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Refereed Papers

Papers

 

  • Wang, Y., Ye, J. and Borchers, D.L. (2022) Automated call detection for acoustic surveys with hierarchically structured calls of varying length. Methods in Ecology and Evolution 13: 1552-1567. https://doi.org/10.1111/2041-210X.13873.

 

 

  • Sharma, R.K., Sharma, K., Borchers, D.L. Bhatnagar, Y.V., Surywanshi, K.S. and Mishra, C. (2021) Spatial variation in population-density of snow leopards in a multiple use landscape in Spiti Valley, Trans-Himalaya. PloS One 16: https://doi.org/10.1371/journal.pone.0250900.

 

  • Durbach, I., Borchers, D.L., Sutherland, C. and Sharma, K. (2021) Fast, flexible alternatives to regular grid designs for spatial capture-recapture. Methods in Ecology and Evolution 12: 298–310. https://doi.org/10.1111/2041-210X.13517.

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  • Bachl, F.E., Lindgren, F., Borchers, D.L. and Illian, J. (2019) inlabru: an R package for Bayesian spatial modelling from ecological survey data. Methods in Ecology and Evolution 10: 760–766. https://doi.org/10.1111/2041-210X.13168.

 

  • Glennie, R., Borchers, D.L., Murchie, M., and Harmsen, B.J. and Foster, R.J. (2019) Open population maximum likelihood spatial capture-recapture. Biometrics, 75: 1345-1355. https://doi.org/10.1111/biom.13078.

 

  • Stevenson, B.C., Borchers, D.L. and Fewster, R.M. (2018) Cluster capture-recapture to account for identification uncertainty on aerial surveys of animal populations. Biometrics 75: 326-336.  https://doi.org/10.1111/biom.12983.

 

  • Loveridge, R., Kidney, D., Ty S., Eang S., Eames, J.C. & Borchers, D.L. 2017. First systematic survey of green peafowl Pavo muticus in northeastern Cambodia reveals a population stronghold and preference for disappearing riverine habitat. Cambodian Journal of Natural History 2: 157–167.

 

 

  • Yuan. Y, Bachl, F.E., Borchers, D.L, Lindgren, F., Illian, J.B., Buckland, S.T., Rue, H. and Gerrodette, T. (2017) Point process models for spatio-temporal distance sampling data from a large-scale survey of blue whales. Annals of Applied Statistics 11: 2270-2297.DOI:10.1214/17-AOAS1078.

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  • Kidney, D, Rawson, B.M., Borchers, D.L., Thomas, L, Marques, T.A. and Stevenson, B. (2016) An efficient acoustic density estimation method with human detectors, applied to gibbons in Cambodia. PloSOne. http://dx.doi.org/10.1371/journal.pone.0155066.

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  • Rekdal, S.L., Hansen, R.G., Borchers, D.L., Bachmann, L., Laidre, K.L., Wiig, O., Nielsen, N.H., Fossette, S., Tervo, O. and Heide-Jørgensen, M.P. (2015). Trends in bowhead whales in West Greenland: Aerial surveys vs. genetic capture-recapture analyses. Marine Mammal Science 31: 133-154.

 

 

  • Burt, M.L., Borchers, D.L., Jenkins, K.J. and Marques, T.A.M. (2014). Using mark-recapture distance sampling methods on line transect surveys. Methods in Ecology and Evolution 5: 1180-1191.

 

 

  • Hammond, P.S., Gillespie, D., Lovell, P., Samarra, F., Swift, R., Macleod, K., Tasker, M., Berggren, P., Borchers, D.L., Burt, M.L., Paxton, C.G.M., Cañadas, A. (2013). Large scale surveys for cetaceans: Line transect assumptions, reliability of abundance estimates and improving survey efficiency – A response to MacLeod. Biological Conservation 170: 338:339.

