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1. Spectral confocal reflection microscopy using a white light source

Author

Booth Martin J., Juškaitis Rimas, and Wilson Tony

Subjects
confocal microscopy, supercontinuum, reflection, spectrometry, Applied optics. Photonics, TA1501-1820, Optics. Light, QC350-467
Abstract

We present a reflection confocal microscope incorporating a white light supercontinuum source and spectral detection. The microscope provides images resolved spatially in three-dimensions, in addition to spectral resolution covering the wavelength range 450-650 nm. Images and reflection spectra of artificial and natural specimens are presented, showing features that are not normally revealed in conventional microscopes or confocal microscopes using discrete-line lasers. The specimens include thin film structures on semiconductor chips, iridescent structures in Papilio blumei butterfly scales, nacre from abalone shells and opal gemstones. Quantitative size and refractive index measurements of transparent beads are derived from spectral interference bands.

Published
2008
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2. Temperature synchronizes temporal variation in laying dates across European hole-nesting passerines

Author

Vriend, S. J. (Stefan J. G.), Grotan, V. (Vidar), Gamelon, M. (Marlene), Adriaensen, F. (Frank), Ahola, M. P. (Markus P.), Alvarez, E. (Elena), Bailey, L. D. (Liam D.), Barba, E. (Emilio), Bouvier, J.-C. (Jean-Charles), Burgess, M. D. (Malcolm D.), Bushuev, A. (Andrey), Camacho, C. (Carlos), Canal, D. (David), Charmantier, A. (Anne), Cole, E. F. (Ella F.), Cusimano, C. (Camillo), Doligez, B. F. (Blandine F.), Drobniak, S. M. (Szymon M.), Dubiec, A. (Anna), Eens, M. (Marcel), Eeva, T. (Tapio), Erikstad, K. E. (Kjell Einar), Ferns, P. N. (Peter N.), Goodenough, A. E. (Anne E.), Hartley, I. R. (Ian R.), Hinsley, S. A. (Shelley A.), Ivankina, E. (Elena), Juskaitis, R. (Rimvydas), Kempenaers, B. (Bart), Kerimov, A. B. (Anvar B.), Kalas, J. A. (John Atle), Lavigne, C. (Claire), Leivits, A. (Agu), Mainwaring, M. C. (Mark C.), Martinez-Padilla, J. (Jesus), Matthysen, E. (Erik), van Oers, K. (Kees), Orell, M. (Markku), Pinxten, R. (Rianne), Reiertsen, T. K. (Tone Kristin), Rytkönen, S. (Seppo), Senar, J. C. (Juan Carlos), Sheldon, B. C. (Ben C.), Sorace, A. (Alberto), Torok, J. (Janos), Vatka, E. (Emma), Visser, M. E. (Marcel E.), Saether, B.-E. (Bernt-Erik), Vriend, S. J. (Stefan J. G.), Grotan, V. (Vidar), Gamelon, M. (Marlene), Adriaensen, F. (Frank), Ahola, M. P. (Markus P.), Alvarez, E. (Elena), Bailey, L. D. (Liam D.), Barba, E. (Emilio), Bouvier, J.-C. (Jean-Charles), Burgess, M. D. (Malcolm D.), Bushuev, A. (Andrey), Camacho, C. (Carlos), Canal, D. (David), Charmantier, A. (Anne), Cole, E. F. (Ella F.), Cusimano, C. (Camillo), Doligez, B. F. (Blandine F.), Drobniak, S. M. (Szymon M.), Dubiec, A. (Anna), Eens, M. (Marcel), Eeva, T. (Tapio), Erikstad, K. E. (Kjell Einar), Ferns, P. N. (Peter N.), Goodenough, A. E. (Anne E.), Hartley, I. R. (Ian R.), Hinsley, S. A. (Shelley A.), Ivankina, E. (Elena), Juskaitis, R. (Rimvydas), Kempenaers, B. (Bart), Kerimov, A. B. (Anvar B.), Kalas, J. A. (John Atle), Lavigne, C. (Claire), Leivits, A. (Agu), Mainwaring, M. C. (Mark C.), Martinez-Padilla, J. (Jesus), Matthysen, E. (Erik), van Oers, K. (Kees), Orell, M. (Markku), Pinxten, R. (Rianne), Reiertsen, T. K. (Tone Kristin), Rytkönen, S. (Seppo), Senar, J. C. (Juan Carlos), Sheldon, B. C. (Ben C.), Sorace, A. (Alberto), Torok, J. (Janos), Vatka, E. (Emma), Visser, M. E. (Marcel E.), and Saether, B.-E. (Bernt-Erik)

