and Oceanography},
	author = {Donald, Derek B. and Bogard, Matthew J. and Finlay, Kerri and Leavitt, Peter R.},
	month = nov,
	year = {2011},
	pages = {2161--2175}
}

@article{dale_rates_2011,
	title = {Rates and regulation of nitrogen cycling in seasonally hypoxic sediments during winter ({Boknis} {Eck}, {SW} {Baltic} {Sea}): {Sensitivity} to environmental variables},
	volume = {95},
	issn = {02727714},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0272771411001739},
	doi = {10.1016/j.ecss.2011.05.016},
	abstract = {This study investigates the biogeochemical processes that control the benthic fluxes of dissolved nitrogen (N) species in Boknis Eck - a 28 m deep site in the Eckernförde Bay (southwestern Baltic Sea). Bottom water oxygen concentrations (O2-BW) fluctuate greatly over the year at Boknis Eck, being well-oxygenated in winter and experiencing severe bottom water hypoxia and even anoxia in late summer. The present communication addresses the winter situation (February 2010). Fluxes of ammonium (NH4+), nitrate (NO3-) and nitrite (NO2-) were simulated using a benthic model that accounted for transport and biogeochemical reactions and constrained with ex situ flux measurements and sediment geochemical analysis. The sediments were a net sink for NO3- (-0.35 mmol m-2 d-1 of NO3-), of which 75\% was ascribed to dissimilatory reduction of nitrate to ammonium (DNRA) by sulfide oxidizing bacteria, and 25\% to NO3- reduction to NO2- by denitrifying microorganisms. NH4+ fluxes were high (1.74 mmol m-2 d-1 of NH4+), mainly due to the degradation of organic nitrogen, and directed out of the sediment. NO2- fluxes were negligible. The sediments in Boknis Eck are, therefore, a net source of dissolved inorganic nitrogen (DIN = NO3- + NO2- + NH4+) during winter. This is in large part due to bioirrigation, which accounts for 76\% of the benthic efflux of NH4+, thus reducing the capacity for nitrification of NH4+. The combined rate of fixed N loss by denitrification and anammox was estimated at 0.08 mmol m-2 d-1 of N2, which is at the lower end of previously reported values. A systematic sensitivity analysis revealed that denitrification and anammox respond strongly and positively to the concentration of NO3- in the bottom water (NO3-BW). Higher O2-BW decreases DNRA and denitrification but stimulates both anammox and the contribution of anammox to total N2 production (\%Ramx). A complete mechanistic explanation of these findings is provided. Our analysis indicates that nitrification is the geochemical driving force behind the observed correlation between \%Ramx and water depth in the seminal study of Dalsgaard et al. (2005). Despite remaining uncertainties, the results provide a general mechanistic framework for interpreting the existing knowledge of N-turnover processes and fluxes in continental margin sediments, as well as predicting the types of environment where these reactions are expected to occur prominently. © 2011 Elsevier Ltd.},
	number = {1},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Dale, A. W. and Sommer, S. and Bohlen, L. and Treude, T. and Bertics, V. J. and Bange, H. W. and Pfannkuche, O. and Schorp, T. and Mattsdotter, M. and Wallmann, K.},
	month = nov,
	year = {2011},
	keywords = {Denitrification, Anammox, Hypoxia, Nitrogen cycle, Modelling, Kiel Bight},
	pages = {14--28}
}

@article{kristensen_fate_1987,
	title = {The fate of organic carbon and nitrogen in experimental marine sediment systems: {Influence} of bioturbation and anoxia.},
	volume = {45},
	abstract = {Lab Experiment with three sed environments 1-worms 2-oxic 3-anoxic. O2 TCO2 and Din flux 2.5 to 3.5 times greater with worms. Much lower PW concentrations of CO2 and DIN. Anoxic cores consumed POC faster than oxic w/o Worms. In intro they say lab studies of oxic vs anoxic show about same rates. oxic 50\% O2 and 50\%NO3. Very steep NO3 profile in oxic and worms but always flux out. However not as big as when oxic seds so difference is denitrification},
	journal = {Journal of Marine Research},
	author = {Kristensen, E and Blackburn, T H},
	year = {1987},
	pages = {231--257}
}

@incollection{fossing_model_2004,
	title = {A model set-up for an oxygen and nutrient flux model for {Aarhus} {Bay} ({Denmark})},
	isbn = {87-7772-793-2},
	abstract = {Most of the organic matter found in the sea is degraded in the seabed. A number of different bacteria are responsible for organic matter degradation. Through their metabolic processes bacteria form inorganic nitrogen and phosphorus compounds that are thus made available for new production. They also produce a number of waste products, such as hydrogen sulphide, that have a great impact on the marine environment. After many years of research, our knowledge of the processes going on in the seabed is substantial. This knowledge forms the basis of a new mathematical model linking the complex material cycles taking place in the seabed and describing the exchange of oxygen and nutrients between seabed and seawater. The construc- tion of the model is described in this report. This report was prepared as a contribu- tion towards developing NERI's expertise within the field of mathematical model- ling.},
	number = {483},
	booktitle = {{NERI} {Technical} {Report}},
	publisher = {National ENvironmental Research Institute, Denmark},
	author = {Fossing, Henrik and Berg, Peter and Thamdrup, Bo and Rysgaard, Søren and Munk, Helene S and Nielsen, Kurt},
	year = {2004},
	pages = {65}
}

@article{mirto_microbial_2000,
	title = {Microbial and meiofaunal response to intensive mussel-farm biodeposition in coastal sediments of the {Western} {Mediterranean}},
	volume = {40},
	issn = {0025326X},
	doi = {10.1016/S0025-326X(99)00209-X},
	abstract = {We studied the impact of organic loads due to the biodeposition of a mussel farm in a coastal area of the Tyrrhenian Sea (Western Mediterranean). Sediment chemistry, microbial and meiofaunal assemblages were investigated from March 1997 to February 1998 on monthly basis at two stations: the first was located under the mussel farm, while the second was at about 1-km distance and served as control. Benthic response to changes in the biodepositional regime was investigated in terms of biochemical composition of the sedimentary organic matter, phytopigment content, bacterial abundance and composition and meiofaunal community structure. A large accumulation of chloroplastic pigments, proteins and lipids was observed under the mussel farm. Such changes in the sedimentary conditions reflected the accumulation of faeces and pseudo-faeces and led to the creation of reducing conditions. Microbial assemblages beneath the mussel cultures increased their densities and displayed, when compared to the control, a larger cyanobacterial importance associated to a strong decrease of the picoeukaryotic cell density. Farm sediments displayed significant changes in meiofaunal density: turbellarian, ostracod and kinorhynch densities decreased significantly, while copepods remained constant or increased possibly profiting of the enrichment in microphytobenthic biomass associated to mussel biodeposits. The comparative analysis of the mussel biodeposition and fish-farm impact on sediments beneath the cultures revealed that mussel farms induced a considerably lower disturbance on benthic community structure. Copyright (C) 2000 Elsevier Science Ltd.},
	number = {3},
	journal = {Marine Pollution Bulletin},
	author = {Mirto, S. and La Rosa, T. and Danovaro, R. and Mazzola, A.},
	year = {2000},
	pmid = {4698869},
	keywords = {Bacteria, Cyanobacteria, Meiofauna, Mediterranean Sea, Mussel farm, Picoeukaryotes},
	pages = {244--252}
}

@techreport{delgado_fish_2003,
	address = {Penang, Malaysia},
	title = {Fish to 2020: supply and demand in changing global markets},
	url = {http://pubs.iclarm.net/resource_centre/WF_356.pdf},
	abstract = {Using a state-of-the art computer model of global supply and demand for food and feed commodities, this book projects the likely changes in the fisheries sector over the next two decades. As prices for most food commodities fall, fish prices are expected to rise, reflecting demand for fish that outpaces the ability of the world to supply it. The model shows that developing countries will consume and produce a much greater share of the world's fish in the future, and trade in fisheries commodities will also increase. The authors show the causes and implications of these and other changes, and argue for specific actions and policies that can improve outcomes for the poor and for the environment.},
	institution = {International Food Policy Research Institute and WorldFish Center},
	author = {Delgado, C. L. and Wada, N. and Rosegrant, M. W. and Meijer, S. and Ahmed, M.},
	year = {2003},
	pages = {226}
}