 

  • Arranz, P., Borchers, D.L., Aguilar Soto, N., Johnson, M. and Cox, M.J. (2014). A new method to study inshore whale cue distribution from land-based observations. Marine Mammal Science 30: 810-818

 

  • Hammond, P.S., Macleod, K., Berggren, P., Borchers, D.L., Burt, M.L., Cañadas, A., Desportes, G., Donovan, G.P., Gilles, A., Gillespie, D., Gordon, J., Hedley, S., Hiby, L., Kuklik, I., Leaper, R., Lehnert, K., Leopold, M., Lovell, P., Øien, N., Paxton, C., Ridoux, V., Rogan, E., Samarra, F., Scheidat, M., Sequeira, M., Siebert, U., Skov, H., Swift, R., Tasker, M.L., Teilmann, J., Van Canneyt, O. and Vázquez, J.A. (2013). Cetacean abundance and distribution in European Atlantic shelf waters to inform conservation and management. Biological Conservation 164: 107-122.

 

 

  • Cox, M.J., Borchers, D.L. and Kelly, N. (2013). nupoint: An R package for density estimation from point transects in the presence of nonuniform animal density. Methods in Ecology and Evolution 4: 589-594.

 

  • Langrock, R., Borchers, D.L. and Skaug, H. (2013). Markov-modulated nonhomogeneous Poisson processes for unbiased estimation of marine mammal abundance. Journal of the American Statistical Association 108: 840-851.

 

  • Efford, M.G. Borchers, D.L. and Mowat, G. (2013). Varying effort in capture-recapture studies. Methods in Ecology and Evolution 4: 629-636.

 

  • Burt, M.L., Borchers, D.L. and Ensor, P. (2012). Trackline detection probability of Antarctic minke whales: Analysis of the BT model experiments conducted on the IWC-SOWER cruises 2005/6-2007/8. Journal of Cetacean Research and Management 12: 307-316.

 

  • 65. Heide-Jørgensen, M.P., Laidre, K.L., Hansen, R.G., Burt, M.L., Borchers, D.L., Hansén, J., Harding, K., Rasmussen, M., Dietz, R and Teilmann, J. (2012). Rate of increase and current abundance of humpback whales in West Greenland. Journal of Cetacean Research and Management 12: 1-14.

 

  • Borchers, D.L. (2012). A non-technical overview of spatially explicit capture–recapture models. Journal of Ornithology 152: 435-444.

 

  • Bernal, M., Stratoudakis, Y., Wood, S., Ibaibarriaga, L., Valdes, L and Borchers, D.L. (2011). A revision of daily egg production estimation methods, with application to Atlanto-Iberian sardine. 1: Daily spawning synchronicity and estimates of egg mortality. ICES Journal of Marine Science 68: 519-527.

 

  • Bernal, M., Stratoudakis, Y., Wood, S., Ibaibarriaga, L., Valdes, L and Borchers, D.L. (2011). A revision of daily egg production estimation methods, with application to Atlanto-Iberian sardine. 2: Spatially and environmentally explicit estimates of egg production. ICES Journal of Marine Science 68: 528-536.

 

  • Cox, M.J., Borchers, D.L., Demer, D.A., Cutter, G.R. and Brierley, A.S. (2011). Estimating Antarctic krill (Eupausia superba) density from multibeam echosounder observations using distance sampling methods. Applied Statistics 60: 301-316. (2nd most cited Applied Statistics paper of 2011-12, as at 7/6/13)

 

  • Buckland, S.T., Laake, J.L. and Borchers, D.L. (2010). Double-observer line transect methods: levels of independence. Biometrics 66: 169-177.

 

  • Heide-Jørgensen, M.P., Laidre, K.L., Simon, M., Rasmussen, M., Burt, M.L. and Borchers, D.L. (2010). Abundance estimates of fin whales in West Greenland in 2007. Journal of Cetacean Research and Management 11: 83-88.

 

  • Heide-Jørgensen, M.P., Laidre, K.L., Burt, M.L., Borchers, D.L., Hansen, R.G., Rasmussen, M. And Fossette, S. (2010). Abundance of narwhals (Monodon monoceros) in Greenland. Journal of Mammalogy 91: 1135-1151.

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  • Borchers, D.L., Marques, T.A., Gunlaugsson, Th. and Jupp, P. (2010). Estimating distance sampling detection functions when distances are measured with errors. Journal of Agricultural, Biological, and Environmental Statistics 15: 346-361.

 

  • Marques, T.A., Buckland, S.T., Borchers, D.L., Tosh, D. and McDonald, R.A. (2010). Point transect sampling along linear features. Biometrics 66:1247-1255.