Abstract

Identifying the environmental drivers of variation in fitness-related traits is a central objective in ecology and evolutionary biology. Temporal fluctuations of these environmental drivers are often synchronized at large spatial scales. Yet, whether synchronous environmental conditions can generate spatial synchrony in fitness-related trait values (i.e., correlated temporal trait fluctuations across populations) is poorly understood. Using data from long-term monitored populations of blue tits (Cyanistes caeruleus, n = 31), great tits (Parus major, n = 35), and pied flycatchers (Ficedula hypoleuca, n = 20) across Europe, we assessed the influence of two local climatic variables (mean temperature and mean precipitation in February-May) on spatial synchrony in three fitness-related traits: laying date, clutch size, and fledgling number. We found a high degree of spatial synchrony in laying date but a lower degree in clutch size and fledgling number for each species. Temperature strongly influenced spatial synchrony in laying date for resident blue tits and great tits but not for migratory pied flycatchers. This is a relevant finding in the context of environmental impacts on populations because spatial synchrony in fitness-related trait values among populations may influence fluctuations in vital rates or population abundances. If environmentally induced spatial synchrony in fitness-related traits increases the spatial synchrony in vital rates or population abundances, this will ultimately increase the risk of extinction for populations and species. Assessing how environmental conditions influence spatiotemporal variation in trait values improves our mechanistic understanding of environmental impacts on populations.