@article{dalsgaard_oxygen_2014,
	title = {Oxygen at {Nanomolar} {Levels} {Reversibly} {Suppresses} {Process} {Rates} and {Gene} {Expression} in {Anammox} and {Denitrification} in the {Oxygen} {Minimum} {Zone} off {Northern} {Chile}},
	volume = {5},
	issn = {2150-7511},
	url = {http://mbio.asm.org/lookup/doi/10.1128/mBio.01966-14},
	doi = {10.1128/mBio.01966-14},
	number = {6},
	journal = {mBio},
	author = {Dalsgaard, Tage and Stewart, Frank J and Thamdrup, Bo and De Brabandere, Loreto and Revsbech, Niels Peter and Ulloa, Osvaldo and Canfield, Don E. and DeLong, Edward F.},
	month = dec,
	year = {2014},
	keywords = {anammox and, and gene expression in, oxygen at nanomolar levels, reversibly suppresses process rates},
	pages = {e01966--14}
}

@article{dong_dissimilatory_2011,
	title = {Dissimilatory reduction of nitrate to ammonium, not denitrification or anammox, dominates benthic nitrate reduction in tropical estuaries},
	volume = {56},
	issn = {00243590},
	url = {http://doi.wiley.com/10.4319/lo.2011.56.1.0279},
	doi = {10.4319/lo.2011.56.1.0279},
	abstract = {We measured benthic denitrification (DN) and dissimilatory reduction of nitrate to ammonium (DNRA) using the isotope-pairing technique in three tropical estuaries in Thailand (Mae Klong), Indonesia (Cisadane), and Fiji (Vunidawa-Rewa) during rainy, dry, and intermediate seasons along the salinity gradient of each estuary. DNRA dominated. Anammox (AN) was measured initially but neither AN activity nor AN bacteria-related 16S ribosomal RNA genes were detected in any of the estuaries. DN was either zero or extremely low, driven by water column nitrate and not from benthic nitrification-DN. N2O was not formed during DN. N2O saturations in estuary water were low, except in the nutrified Indonesian estuary, and tropical estuaries are therefore likely to be only small sources of N2O. Benthic nitrate reduction was nitrate limited; when nitrate was enhanced experimentally, DN increased slightly, but DNRA increased proportionately much more. Predominance of DNRA over DN in tropical estuaries may be due both to an energetic advantage (greater standard free energy change, DG degrees) of nitrate ammonifiers over denitrifiers when competing for limited nitrate, and also to higher affinity for nitrate by the nitrate ammonifiers. At tropical temperatures the three processes occur in the order DNRA {\textbackslash}textgreater DN {\textbackslash}textgreater AN. In contrast, temperate estuaries, at lower temperature and higher nitrate concentrations, exhibit proportionately greater levels of AN and DN. The Cisadane estuary became anoxic during the dry season, with high ammonium and sulfide, but no nitrate reduction because of lack of nitrate. Addition of nitrate stimulated high rates of autotrophic DN driven by sulfide, but not DNRA.},
	number = {1},
	journal = {Limnology and Oceanography},
	author = {Dong, Liang F. and Sobey, Milika Naqasima and Smith, Cindy J and Rusmana, Iman and Phillips, Wayne and Stott, Andrew and Osborn, A. Mark and Nedwell, David B.},
	month = jan,
	year = {2011},
	keywords = {AMMONIFICATION, BALTIC SEA, FLUXES, MARINE-SEDIMENTS, NITRITE, NITROUS-OXIDE PRODUCTION, RIVER, SALT-MARSH SEDIMENT, SPECTROPHOTOMETRIC DETERMINATION, UNITED-KINGDOM},
	pages = {279--291}
}

@incollection{ward_nitrification_2000,
	title = {Nitrification and the marine nitrogen cycle},
	isbn = {0-471-29993-6},
	abstract = {1. Nitrification is performed by chemolithoautotrophic bacteria that obtain metabolic energy for CO2 fixation from the oxidation of inorganic nitrogen compounds, resulting in the net transformation of ammonia to nitrate. 2. Both nitrite-and ammonia-oxidizing nitrifiers are Proteobacteria. The ammonia oxidizers are closely related both phylogenetically and metabolically to methanotrophic bacteria. 3. Nitrification rates are highest near the base of the euphotic zone in the open ocean, and in sediments in the coastal region. High nitrate concentrations in deep water probably result from slow accumulation due to low nitrification rates coupled to the absence of a significant sink for nitrate in oxygenated deep water. 4. Environmental factors with mediate the rate of nitrification include light intensity, substrate concentration and oxygen concentration. Nitrification is subject to inhibition by a number of different chemicals, which may influence its rate in the environment. 5. Nitrification has been implicated in the production of nitric and nitrous oxides in the ocean. Trace gas production is enhanced at low oxygen tensions. In oxygen minimum zones, nitrification is coupled to denitrification, leading to net loss of fixed nitrogen.},
	booktitle = {Microbial {Ecology} of the {Oceans}},
	publisher = {Wiley-Liss, Inc.},
	author = {Ward, Bess B},
	editor = {Kirchman, David L.},
	year = {2000},
	doi = {10.1007/s00027–},
	pages = {427--453}
}

@article{wu_impact_1994,
	title = {Impact of {Marine} {Fish} {Farming} on {Water}-{Quality} and {Bottom} {Sediment} - a {Case}-{Study} in the {Subtropical} {Environment}},
	volume = {38},
	abstract = {Field studies were carried out to determine and compare the impact of marine fish farming activities on the water quality and bottom sediment at four fish culture sites with different hydrographic and culture conditions in a sub-tropical environment where trash fish is used as feed. The major impact identified was on the sea bottom, resulting in the development of reducing and anoxic sediments, high sediment oxygen demand, production of hydrogen sulphide and elimination/decrease in benthos. The impact on water quality was less conspicuous. A decrease in dissolved oxygen was observed at all sites while increases in ammonia, inorganic P, nitrate and nitrite were observed only at sites with poor tidal flushing and high stocking density. However, no significant changes in total suspended solids, light extinction coefficient, chlorophyll a, phaeopigment and E. coli were found near the fish rafts at any sites. Environmental impacts vary considerably between sites, and were significantly reduced at sites with good water circulation and low stocking density. Despite the high organic and nutrient loadings generated by marine fish farming activities, the impacts on water quality and sediments at all sites were localised and did not appear to extend beyond a distance of 1-1.5 km from the fish rafts. Results of the present study also do not support the suggestion that marine fish farming activities have caused eutrophication on a large scale.},
	number = {2},
	journal = {Marine Environmental Research},
	author = {Wu, Rudolf S S and Lam, K S and Mackay, D W and Lau, T C and Yam, V},
	year = {1994},
	keywords = {oxygen, nitrogen, nitrification, carbon, pollution, sea},
	pages = {115--145}
}

@techreport{fao_state_2016,
	address = {Rome},
	title = {The {State} of {World} {Fisheries} and {Aquaculture} 2016. {Contributing} to food security and nutrition for all},
	url = {http://www.fao.org/3/a-i3720e.pdf},
	author = {{FAO}},
	year = {2016},
	pages = {200}
}

@article{wu_environmental_1995,
	title = {The {Environmental} {Impact} of {Marine} {Fish} {Culture} : {Towards} a {Sustainable} {Future}},
	volume = {31},
	number = {4-12},
	journal = {Marine Pollution Bulletin},
	author = {Wu, Rudolf S S},
	year = {1995},
	pages = {159--166}
}

@article{tett_general_1978,
	title = {The {General} {Annual} {Cycle} of {Chlorophyll} {Standing} {Crop} in {Loch} {Creran}},
	volume = {66},
	issn = {00220477},
	url = {http://www.jstor.org/stable/2259190 http://www.jstor.org/stable/2259190?origin=crossref},
	doi = {10.2307/2259190},
	number = {1},
	journal = {The Journal of Ecology},
	author = {Tett, Paul and Wallis, Andrew},
	month = mar,
	year = {1978},
	pages = {227}
}