 

  • Heide-Jørgensen, M.P., Laidre, K.L., Borchers, D.L. Stem, H. and Simon, M.J. (2010). The effect of sea ice loss on beluga whales. Polar Research 29:198-208.

 

  • Fewster, R.M., Buckland, S.T., Burnham, K.P., Borchers, D.L., Jupp, P.E., Laake, J.L. and Thomas, L.J. (2009). Estimating the encounter rate variance in distance sampling. Biometrics 65: 225-236. (Adopted as primary increment in Distance software, Release 6, July 2009. Distance 6 had gained 8500 users as of November 2011. The journal's 5th most cited paper from 2009.)

 

  • Borchers, D.L., Pike, D., Gunlaugsson, Th. and Vikingson, G. (2009). Minke whale abundance estimation from the NASS 1987 and 2001 cue counting surveys taking account of distance estimation errors. North Atlantic Marine Mammal Commission Publications, Volume 7: North Atlantic Sightings Surveys (1987-2001): 95-110.

 

  • Cañadas, A., Donovan, G., Desportes, G. and Borchers, D.L. (2009). A short review of the distribution of short-beaked common dolphins (Delphinus delphis) in the central and eastern North Atlantic with an abundance estimate for part of this area. North Atlantic Marine Mammal Commission Publications, Volume 7: North Atlantic Sightings Surveys (1987-2001): 201-220.

 

  • Efford, M.G., Dawson, D. and Borchers, D.L. (2009). Population density estimated from locations of individuals on a passive detector array. Ecology 90: 2676-2682.

 

  • Efford, M.G., Borchers, D.L. and Byrom, A.E. (2008). Density estimation by spatially explicit capture-recapture: likelihood-based methods. In: D.L. Thompson, E.G. Cooch, M.J. Conroy (eds), Modeling Demographic Processes in Marked Populations. Springer, New York. pp 255-269.

 

  • Heide-Jørgensen, M.P., Borchers, D.L., Witting,L., Simon, M.J., Laidre, K.L., Rosing-Asvid, A. and Pike, D.G. (2008). Estimates of large whale abundance in West Greenland waters from an aerial survey in 2005. Journal of Cetacean Research and Management 10:119-129.

 

  • Fewster, R.M., Southwell, C., Borchers, D.L., Buckland, S.T. and Pople, A.R. (2008). The influence of animal mobility on the assumption of uniform distances in aerial line-transect surveys. Wildlife Research 35: 275-288.

 

  • Southwell, C., Paxton, C.G.M. and Borchers, D.L. (2008). Detectability of penguins in aerial surveys over the pack-ice off Antarctica. Wildlife Research 35: 349-357.

 

  • Borchers, D.L. and Efford, M. (2008). Spatially explicit maximum likelihood methods for capture-recapture studies. Biometrics 64: 377-385. (The journal's most cited paper from 2008.)

 

  • Southwell, C., Paxton, C.G.M., Borchers, D.L., Boveng, P., Rogers, T., de la Mare, W.K. (2008). Uncommon or cryptic? Challenges in estimating leopard seal abundance by conventional but state-or-the-art methods. Deep-Sea Research 55: 519-531.

 

  • Bernal, M., Ibaibarriaga, L., Lago de Lanzos, A., Lonergan, M. Hernandez, C. Franco, C. Rasines, I., Valdes, L. and Borchers, D.L. (2008). Using multinomial models to analyse data from sardine incubation experiments; a review of advances in fish egg incubation analysis techniques. ICES Journal of Marine Science 65: 51-59

 

  • Buckland, S.T., Borchers, D.L., Johnston, A., Henrys, P.A. and Marques, L. (2007). Line transect methods for plant surveys. Biometrics 63: 989-998.

 

  • Heide-Jorgensen, M.P., Laidre, K., Borchers, D.L., Samarra, F. and Stern, H. (2007). Increasing abundance of bowhead whales in west Greenland. Biology Letters 3: 577-580.

 

  • Southwell, C., Borchers, D.L., Paxton, C.G.M., Burt, M.L. and de la Mare, W. (2007). Estimation of detection probability in aerial surveys of Antarctic pack-ice seals. Journal of Agricultural, Biological, and Environmental Statistics 12: 41-54.

 

  • Southwell, C., Paxton, C.G.M., Borchers, D.L., Boveng, P. and de la Mare, W. (2007). Taking account of dependent species in management of the Southern Ocean krill fishery: estimating crabeater seal abundance off east Antarctica. Journal of Applied Ecology 45: 622-631.

 

  • Ibaibarriaga, L., Bernal, M., Motos, L., Uriarte, A., Lonergan, M.E., Borchers, D.L. and Wood, S.N. (2007). Estimation of development properties of stage-classified biological processes using multinomial models: a case study of the Bay of Biscay anchovy (Engraulis encrasicolis, L.) egg development. Canadian Journal of Fisheries and Aquatic Sciences 64: 539-553.

 

  • Borchers, D.L., Laake, J.L., Southwell, C. and Paxton, C.G.M. (2006). Accommodating unmodelled heterogeneity in double-observer distance sampling surveys. Biometrics 62: 372-378. (Primary increment in Distance 5, 2006, and further releases. Biometrics' 8th most cited paper from 2006.)

 

  • Buckland, S.T., Summers, R.W., Borchers, D.L. and Thomas, L.J. (2005). Point transect sampling with traps or lures. Journal of Applied Ecology 43: 377-384.

 

  • Borchers, D.L. (2005). Estimating detection probability from line transect cetacean surveys when detection on the line is not certain: an overview. in Thomsen, F., Ugarte, F and Evans, P.G.H. (eds) Proceedings of the workshop on estimation of g(0) in line transect surveys of cetaceans. ECS Newsletter 44 – Special Issue. 46pp.

 

  • Cañadas, A., Desportes, G. and Borchers, D.L. (2004). The estimation of the detection function and g(0) for short-beaked common dolphins (Delphinis delphis), using double-platform data collected during the NASS-95 Faroese survey. Journal of Cetacean Research and Management 6: 191-198.

 

  • Southwell, C., de la Mare, B., Borchers, D.L. and Burt, L. (2004). Shipboard line transect surveys of Crabeater seal abundance in the pack-ice off eastern Antarctica: evaluation of assumptions. Marine Mammal Science 20: 602-620.

 

  • Stratoudakis, Y., Bernal, M., Borchers, D.L., Borges, M.F., Cardador, F. (2003). Changes in the distribution of sardine eggs and larvae off Portugal, 1985-2000. Fisheries Oceanography 12: 49-60.

 

  • Clarke, E.D., Spear, L., McCracken, M., Marques, F.F.C., Borchers, D.L., Buckland, S.T. and Ainley, D.G. (2003). Validating the use of generalised additive models and at-sea surveys to estimate size and temporal trends of seabird populations. Journal of Applied Ecology 40: 278-292.

 

  • Butterworth, D.S., Borchers, D.L., and Punt, A.E. (2002). Dynamic response analysis for the eastern North Pacigic gray whale population: An alternative approach. Journal of Cetacean Research and Management 4: 77-83.

 

  • Hammond, P.S, Berggren, P., Benke, H., Borchers, D.L., Collet, A., Heide-Jørgensen, M.P., Heimlich-Boran, S., Hiby, A.R. Leopold, M.F. Øien. (2002). Abundance of harbour porpoises and other cetaceans in the North Sea and adjacent waters. Journal of Applied Ecology 39: 361-376. (4th most cited Journal of Applied Ecology paper from 2002.)

 

  • Buckland, S.T., Thomas, L, Marques, F.F.C., Strindberg, S., Hedley, S.L., Pollard, J.H., Borchers, D.L. and Burt, M.L. (2002). Distance sampling: recent advances and future directions. In Anderson, Barnett, Chatwin and El-Shaarawi (eds). Quantitative methods for Current Environmental Issues. Springer.

 

  • Thomas, L., Buckland, S.T., Burnham, K.P., Anderson, D.R., Laake, J.L., Borchers, D.L. and Strindberg, S. (2002). Distance sampling. In Encyclopedia of Environmetrics. A.H. El-Shaarawi & W. W. Piegorsch. John Wiley & Sons, Chichester, 544-552.