@techreport{fao_aquaculture_2010,
	address = {Rome},
	title = {Aquaculture {Development} - 4. {Ecosystem} approach to aquaculture},
	abstract = {These Technical Guidelines have been developed to support sections of the FAOs Code of Conduct for Responsible Fisheries on aspects of genetic resource management in aquaculture. Guidance is provided on broodstock management and domestication, genetic improvement programmes, dissemination programmes for genetically improved fish, economic considerations in genetic improvement programmes, risk assessment and monitoring, culture based fisheries, conservation of fish genetic resources, gene banks, a precautionary approach and public relations. The effective management of genetic resources, risk assessment and monitoring can help promote responsible aquaculture by increasing production output and efficiency and help minimize adverse impacts on the environment. These benefits of the responsible application of genetic principles to aquaculture should be communicated to consumers, policy-makers, scientists and others interested in responsible fisheries and aquaculture.},
	number = {4},
	institution = {FAO},
	author = {{FAO}},
	year = {2010},
	doi = {10.1080/13657300209380305},
	pmid = {807465},
	pages = {53pp}
}

@article{jantti_jantti_2012,
	title = {Jäntti and {Hietanen} 2012 {HYPOXIA} {DNRA} {DNF} {EUTROPHICATION}.pdf},
	volume = {41},
	doi = {10.1007/s13280-011-0233-6},
	journal = {AMBIO},
	author = {Jäntti, Helena and Hietanen, Susanna},
	year = {2012},
	keywords = {Nitrogen, Denitrification, DNRA, Hypoxia, Sediment, Baltic Sea},
	pages = {161--169}
}

@article{sara_use_2006,
	title = {Use of stable isotopes to investigate dispersal of waste from fish farms as a function of hydrodynamics},
	volume = {313},
	issn = {0171-8630, 1616-1599},
	url = {https://www.int-res.com/abstracts/meps/v313/p261-270/},
	doi = {10.3354/meps313261},
	abstract = {Stable isotopes were used to examine differential effects of fish farm waste on the water column and sediments. To achieve this objective, we chose 3 marine fish farms located along the coast of Sicily (Mediterranean Sea) as point-source disturbances, and a control area. The hypothesis that carbon and nitrogen isotope composition of particulate (POM) and sedimentary (SOM) organic matter varied with increasing distance (from cages to 1000 m) was tested at 3 levels of hydrodynamics: low (mean velocity of current [MVC] {\textasciitilde}12 cm s–1), intermediate (MVC {\textasciitilde}22 cm s–1), and high (MVC {\textasciitilde}40 cm s–1). Different isotopic signals from allochthonous (fish waste) over natural (phytoplankton, terrigenous, and sand microflora) inputs allowed identification of the ‘spatial effect regime’ of fish farming. The increasing water current velocities seem to proportionally enlarge the relative area of influence of the cages, particularly on sediments. At low hydrodynamics, an increasing contribution of terrigenous signals was inferred: POM and SOM showing a depleted gradient of C (ranging from –22.0 to –24.0‰) and N (from 5.0 to 2.0‰). At an intermediate hydrodynamic level, C and N showed a slight increase in waste contribution, particularly in POM (δ15N from 2.6 to {\textasciitilde}4.0‰). At high hydrodynamics, an enriching isotopic gradient (δ15NPOM-SOM from 1.8 to 4.6‰) suggested a notable contribution of fish waste. Accordingly, the dispersal of waste from the cages seemed to be related to movements at the bottom of the water column, confirming the recently identified role played by resuspension movements.},
	language = {en},
	urldate = {2019-05-08},
	journal = {Marine Ecology Progress Series},
	author = {Sarà, G. and Scilipoti, D. and Milazzo, M. and Modica, A.},
	month = may,
	year = {2006},
	keywords = {Fish farming, Sediment, Stable isotopes, Hydrodynamics, Mediterranean, Impact, Water column},
	pages = {261--270},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\YT2A3K5S\\Sarà et al. - 2006 - Use of stable isotopes to investigate dispersal of.pdf:application/pdf;Snapshot:C\:\\Users\\chand\\Zotero\\storage\\7TR32XK9\\p261-270.html:text/html}
}

@article{broch_spatiotemporal_2017,
	title = {Spatiotemporal {Dispersal} and {Deposition} of {Fish} {Farm} {Wastes}: {A} {Model} {Study} from {Central} {Norway}},
	volume = {4},
	issn = {2296-7745},
	shorttitle = {Spatiotemporal {Dispersal} and {Deposition} of {Fish} {Farm} {Wastes}},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2017.00199/full},
	doi = {10.3389/fmars.2017.00199},
	abstract = {Abstract A spatially explicit coupled hydrodynamic-mass transport model system was used to simulate dispersal of particulate organic matter from Atlantic salmon (Salmo salar) farming in central Norway. Model setups of 32 m horizontal resolution were run for periods of up to 650 days for 3 sites of different oceanographic characteristics: one fjord location, one medium-exposed location influenced by fjord water and one coastal location. Records on feed used for each cage at each location were converted to feces released based on a published mass balance model. The results from the simulations were compared with scores from corresponding mandatory benthic surveys (MOM-B) of the sediment layer beneath the farms. The correspondence between simulated and measured thickness of the sediment layer was good, and improved with the inclusion of resuspension processes. At all sites the distribution of organic matter in the bottom layer was non-homogeneous, with significant temporal variation and transport and settling of matter up to at least 0.5 km away from one of the farms. Our results indicate that the monitoring practice used in Norway until now, with a few sediment grab samples taken mainly within the fish farm, may not adequately determine the areal impacts of all salmon farming operations. The patchy distribution of organic matter and the correspondence between simulation and survey results is attributed to the use of full 3D current fields of a high spatiotemporal resolution and a good model for resuspension processes that some previous model studies have failed to properly account for.},
	language = {English},
	urldate = {2019-05-08},
	journal = {Frontiers in Marine Science},
	author = {Broch, Ole J. and Daae, Ragnhild L. and Ellingsen, Ingrid H. and Nepstad, Raymond and Bendiksen, Eldar Å and Reed, Jenny L. and Senneset, Gunnar},
	year = {2017},
	keywords = {aquaculture dispersal model, Aquaculture effects, Depositional model, Environmental effects, Fish farm wastes, Hydrodynamic modeling},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\2E9E7RRW\\Broch et al. - 2017 - Spatiotemporal Dispersal and Deposition of Fish Fa.pdf:application/pdf}
}