 

  • Bernal, M., Borchers, D.L., Valdés, L., Lago de Lanzós, A. and Buckland, S.T. (2001). A new ageing method for eggs of fish species with daily spawning synchronicity. Canadian Journal of Fisheries and Aquatic Sciences 58: 2330-2340.

 

  • Marques, F.F.C., Buckland, S.T., Goffin, D., Dixon, C.E. Borchers, D.L., Mayle, B.A. and Peace, A.J. (2001). Estimating deer abundance from line transect surveys of dung: sika deer in southern Scotland. Journal of Applied Ecology 38: 349-363.

 

  • Hedley, S. L., Buckland, S.T. and Borchers, D.L. (2001). Spatial modelling from line transect data. Journal of Cetacean Research Management 1: 255-264.

 

  • Buckland, S.T., Goudie, I.B.J. and Borchers, D.L. (2000). Wildlife population assessment: past developments and future directions. Biometrics 56: 1-12.

 

  • Buckland, S.T., Augustin, N.H., Trenkel, V.M., Elston, D.A. and Borchers, D.L. (2000). Simulated inference, with applications to wildlife population assessment. Metron 58: 1-22.

 

  • Borchers, D.L. (1999). Composite mark-recapture line transect surveys. In Garner, G.W., Amstrup, S.C., Laake, J.L., Manly, B.F., McDonald, L.L. and Robertson, D.G. (eds) Marine Mammals Survey and Assessment Methods. Balkema, Rotterdam: 115-126.

 

  • Borchers, D.L., Zucchini, W. and Fewster, R.M. (1998). Mark-recapture models for line transect surveys. Biometrics 54: 1207-1220. (Biometrics editor's choice as best Biometrics paper in 1997 and 1998.) (Editor's Invited Paper at the International Biometrics Conference, Cape Town, 1998. Primary increment in Distance software, Release 5, 2006. Release 5 gained 8,200 users before the next release.)

 

  • Borchers, D.L., Buckland, S.T., Goedhart, P.W., Clarke, E.D. and Hedley, S.L. (1998). Horvitz-Thompson estimators for line transect surveys. Biometrics 54: 1221-1237.

 

  • Augustin, N.H., Borchers, D.L., Buckland, S.T. Clarke, E.D. and Walsh, M. (1998). Spatio-temporal models to improve the annual egg production method. Canadian Journal of Fisheries and Aquatic Sciences 55: 2608-2621.

 

  • Borchers, D.L., Buckland, S.T., Priede, I.G. and Ahmadi, S. (1997). Improving the precision of the daily egg production method using generalized additive models. Canadian Journal of Fisheries and Aquatic Sciences 54: 2727-2742.

 

  • Borchers, D.L., Richardson, A. and Motos, L. (1997). Modelling the spatial distribution of fish eggs using generalized additive models. Ozeanografika 2: 103-120.

 

  • Punt, A.E., Cooke, J.G., Borchers, D.L. and Strindberg, S. (1997). Estimating the extend of additional variance for southern hemisphere minke whales from the results of the IWC/IDCR cruises. Reports of the International Whaling Commission 47: 431-434.

 

  • Hedley, S.L., Borchers, D.L. and Buckland, S.T. (1997). A review of analysis options for implementation in the IWC database and estimation software system. Reports of the International Whaling Commission 47: 885-895.

 

  • Augustin, N.H., Borchers, D.L., Mugglestone, M.A. and Buckland, S.T. (1996). Regression methods with spatially referenced data, Aspects of Applied Biology 46: 67-74.

 

  • Punt, A.E., Cooke, J.G. and Borchers, D.L. (1996). Estimating the extent of process error for southern hemisphere minke whales from the results of the IWC/IDCR cruises. Reports of the International Whaling Commission 46: 113.

 

  • Borchers, D.L. (1995). A summary of IWC methods and recommendations for inter-annual comparisons of southern hemisphere minke whale abundance estimates from IDCR cruises. Reports of the International Whaling Commission 45: 112-113.

 

  • Borchers, D.L. (1994). Methods of estimating mean school size from IWC sightings survey data. Reports of the International Whaling Commission 44: 429-437.