@incollection{yokoyama_macrobenthos_2007,
	address = {Dordrecht},
	series = {Methods and {Technologies} in {Fish} {Biology} and {Fisheries}},
	title = {Macrobenthos as {Biological} {Indicators} to {Assess} the {Influence} of {Aquaculture} on {Japanese} {Coastal} {Environments}},
	isbn = {978-1-4020-6148-6},
	url = {https://doi.org/10.1007/978-1-4020-6148-6_22},
	abstract = {To delineate patterns in the gradients of macrobenthic communities around fish farms and to generate site-selection guidelines for sustainable fish farms, a quantitative survey was conducted in August-September 1998 and in February 1999 in fishfarming areas along the coast of Kumano-nada, central Japan. The biomass peaked in sediments containing 1.2 mg=g of total nitrogen or 9.2 mg=g of total organic carbon, suggesting that these values are indicative of possible aerobic mineralization of the loaded organic wastes. Macrobenthos was scarcely found in sediments with acid-volatile sulfides (AVS) {\textgreater}1.9 mg S=g, which suggests critical AVS conditions for maintaining sustainable and environmentally “friendly” aquaculture. An index, “ED,” which serves as an index for bathymetry of the sampling site, was devised. ED was highly correlated with four community parameters (biomass, density, species diversity, and species richness) and with five environmental factors (sediment total nitrogen, total organic carbon, total phosphorus and acid-volatile sulfides, and bottom-water dissolved oxygen). Compared with small-scale farms, environmental deterioration and decline in macrofauna were obvious in large-scale farms (\_600 t=yr of fish production) that were located in inner parts of embayments and that had comparatively high ED values. However, in areas near open waters and that had comparatively low ED values, the impacts of aquacultural activities were not clear. These findings suggest that the variation in macrobenthos and environmental factors found in the study area was attributable principally to the area’s bathymetry and, secondly, to aquacultural activities. Seven assemblages, recognized on the basis of cluster analysis, were placed in a gradient of ED versus fish production. These assemblages were classified into three groups: a group characteristic of a healthy zone, a group characteristic of a cautionary zone, and a group characteristic of a critical zone. As fish production increased, the location of the assemblage characteristic of the cautionary zone shifted to more open, deeper areas (lower ED values). An azoic-site group was composed of large-scale farms in a stagnant basin. The community type of the macrobenthos in the vicinity of open-water, net-pen fish farms is an indicator of the condition and assimilative capacity of the benthic environment in that area and can be used to evaluate the suitability of the site for continued fish farming. The index of embayment degree, ED, can be used as a simple and effective substitute indicator for this evaluation.},
	language = {en},
	urldate = {2019-05-15},
	booktitle = {Ecological and {Genetic} {Implications} of {Aquaculture} {Activities}},
	publisher = {Springer Netherlands},
	author = {Yokoyama, Hisashi and Nishimura, Akifumi and Inoue, Misa},
	editor = {Bert, Theresa M.},
	year = {2007},
	doi = {10.1007/978-1-4020-6148-6_22},
	keywords = {Fish Farm, Fish Production, Organic Input, Total Nitrogen, Total Organic Carbon, ecological indicators, waste impacts},
	pages = {407--423},
	file = {Springer Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\YGGWKLNH\\Yokoyama et al. - 2007 - Macrobenthos as Biological Indicators to Assess th.pdf:application/pdf}
}

@article{soetaert_reactive_2012,
	title = {Reactive transport in aquatic ecosystems: {Rapid} model prototyping in the open source software {R}},
	volume = {32},
	journal = {Environmental Modelling \& Software},
	author = {Soetaert, Karline and Meysman, Filip J.R.},
	year = {2012},
	pages = {49--60}
}

@article{beam_biological_2018,
	title = {Biological rejuvenation of iron oxides in bioturbated marine sediments},
	volume = {12},
	copyright = {2018 International Society for Microbial Ecology},
	issn = {1751-7370},
	url = {https://www.nature.com/articles/s41396-017-0032-6},
	doi = {10.1038/s41396-017-0032-6},
	abstract = {The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although biological processes that catalyze the reductive side of the iron cycle are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments—resulting in the formation of iron oxides. Here we show that a potential source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, presumably enhanced by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments, and predicted to annually produce 8 × 1015 g of Fe in sedimentary iron oxides—55 times larger than the annual flux of iron oxides deposited by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments—despite their low numerical abundance—yet exert a disproportionate impact via the rejuvenation of iron oxides.},
	language = {En},
	number = {5},
	urldate = {2019-06-27},
	journal = {The ISME Journal},
	author = {Beam, Jacob P. and Scott, Jarrod J. and McAllister, Sean M. and Chan, Clara S. and McManus, James and Meysman, Filip J. R. and Emerson, David},
	month = may,
	year = {2018},
	keywords = {bioturbation, iron},
	pages = {1389},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\9U42GYE3\\Beam et al. - 2018 - Biological rejuvenation of iron oxides in bioturba.pdf:application/pdf;Snapshot:C\:\\Users\\chand\\Zotero\\storage\\DBWITN6L\\s41396-017-0032-6.html:text/html}
}

@article{koretsky_quantifying_2002,
	title = {Quantifying bioirrigation using ecological parameters: a stochastic approach†},
	volume = {3},
	issn = {1467-4866},
	shorttitle = {Quantifying bioirrigation using ecological parameters},
	url = {https://doi.org/10.1186/1467-4866-3-17},
	doi = {10.1186/1467-4866-3-17},
	abstract = {Irrigation by benthic macrofauna has a major influence on the biogeochemistry and microbial community structure of sediments. Existing quantitative models of bioirrigation rely primarily on chemical, rather than ecological, information and the depth-dependence of bioirrigation intensity is either imposed or constrained through a data fitting procedure. In this study, stochastic simulations of 3D burrow networks are used to calculate mean densities, volumes and wall surface areas of burrows, as well as their variabilities, as a function of sediment depth. Burrow networks of the following model organisms are considered: the polychaete worms Nereis diversicolor and Schizocardium sp., the shrimp Callianassa subterranea, the echiuran worm Maxmuelleria lankesteri, the fiddler crabs Uca minax, U. pugnax and U. pugilator, and the mud crabs Sesarma reticulatum and Eurytium limosum. Consortia of these model organisms are then used to predict burrow networks in a shallow water carbonate sediment at Dry Tortugas, FL, and in two intertidal saltmarsh sites at Sapelo Island, GA. Solute-specific nonlocal bioirrigation coefficients are calculated from the depth-dependent burrow surface areas and the radial diffusive length scale around the burrows. Bioirrigation coefficients for sulfate obtained from network simulations, with the diffusive length scales constrained by sulfate reduction rate profiles, agree with independent estimates of bioirrigation coefficients based on pore water chemistry. Bioirrigation coefficients for O2 derived from the stochastic model, with the diffusion length scales constrained by O2 microprofiles measured at the sediment/water interface, are larger than irrigation coefficients based on vertical pore water chemical profiles. This reflects, in part, the rapid attenuation with depth of the O2 concentration within the burrows, which reduces the driving force for chemical transfer across the burrow walls. Correction for the depletion of O2 in the burrows results in closer agreement between stochastically-derived and chemically-derived irrigation coefficient profiles.},
	number = {1},
	urldate = {2019-07-03},
	journal = {Geochemical Transactions},
	author = {Koretsky, Carla M. and Meile, Christof and Van Cappellen, Philippe},
	month = feb,
	year = {2002},
	pages = {17},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\4DKE2TVD\\Koretsky et al. - 2002 - Quantifying bioirrigation using ecological paramet.pdf:application/pdf;Snapshot:C\:\\Users\\chand\\Zotero\\storage\\GDS37FUY\\1467-4866-3-17.html:text/html}
}

@article{hale_characterizations_2014,
	title = {Characterizations of how species mediate ecosystem properties require more comprehensive functional effect descriptors},
	volume = {4},
	copyright = {2014 Nature Publishing Group},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/srep06463},
	doi = {10.1038/srep06463},
	abstract = {The importance of individual species in mediating ecosystem process and functioning is generally accepted, but categorical descriptors that summarize species-specific contributions to ecosystems tend to reference a limited number of biological traits and underestimate the importance of how organisms interact with their environment. Here, we show how three functionally contrasting sediment-dwelling marine invertebrates affect fluid and particle transport - important processes in mediating nutrient cycling - and use high-resolution reconstructions of burrow geometry to determine the extent and nature of biogenic modification. We find that individual functional effect descriptors fall short of being able to adequately characterize how species mediate the stocks and flows of important ecosystem properties and that, in contrary to common practice and understanding, they are not substitutable with one another because they emphasize different aspects of species activity and behavior. When information derived from these metrics is combined with knowledge of how species behave and modify their environment, however, detailed mechanistic information emerges that increases the likelihood that a species functional standing will be appropriately summarized. Our study provides evidence that more comprehensive functional effect descriptors are required if they are to be of value to those tasked with projecting how altered biodiversity will influence future ecosystems.},
	language = {en},
	urldate = {2019-07-03},
	journal = {Scientific Reports},
	author = {Hale, R. and Mavrogordato, M. N. and Tolhurst, T. J. and Solan, M.},
	month = sep,
	year = {2014},
	pages = {6463},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\Y7352Q22\\Hale et al. - 2014 - Characterizations of how species mediate ecosystem.pdf:application/pdf;Snapshot:C\:\\Users\\chand\\Zotero\\storage\\F394H4DM\\srep06463.html:text/html}
}

@article{renz_are_2013,
	title = {Are similar worms different? {A} comparative tracer study on bioturbation in the three sibling species {Marenzelleria} arctia, {M}. viridis, and {M}. neglecta from the {Baltic} {Sea}},
	volume = {58},
	copyright = {© 2013, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	issn = {1939-5590},
	shorttitle = {Are similar worms different?},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.4319/lo.2013.58.6.2046},
	doi = {10.4319/lo.2013.58.6.2046},
	abstract = {The invasive spionid polychaetes of the genus Marenzelleria spp., consisting of the three sibling species M. neglecta, M. viridis, and M. arctia, has been found in the Baltic Sea since the 1980s. Because of difficulties in species identification, little is known about species-dependent sediment reworking and solute transport. The closely related species are apparently similar in feeding and sediment-dwelling behavior, but size and burrowing depth indicate differences in bioturbation and the biogeochemical consequences thereof. To investigate these potential differences, a tracer experiment with artificial particles (luminophores) and solute tracer (bromide) was conducted. Polychaetes were identified to species level using a molecular genetic key. Modeled results show that all three species display markedly low particle reworking rates with biodiffusion coefficients (Db) of 1.76 cm2 yr−1 (M. viridis) and 0.07 cm2 yr−1 (M. neglecta) at an abundance of 1273 individuals m−2 and 0.44 cm2 yr−1 (M. arctia) at twice that abundance. Nonlocal transport coefficients are negligible in all cases. Solute transport by M. neglecta and M. viridis are more similar to one another than to M. arctia, whose solute transport mode is much more diffusive in character (10.9-fold enhanced diffusivity with nonlocal irrigation coefficients [α] of 55.3 yr−1) than that of the two other species, which affect tracer distributions in the sediment predominantly through a nonlocal, advective transport mode (α of 108.9 yr−1 M. viridis and 130.9 yr−1 M. neglecta). Thus, a functional grouping of the sibling species in terms of bioirrigation is not recommended.},
	language = {en},
	number = {6},
	urldate = {2019-07-03},
	journal = {Limnology and Oceanography},
	author = {Renz, Judith R. and Forster, Stefan},
	year = {2013},
	keywords = {bioturbation, bioirrigation},
	pages = {2046--2058},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\WQYS7SXC\\Renz and Forster - 2013 - Are similar worms different A comparative tracer .pdf:application/pdf;Snapshot:C\:\\Users\\chand\\Zotero\\storage\\4NHZLXZ9\\lo.2013.58.6.html:text/html}
}

@misc{furukawa_bioirrigation_2001,
	type = {Text},
	title = {Bioirrigation modeling in experimental benthic mesocosms},
	url = {https://orst.library.ingentaconnect.com/content/jmr/jmr/2001/00000059/00000003/art00004#},
	language = {en},
	urldate = {2019-07-03},
	author = {Furukawa, Yoko and Bentley, Samuel J. and Lavoie, Dawn L.},
	month = may,
	year = {2001},
	doi = {info:doi/10.1357/002224001762842262},
	file = {Snapshot:C\:\\Users\\chand\\Zotero\\storage\\QE7EYDM3\\art00004.html:text/html}
}

@article{wrede_organism_2018,
	title = {Organism functional traits and ecosystem supporting services – {A} novel approach to predict bioirrigation},
	volume = {91},
	issn = {1470-160X},
	url = {http://www.sciencedirect.com/science/article/pii/S1470160X18302796},
	doi = {10.1016/j.ecolind.2018.04.026},
	abstract = {Increasing anthropogenic activities on land and at sea underline the demand for easily applicable indices to effectively predict human mediated changes in ecosystem functioning. Here, we propose a novel bioirrigation index (IPc) that is based on body mass, abundance, burrow type, feeding type and injection pocket depth of bottom dwelling animals. The index was validated with combined field (in situ communities) and manipulative (single species) experiments. Results from both community and single-species experimental incubations indicate that IPc is able to predict the bioirrigation rate in different sediment types (mud, fine sand, sand). The trait-based index thus demonstrates robustness in the prediction of animal-mediated functional processes that support biogeochemical functions under variable environmental conditions. Accordingly, we argue that trait-based indices provide a useful tool for the quantitative prediction of ecosystem processes as effect traits provide a direct link to the behavioral mechanisms that drive ecosystem functioning.},
	urldate = {2019-07-03},
	journal = {Ecological Indicators},
	author = {Wrede, Alexa and Beermann, Jan and Dannheim, Jennifer and Gutow, Lars and Brey, Thomas},
	month = aug,
	year = {2018},
	keywords = {Bioturbation, Biogeochemical cycling, Bentho-pelagic coupling, Bioturbation potential, Marine Strategy Framework Directive, Trait based indices},
	pages = {737--743},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\BBLXD26S\\Wrede et al. - 2018 - Organism functional traits and ecosystem supportin.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\chand\\Zotero\\storage\\AVLX9PZJ\\S1470160X18302796.html:text/html}
}

@article{renz_community_2018,
	title = {Community bioirrigation potential ({BIPc}), an index to quantify the potential for solute exchange at the sediment-water interface},
	volume = {141},
	issn = {0141-1136},
	url = {http://www.sciencedirect.com/science/article/pii/S0141113618302526},
	doi = {10.1016/j.marenvres.2018.09.013},
	abstract = {Bioirrigation
the animal-induced exchange of solutes between pore water and overlying water - is a key process in sediments with profound implications for biogeochemical processes such as nutrient cycling and organic matter regeneration at the sediment water interface. There is an urgent need to understand how a changing environment will affect the irrigation activity of macrofauna and vice versa. A shift in species composition (e.g. from deep burrowing species to smaller, more opportunistic and shallow burrowing species) will have large effects on bioirrigation and thus on ecosystem function (such as benthic pelagic coupling). Considering the difficulties to determine area-covering rates of bioirrigation (e.g. in terms tracer-based fluxes) and the complexity of interactions of multiple species in the community that prohibit a direct measure of bioirrigation attributable to each species, a mechanistically-based approach is needed to predict relative intensities of bioirrigation activity based on the fundamental functional traits. We propose a conceptual framework to develop an index of bioirrigation that takes into account the biological mechanisms of bioirrigation and provides a simplified, yet functionally based approach to quantify the bioirrigation potential of benthic communities. We developed the community bioirrigation potential (BIPc) that provides a biomass- and abundance-weighted scoring system considering functional traits related to pore water and solute exchange. It may be used as a supplement to established methods to assess the function of marine soft sediments related bioirrigation. In analogy to the particle-related community bioturbation potential of Solan et al. (2004), context dependent organismal traits that affect ventilation and bioirrigation (feeding type, morphology of burrows, and burrowing depth) are combined with the data on abundance and biomass of the respective species. These are subsequently summed up to a community bioirrigation potential (BIPc). This review considers ecological traits relevant for bioirrigation and their classification into a bioirrigation index. Furthermore the necessary simplifications in the index (e.g. limiting its applicability to interfacial nutrient fluxes) are discussed. We also provide a working example from the southwestern Baltic Sea to illustrate the practical application of the index and a compilation of key species related to this area containing their classification into the considered bioirrigation traits.},
	urldate = {2019-07-03},
	journal = {Marine Environmental Research},
	author = {Renz, J. R. and Powilleit, M. and Gogina, M. and Zettler, M. L. and Morys, C. and Forster, S.},
	month = oct,
	year = {2018},
	keywords = {Macrofauna, Baltic Sea, Benthic community, Classification, Ecosystem function},
	pages = {214--224},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\ICQ3T585\\Renz et al. - 2018 - Community bioirrigation potential (BIPc), an index.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\chand\\Zotero\\storage\\6J6HPKKT\\S0141113618302526.html:text/html}
}