 

  • Borchers, D.L. (1994). Rough estimates of humpback whale abundance south of 30S. Reports of the International Whaling Commission 44: 107.

 

  • Cockroft, V.G., Ross, G.J.B., Peddemors, V.M., Borchers, D.L. (1992). Estimates of abundance and undercounting of bottlenose dolphins off northern Natal, South Africa. South African Journal of Wildlife Research 22: 102109.

 

  • Butterworth, D.S., Punt, A.E., Bergh, M.O. and Borchers, D.L. (1992). Assessment and management of South African marine resources during the period of the Benguela Ecology Programme: Key lessons and future directions. South African Journal of Marine Science 12: 989-1004.

 

  • Butterworth, D.S. and Borchers, D.L. (1990). Comparison of Antarctic minke school densities in closing and passing (with IO) mode. Reports of the International Whaling Commission 40: 142-143.

 

  • Borchers, D.L. and Haw, M.D. (1990). Analysis of the School Identity and Cuecounting experiments conducted on the 1988/89 Antarctic sightings survey. Reports of the International Whaling Commission 40: 277-288.

 

  • Borchers, D.L. and Haw, M.D. (1990). Determination of minke whale response to a transiting survey vessel from visual tracking of sightings. Reports of the International Whaling Commission 40: 257270.

 

  • Borchers, D.L. (1989). Calculations of mean school size and effective strip search width for surveys conducted in Area II in 1986/87. Reports of the International Whaling Commission 39: 80.

 

  • Borchers, D.L. (1989). Estimates of g(0) based on duplicate sightings of whales during surveys in Area II in 1986/87. Reports of the International Whaling Commission 39: 80.

 

  • Butterworth, D.S. and Borchers, D.L. (1988). Estimates of g(0) for minke schools from the results of the independent observer experiment on the 1985/86 and 1986/87 IWC/IDCR Antarctic assessment cruises. Reports of the International Whaling Commission 38: 302-313.

 

  • Butterworth, D.S. and Borchers, D.L. (1988). Kelker strip estimates of minke whale density in strata adopted for the analysis of the 1978/79-1983/84 sightings data in SC/39/Mi18. Reports of the International Whaling Commission 38: 81.

Software

An R package for animal abundance estimation via conventional, multiple covariate and mark-recapture distance sampling. Detection function fitting is performed via maximum likelihood. Also included are diagnostics and plotting for fitted detection functions.

Authors: Laake. J.L, Borchers, D.L., Thomas, L., Miller, D. and Bishop, J.

 

An R package for line transect abundance estimation when animals are stochastically available for detection (due to diving under water, for example). Based on methods of this papre: Borchers, D.L., Zucchini, W., Heide-Jørgenssen, M.P., Canadas, A. and Langrock, R. (2013). Using hidden Markov models to deal with availability bias on line transect surveys. Biometrics 69: 703-713. Currently updating to incrporate double-observer methods, similar to this paper: Borchers, D.L. and Langrock, R. (in press) Double-observer line transect surveys with Markov-modulated Poisson process models for overdispersed animal availability. Biometrics.

Authors: Borchers, D.L. and, Jefferson, C.

 

  • admbsecr: github (superceded by package ascr)

An R package for spatial capture-recapture density estimation using spatial capture histories and supplementary information (signal strength, time of acoustic signal arrival, estimated bearing, and/or estimated distance to detections). It uses AD Model Builder (see here) to obtain maximum likelihood estimates of parameters. This is faster than the package secr (available here) except when there are very few model parameters to be estimated, the more so the greater the number of parameters to be estimated. It is not nearly as general as secr but secr accommodates only signal strength as supplementary information. Estimation methods are described in Borchers, D.L., Stevenson, B.C., Kidney, D., Thomas, L.J. and Marques, T.A. (2015) A unifying model for capture-recapture and distance sampling surveys. Journal of the American Statistical Association 110: 195-204 and Stevenson, B.C., Borchers, D.L., Altwegg, R., Swift, R.J., Gillespie, D.M. and Measey, G.J. (2015). An acoustic spatially explicit capture-recapture method for estimating density of visually cryptic species. Methods in Ecology and Evolution 6: 38-48. and .

Authors: Stevenson, B.C. and Borchers, D.L.

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Software
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