@article{quintana_functional_2018,
	title = {Functional {Performance} of {Three} {Invasive} {Marenzelleria} {Species} {Under} {Contrasting} {Ecological} {Conditions} {Within} the {Baltic} {Sea}},
	volume = {41},
	issn = {1559-2731},
	url = {https://doi.org/10.1007/s12237-018-0376-9},
	doi = {10.1007/s12237-018-0376-9},
	abstract = {A 4-week laboratory experiment investigated the behaviour (survival and bioirrigation) and impact of the invasive polychaetes Marenzelleria viridis, M. neglecta and M. arctia on sediment-water solutes exchange, porewater chemistry, and Fe and P interactions in high-salinity sandy sediment (HSS) and low-salinity muddy sediment (LSM) from the Baltic Sea. M. viridis showed deep burrowing with efficient bioirrigation (11 L m−2 day−1) and high survival (71\%) in HSS, while M. arctia exhibited shallow burrowing with high bioirrigation (12 L m−2 day−1) and survival (88\%) in LSM. M. neglecta behaved poorly in both ecological settings (bioirrigation, 5–6 L m−2 day−1; survival, 21–44\%). The deep M. viridis bioirrigation enhanced total microbial CO2 (TCO2) production in HSS by 175\% with a net efflux of NH4+ and PO43−, at rates 3- to 27-fold higher than for the other species. Although the shallow and intense bioirrigation of M. arctia in LSM stimulated microbial TCO2 production to some extent (61\% enhancement), the nutrient fluxes close to zero indicate that it effectively prevented the P release. Porewater Fe:PO43− ratios revealed that the oxidizing effect of M. arctia bioirrigation increased the PO43− adsorption capacity of LSM twofold relative to defaunated controls while no buffering of PO43− was detected in M. viridis HSS treatment. Therefore, the different behaviour of the three species in various environments and the sharp contrast between M. viridis and M. arctia effects on C, N and P cycling must be considered carefully when the ecological role of Marenzelleria species in the Baltic Sea is evaluated.},
	language = {en},
	number = {6},
	urldate = {2019-07-05},
	journal = {Estuaries and Coasts},
	author = {Quintana, Cintia O. and Raymond, Caroline and Nascimento, Francisco J. A. and Bonaglia, Stefano and Forster, Stefan and Gunnarsson, Jonas S. and Kristensen, Erik},
	month = sep,
	year = {2018},
	keywords = {Eutrophication, Sediment biogeochemistry, Bioirrigation, Nutrient cycling, Invasive species, P retention},
	pages = {1766--1781},
	file = {Springer Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\C5GQTGUT\\Quintana et al. - 2018 - Functional Performance of Three Invasive Marenzell.pdf:application/pdf}
}

@article{mermillod-blondin_influence_2004,
	title = {Influence of bioturbation by three benthic infaunal species on microbial communities and biogeochemical processes in marine sediment},
	volume = {36},
	issn = {0948-3055, 1616-1564},
	url = {https://www.int-res.com/abstracts/ame/v36/n3/p271-284/},
	doi = {10.3354/ame036271},
	abstract = {Benthic invertebrates play a key role in the physical, chemical, and biological properties of the marine water-sediment interface. The influences of invertebrates on biogeochemical processes have mainly been attributed to their sediment
reworking and bioirrigation activities. The aim of this study was to compare the influences of bioturbation activities by 3 dominant species of shallow water habitats (Cerastoderma edule, Corophium volutator, and Nereis diversicolor)
on microbial communities and biogeochemical processes in sediment cores. C. edule acted as a biodiffuser, mixing surface particles in the top 2 cm of the sediment. Despite this mixing activity, this species had little effect on O2
consumption, water exchange between the water column and the sediment, microbial characteristics, and release of nutrients from the sediment. In contrast, C. volutator and N. diversicolor produced burrows in the sediment that allowed
transport of surface particles into biogenic structures. These 2 species doubled the solute exchange between the water column and the sediment. Such modifications of sediment structure and solute transport increased the O2 consumption and the
release of nutrients from the sediment. Both C. volutator and N. diversicolor stimulated the microbial communities as indicated by higher percentages of active bacteria. Reduction of the numbers of sulphate reducing bacteria was observed
when the 3 invertebrates were present and could be attributed to the penetration of O2 due to animal activities. N. diversicolor had a greater influence than C. volutator on pore water chemistry, ammonium release, and active
bacteria. As N. diversicolor burrowed deeper in the sediment than C. volutator, it irrigated a greater volume of sediment. The modes of sediment reworking and structure building, irrigation behaviour, and burrowing depths were factors
sufficient to assign the 3 species into different functional groups.},
	language = {en},
	number = {3},
	urldate = {2019-07-05},
	journal = {Aquatic Microbial Ecology},
	author = {Mermillod-Blondin, F. and Rosenberg, R. and François-Carcaillet, F. and Norling, K. and Mauclaire, L.},
	month = sep,
	year = {2004},
	keywords = {Bioturbation, Cerastoderma edule, Corophium volutator, Functional groups, Microbial activity, Nereis diversicolor, Organic matter processing},
	pages = {271--284},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\8BJADT6X\\Mermillod-Blondin et al. - 2004 - Influence of bioturbation by three benthic infauna.pdf:application/pdf;Snapshot:C\:\\Users\\chand\\Zotero\\storage\\EBXMC25X\\p271-284.html:text/html}
}

@article{volkenborn_effects_2007-1,
	title = {Effects of bioturbation and bioirrigation by lugworms ({Arenicola} marina) on physical and chemical sediment properties and implications for intertidal habitat succession},
	volume = {74},
	issn = {0272-7714},
	url = {http://www.sciencedirect.com/science/article/pii/S0272771407001394},
	doi = {10.1016/j.ecss.2007.05.001},
	abstract = {Sediment destabilization by sediment-reworking organisms is common in coastal aquatic environments, but the potential of bioturbation to inhibit shoreline succession has not been suggested previously. The lugworm Arenicola marina is a widespread and dominant large burrower at European Atlantic shores, and a major source of bioturbation and bioirrigation on the extensive intertidal flats in the Wadden Sea (eastern North Sea). The hypothesis that lugworm activities inhibit the successive development from sandy to muddy sediments in depositional embayments has been tested by a large-scale exclusion field experiment. Changes in sediment properties indicate a progressive clogging of interstices with fine particles and organic matter, resulting in lower sediment permeability in exclusion areas compared to lugworm inhabited control areas. Chlorophyll content in the surface layer was consistently higher in the absence of lugworms. Lack of sub-surface irrigation in the absence of lugworms combined with reduced sediment permeability resulted in increased concentrations of ammonium, phosphate, silicate, and sulphide in the pore-water. Concentrations {\textgreater}100μM of sulphide gave rise to toxic conditions for macrofauna. The effects of lugworms on sediment characteristics were more conspicuous in fine than in medium sand. It is concluded that A. marina contributes to the maintenance of permeable sand and thereby sustaining suitable conditions for the lugworm population itself. Without this “ecosystem engineer” mud flats would greatly expand at the expense of sand flats in the Wadden Sea.},
	number = {1},
	urldate = {2019-07-05},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Volkenborn, N. and Hedtkamp, S. I. C. and van Beusekom, J. E. E. and Reise, K.},
	month = aug,
	year = {2007},
	keywords = {bioturbation, bioirrigation, ecosystem engineering, intertidal sand, sediment properties, Wadden Sea},
	pages = {331--343},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\BC2CKC8G\\Volkenborn et al. - 2007 - Effects of bioturbation and bioirrigation by lugwo.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\chand\\Zotero\\storage\\EGX4KSQT\\S0272771407001394.html:text/html}
}

@article{vasquez-cardenas_species-specific_2016,
	title = {Species-specific effects of two bioturbating polychaetes on sediment chemoautotrophic bacteria},
	volume = {549},
	issn = {0171-8630, 1616-1599},
	url = {https://www.int-res.com/abstracts/meps/v549/p55-68/},
	doi = {10.3354/meps11679},
	abstract = {Bioturbation has major impacts on sediment biogeochemistry, which can be linked to the functional traits of the macrofauna involved. Nereis (Hediste) diversicolor and Marenzelleria viridis are 2 functionally different bioturbating polychaetes that strongly affect the ecology and biogeochemistry of coastal sediments. However, the different effects of these polychaetes on the activity and composition of microbial communities and on chemoautotrophic bacteria have not been extensively studied. We performed experiments with sediment aquaria that contained each species separately as well as a non-bioturbated control. Bacterial communities in different sediment zones (surface, burrow, subsurface) were characterized by phospholipid-derived fatty acid analysis combined with stable isotope labeling (13C bicarbonate) to quantify the dark CO2 fixation by chemoautotrophic bacteria. Pore water chemistry (ΣH2S and dissolved inorganic carbon) was additionally assessed in each treatment. The strong ventilation but low bioirrigation capacity in the open-ended burrows of N. diversicolor resulted in enhanced aerobic chemoautotrophic activity, potentially by sulfur oxidizing and nitrifying bacteria along the burrow. In contrast, slower ventilation and higher irrigation by M. viridis induced an advective mode of pore water transport. This promotes anaerobic chemoautotrophy around the blind-ended burrow and within the subsurface sediment. Sulfate-reducing bacteria were the dominant anaerobic chemoautotrophs that probably disproportionate sulfur. In conclusion, our analysis shows that bioturbating fauna influence the microbial community and chemoautotrophic activity in sediments, but that the effect strongly depends on the structure of the burrow and on species-specific ventilation behavior and irrigation capacity.},
	language = {en},
	urldate = {2019-07-05},
	journal = {Marine Ecology Progress Series},
	author = {Vasquez-Cardenas, Diana and Quintana, Cintia Organo and Meysman, Filip J. R. and Kristensen, Erik and Boschker, Henricus T. S.},
	month = may,
	year = {2016},
	keywords = {Fatty acids, Dark carbon fixation, Marenzelleria viridis, Microbes, Nereis (Hediste) diversicolor, PLFA, Stable isotope probing},
	pages = {55--68},
	file = {Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\N9K9LPQI\\Vasquez-Cardenas et al. - 2016 - Species-specific effects of two bioturbating polyc.pdf:application/pdf;Snapshot:C\:\\Users\\chand\\Zotero\\storage\\W6DVARMH\\p55-68.html:text/html}
}

@article{wrede_who_2017,
	title = {Who really matters: {Influence} of {German} {Bight} key bioturbators on biogeochemical cycling and sediment turnover},
	volume = {488},
	issn = {0022-0981},
	shorttitle = {Who really matters},
	url = {http://www.sciencedirect.com/science/article/pii/S0022098117300011},
	doi = {10.1016/j.jembe.2017.01.001},
	abstract = {Loss of bioturbating key species from marine sediments has been shown to strongly reduce benthic biogeochemical cycling and ecosystem functioning. It is thus of paramount importance to identify key bioturbators and quantify their effect on biogeochemical processes. To do so trait based community and species bioturbation potential (BPc and BPi) was mapped for 423 North Sea stations in the German Bight. Mapping of BPc and BPi identified Amphiura filiformis, Echinocardium cordatum and Nucula nitidosa as major bioturbating species in the German Bight. The effects of these species on benthic nutrient flux (i.e., changing concentrations of silicate ∆[SiO2], ammonium ∆[NH4+], nitrate ∆[NO3−] and nitrite ∆[NO2−]) were quantified in laboratory experiments together with their bioturbation rate (Db) and bioirrigation activity. The experiments indicated that mapped species bioturbation potential (BPi) may be a poor tool for identifying key bioturbators while calculated experimental BPi (expBPi) was a good indicator for species impact on biogeochemical cycling. Out of the three investigated species only E. cordatum significantly influenced biogeochemical cycling, whereas the effect of A. filiformis remained inconclusive potentially because arm damage and regeneration may affect the bioturbation activity of many individuals. The bivalve N. nitidosa showed only little impact on biogeochemical cycling, although this species was found to be an active bioturbator. Accordingly, E. cordatum may be considered one of the most important contributors to biogeochemical cycling at the sediment-water interface in the German Bight.},
	urldate = {2019-07-05},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Wrede, Alexa and Dannheim, Jennifer and Gutow, Lars and Brey, Thomas},
	month = mar,
	year = {2017},
	keywords = {Bioirrigation, Bioturbation potential, Sediment reworking},
	pages = {92--101},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\chand\\Zotero\\storage\\P7KRLW7L\\Wrede et al. - 2017 - Who really matters Influence of German Bight key .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\chand\\Zotero\\storage\\NFLPVW6W\\S0022098117300011.html:text/html}
}

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@article{pavlov_eegmanylabs_2020,
 abstract = {There is growing awareness across the neuroscience community that the replicability of findings on the relationship between brain activity and cognitive phenomena can be improved by conducting studies with high statistical power that adhere to well-defined and standardized analysis pipelines. Inspired by efforts from the psychological sciences, and with the desire to examine some of the foundational findings using electroencephalography (EEG), we have launched #EEGManyLabs, a large-scale international collaborative replication effort. Since its discovery in the early 20th century, EEG has had a profound influence on our understanding of human cognition, but there is limited evidence on the replicability of some of the most highly cited discoveries. After a systematic search and selection process, we have identified 27 of the most influential and continually cited studies in the field. We plan to directly test the replicability of key findings from 20 of these studies in teams of at least three independent laboratories. The design and protocol of each replication effort will be submitted as a Registered Report and peer-reviewed prior to data collection. Prediction markets, open to all EEG researchers, will be used as a forecasting tool to examine which findings the community expects to replicate. This project will update our confidence in some of the most influential EEG findings and generate a large open access database that can be used to inform future research practices. Finally, through this international effort, we hope to create a cultural shift towards inclusive, high-powered multi-laboratory collaborations.},
 author = {Pavlov, Yuri G. and Adamian, Nika and Appelhoff, Stefan and Arvaneh, Mahnaz and Christopher Benwell, Ph D. and Beste, Christian and Bland, Amy and Bradford, Daniel E. and Bublatzky, Florian and Busch, Niko and Clayson, Peter E. and Cruse, Damian and Czeszumski, Artur and Almenberg, Anna Dreber and Dumas, Guillaume and Ehinger, Benedikt Valerian and Ganis, Giorgio and He, Xun and Hinojosa, José Antonio and Huber-Huber, Christoph and Inzlicht, Michael and Jack, Bradley N. and Johannesson, Magnus and Jones, Rhiannon and Kaltwasser, Laura and Karimi-Rouzbahani, Hamid and König, Peter and Kouara, Layla and Kulke, Louisa and Ladouceur, Cecile and Langer, Nicolas and Liesefeld, Heinrich R. and Luque, David and MacNamara, Annmarie and Muthuraman, Muthuraman and Neal, Lauren and Nilsonne, Gustav and Galán, Julia Guiomar Niso and Ocklenburg, Sebastian and Oostenveld, Robert and Pernet, Dr Cyril and Pourtois, Gilles and Ruzzoli, Manuela and Sass, Sarah and Schaefer, Alexandre and Senderecka, Magdalena and Tamnes, Christian K. and Tognoli, Emmanuelle and Vugt, Marieke K. van and Verona, Edelyn and Vloeberghs, Robin and Welke, Dominik and Wessel, Jan and Zakharov, Ilya and Mushtaq, Faisal},
 doi = {10.31234/osf.io/528nr},
 file = {Pavlov et al_2020_.pdf:C\:\\Users\\Pavlov\\Zotero\\storage\\GSYMLCIH\\Pavlov et al_2020_.pdf:application/pdf},
 journal = {PsyArXiv},
 keywords = {⛔ No DOI found, Cognitive Neuroscience, Cognitive Psychology, EEG, ERP, ManyLabs, Meta-science, Neuroscience, Open Science, Replication, Social and Behavioral Sciences},
 month = {November},
 shorttitle = {#EEGManyLabs},
 title = {#EEGManyLabs: Investigating the Replicability of Influential EEG Experiments},
 url = {https://psyarxiv.com/528nr/},
 urldate = {2020-11-27},
 year = {2020}
}

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  author = {Kyriakos Schwarz and Ahmed Allam and Nicolas Andres Perez Gonzalez and Michael Krauthammer},
  doi = {https://doi.org/10.1186/s12859-021-04325-y},
  journal = {BMC Bioinformatics},
  title={AttentionDDI: Siamese Attention-based Deep Learning method for drug-drug interaction predictions},
  url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04325-y#Fun},
}

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text:
DESCRIPTION = "initramfs image to be used together with SiFive Unleashed board \
as the board currently only supports booting from a ramdisk image"

# Do not pollute the initrd image with rootfs features
IMAGE_FEATURES = ""

export IMAGE_BASENAME = "${MLPREFIX}riscv-initramfs-image"
IMAGE_LINGUAS = ""

LICENSE = "MIT"

IMAGE_FSTYPES += "${INITRAMFS_FSTYPES}"
inherit core-image

IMAGE_ROOTFS_SIZE = "8192"
IMAGE_ROOTFS_EXTRA_SPACE = "0"

BAD_RECOMMENDATIONS += "busybox-syslog"

# WIC is not compatible with an initramfs image, also enabling WIC would cause
# an circular dependency.
IMAGE_FSTYPES:remove = " wic wic.gz"

repository: YoeDistro/meta-riscv

repo_name: YoeDistro/meta-riscv

extension: bb


text:
@article{Bondaruk-2020-Assessing,
    title = "Assessing the state of the art in Discrete Global Grid Systems: OGC criteria and present functionality",
    author = "Bondaruk, Ben  and
      Roberts, Steven A.  and
      Robertson, Colin",
    journal = "Geomatica, Volume 74, Issue 1",
    volume = "74",
    number = "1",
    year = "2020",
    publisher = "Canadian Science Publishing",
    url = "https://aclanthology.org/G20-53001",
    doi = "10.1139/geomat-2019-0015",
    pages = "9--30",
    abstract = "The continuous growth of available geospatial data requires new methods for its integration, analysis, and visualization to be explored and implemented in software available to the geospatial community. Discrete Global Grid Systems (DGGS) are an emerging method for spatial data handling in the digital earth framework. DGGS are hierarchical data structures for discretizing the Earth{'}s surface that have seen considerable theoretical development over the last two decades. In this paper, four software implementations are reviewed, dggridR, H3, OpenEAGGR, and S2, to explore their potential applications in data modelling and GIS, as well as their performance. These software implementations were also evaluated against the recently published Open Geospatial Consortium (OGC) abstract specification. The results indicate great potential and versatility for utilizing such systems in geospatial analysis, if basic methods for converting and handling spatial features are further developed. The performance of these systems is shown to be highly scalable and operational with datasets of various sizes. Yet, it is demonstrated that the current software implementations generally fall short of fulfilling all of the OGC requirements or it was not possible to confirm their compliance. The assessment here identified that further enhancements, endorsement of OGC criteria, and their explicit acknowledgment within official documentation remain key research needs for the evaluated software packages. Further work developing operational DGGS that solve real world problems may promote greater community adoption and integration of DGGS data structures into commonly used geospatial platforms.",
}

repository: gwf-uwaterloo/gwf-publications

repo_name: gwf-uwaterloo/gwf-publications

branch_name: refs/heads/main

gha_language: Python


text:
@inproceedings{shakoor2017data,
 author = {Shakoor, Modesar and Gao, Jiaying and Liu, Zeliang and Liu, Wing Kam},
 booktitle = {International Workshop on Meshfree Methods for Partial Differential Equations},
 organization = {Springer},
 pages = {135--148},
 title = {A Data-Driven Multiscale Theory for Modeling Damage and Fracture of Composite Materials},
 year = {2017}
}


text:
@article{Alexandrou:2018sjm,
      author         = "Alexandrou, C. and Bacchio, S. and Constantinou, M. and
                        Finkenrath, J. and Hadjiyiannakou, K. and Jansen, K. and
                        Koutsou, G. and Vaquero Aviles-Casco, A.",
      title          = "{Proton and neutron electromagnetic form factors from
                        lattice QCD}",
      journal        = "Phys. Rev.",
      volume         = "D100",
      year           = "2019",
      number         = "1",
      pages          = "014509",
      doi            = "10.1103/PhysRevD.100.014509",
      eprint         = "1812.10311",
      archivePrefix  = "arXiv",
      primaryClass   = "hep-lat",
      reportNumber   = "DESY-18-033, DESY 18-033",
      SLACcitation   = "%%CITATION = ARXIV:1812.10311;%%"
}
@article{Alexandrou:2019lfo,
      author         = "Alexandrou, Constantia and Cichy, Krzysztof and
                        Constantinou, Martha and Hadjiyiannakou, Kyriakos and
                        Jansen, Karl and Scapellato, Aurora and Steffens,
                        Fernanda",
      title          = "{Systematic uncertainties in parton distribution
                        functions from lattice QCD simulations at the physical
                        point}",
      journal        = "Phys. Rev.",
      volume         = "D99",
      year           = "2019",
      number         = "11",
      pages          = "114504",
      doi            = "10.1103/PhysRevD.99.114504",
      eprint         = "1902.00587",
      archivePrefix  = "arXiv",
      primaryClass   = "hep-lat",
      reportNumber   = "DESY-19-001",
      SLACcitation   = "%%CITATION = ARXIV:1902.00587;%%"
}
@article{Alexandrou:2019mdw,
      author         = "Alexandrou, Constantia and Bacchio, Simone and
                        Constantinou, Martha and Howarth, Dean and Lauer, Colin
                        and Hadjiyiannakou, Kyriakos and Koutsou, Giannis and
                        Jansen, Karl",
      title          = "{Investigating volume effects for N$_f$=2 twisted clover
                        fermions at the physical point}",
      booktitle      = "{Proceedings, 36th International Symposium on Lattice
                        Field Theory (Lattice 2018): East Lansing, MI, United
                        States, July 22-28, 2018}",
      journal        = "PoS",
      volume         = "LATTICE2018",
      year           = "2019",
      pages          = "314",
      doi            = "10.22323/1.334.0314",
      eprint         = "1904.10013",
      archivePrefix  = "arXiv",
      primaryClass   = "hep-lat",
      SLACcitation   = "%%CITATION = ARXIV:1904.10013;%%"
}
@article{Alexandrou:2019ali,
      author         = "Alexandrou, C. and others",
      title          = "{Moments of nucleon generalized parton distributions from
                        lattice QCD simulations at physical pion mass}",
      journal        = "Phys. Rev.",
      volume         = "D101",
      year           = "2020",
      number         = "3",
      pages          = "034519",
      doi            = "10.1103/PhysRevD.101.034519",
      eprint         = "1908.10706",
      archivePrefix  = "arXiv",
      primaryClass   = "hep-lat",
      SLACcitation   = "%%CITATION = ARXIV:1908.10706;%%"
}
@article{Alexandrou:2019olr,
      author         = "Alexandrou, C. and Bacchio, S. and Constantinou, M. and
                        Finkenrath, J. and Hadjiyiannakou, K. and Jansen, K. and
                        Koutsou, G.",
      title          = "{Nucleon strange electromagnetic form factors}",
      journal        = "Phys. Rev.",
      volume         = "D101",
      year           = "2020",
      number         = "3",
      pages          = "031501",
      doi            = "10.1103/PhysRevD.101.031501",
      eprint         = "1909.10744",
      archivePrefix  = "arXiv",
      primaryClass   = "hep-lat",
      SLACcitation   = "%%CITATION = ARXIV:1909.10744;%%"
}
@article{Alexandrou:2019tmk,
      author         = "Alexandrou, Constantia and Berlin, Joshua and Finkenrath,
                        Jacob and Leontiou, Theodoros and Wagner, Marc",
      title          = "{Tetraquark interpolating fields in a lattice QCD
                        investigation of the $D_{s0}^\ast(2317)$ meson}",
      journal        = "Phys. Rev.",
      volume         = "D101",
      year           = "2020",
      number         = "3",
      pages          = "034502",
      doi            = "10.1103/PhysRevD.101.034502",
      eprint         = "1911.08435",
      archivePrefix  = "arXiv",
      primaryClass   = "hep-lat",
      SLACcitation   = "%%CITATION = ARXIV:1911.08435;%%"
}