Published
2023

5. Expert range maps of global mammal distributions harmonised to three taxonomic authorities

Author

Marsh, CJ, Sica, YV, Burgin, CJ, Dorman, WA, Anderson, RC, del Toro Mijares, I, Vigneron, JG, Barve, V, Dombrowik, VL, Duong, M, Guralnick, R, Hart, JA, Maypole, JK, McCall, K, Ranipeta, A, Schuerkmann, A, Torselli, MA, Lacher, T, Mittermeier, RA, Rylands, AB, Sechrest, W, Wilson, DE, Abba, AM, Aguirre, LF, Arroyo-Cabrales, J, Astua, D, Baker, AM, Braulik, G, Braun, JK, Brito, J, Busher, PE, Burneo, SF, Camacho, MA, Cavallini, P, de Almeida Chiquito, E, Cook, JA, Cserkesz, T, Csorba, G, Cuellar Soto, E, da Cunha Tavares, V, Davenport, TRB, Demere, T, Denys, C, Dickman, CR, Eldridge, MDB, Fernandez-Duque, E, Francis, CM, Frankham, G, Franklin, WL, Freitas, T, Friend, JA, Gadsby, EL, Garbino, GST, Gaubert, P, Giannini, N, Giarla, T, Gilchrist, JS, Gongora, J, Goodman, SM, Gursky-Doyen, S, Hacklander, K, Hafner, MS, Hawkins, M, Helgen, KM, Heritage, S, Hinckley, A, Hintsche, S, Holden, M, Holekamp, KE, Honeycutt, RL, Huffman, BA, Humle, T, Hutterer, R, Ibanez Ulargui, C, Jackson, SM, Janecka, J, Janecka, M, Jenkins, P, Juskaitis, R, Juste, J, Kays, R, Kilpatrick, CW, Kingston, T, Koprowski, JL, Krystufek, B, Lavery, T, Lee, TE, Leite, YLR, Novaes, RLM, Lim, BK, Lissovsky, A, Lopez-Antonanzas, R, Lopez-Baucells, A, MacLeod, CD, Maisels, FG, Mares, MA, Marsh, H, Mattioli, S, Meijaard, E, Monadjem, A, Morton, FB, Musser, G, Nadler, T, Norris, RW, Ojeda, A, Ordonez-Garza, N, Pardinas, UFJ, Patterson, BD, Pavan, A, Pennay, M, Pereira, C, Prado, J, Queiroz, HL, Richardson, M, Riley, EP, Rossiter, SJ, Rubenstein, DI, Ruelas, D, Salazar-Bravo, J, Schai-Braun, S, Schank, CJ, Schwitzer, C, Sheeran, LK, Shekelle, M, Shenbrot, G, Soisook, P, Solari, S, Southgate, R, Superina, M, Taber, AB, Talebi, M, Taylor, P, Vu Dinh, T, Ting, N, Tirira, DG, Tsang, S, Turvey, ST, Valdez, R, Van Cakenberghe, V, Veron, G, Wallis, J, Wells, R, Whittaker, D, Williamson, EA, Wittemyer, G, Woinarski, J, Zinner, D, Upham, NS, Jetz, W, Marsh, CJ, Sica, YV, Burgin, CJ, Dorman, WA, Anderson, RC, del Toro Mijares, I, Vigneron, JG, Barve, V, Dombrowik, VL, Duong, M, Guralnick, R, Hart, JA, Maypole, JK, McCall, K, Ranipeta, A, Schuerkmann, A, Torselli, MA, Lacher, T, Mittermeier, RA, Rylands, AB, Sechrest, W, Wilson, DE, Abba, AM, Aguirre, LF, Arroyo-Cabrales, J, Astua, D, Baker, AM, Braulik, G, Braun, JK, Brito, J, Busher, PE, Burneo, SF, Camacho, MA, Cavallini, P, de Almeida Chiquito, E, Cook, JA, Cserkesz, T, Csorba, G, Cuellar Soto, E, da Cunha Tavares, V, Davenport, TRB, Demere, T, Denys, C, Dickman, CR, Eldridge, MDB, Fernandez-Duque, E, Francis, CM, Frankham, G, Franklin, WL, Freitas, T, Friend, JA, Gadsby, EL, Garbino, GST, Gaubert, P, Giannini, N, Giarla, T, Gilchrist, JS, Gongora, J, Goodman, SM, Gursky-Doyen, S, Hacklander, K, Hafner, MS, Hawkins, M, Helgen, KM, Heritage, S, Hinckley, A, Hintsche, S, Holden, M, Holekamp, KE, Honeycutt, RL, Huffman, BA, Humle, T, Hutterer, R, Ibanez Ulargui, C, Jackson, SM, Janecka, J, Janecka, M, Jenkins, P, Juskaitis, R, Juste, J, Kays, R, Kilpatrick, CW, Kingston, T, Koprowski, JL, Krystufek, B, Lavery, T, Lee, TE, Leite, YLR, Novaes, RLM, Lim, BK, Lissovsky, A, Lopez-Antonanzas, R, Lopez-Baucells, A, MacLeod, CD, Maisels, FG, Mares, MA, Marsh, H, Mattioli, S, Meijaard, E, Monadjem, A, Morton, FB, Musser, G, Nadler, T, Norris, RW, Ojeda, A, Ordonez-Garza, N, Pardinas, UFJ, Patterson, BD, Pavan, A, Pennay, M, Pereira, C, Prado, J, Queiroz, HL, Richardson, M, Riley, EP, Rossiter, SJ, Rubenstein, DI, Ruelas, D, Salazar-Bravo, J, Schai-Braun, S, Schank, CJ, Schwitzer, C, Sheeran, LK, Shekelle, M, Shenbrot, G, Soisook, P, Solari, S, Southgate, R, Superina, M, Taber, AB, Talebi, M, Taylor, P, Vu Dinh, T, Ting, N, Tirira, DG, Tsang, S, Turvey, ST, Valdez, R, Van Cakenberghe, V, Veron, G, Wallis, J, Wells, R, Whittaker, D, Williamson, EA, Wittemyer, G, Woinarski, J, Zinner, D, Upham, NS, and Jetz, W

Abstract

AIM: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). LOCATION: Global. TAXON: All extant mammal species. METHODS: Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). RESULTS: Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. MAIN CONCLUSION: Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.

Published
2022

6. Bird populations most exposed to climate change are less sensitive to climatic variation

Author

Bailey, L. D. (Liam D.), van de Pol, M. (Martijn), Adriaensen, F. (Frank), Arct, A. (Aneta), Barba, E. (Emilio), Bellamy, P. E. (Paul E.), Bonamour, S. (Suzanne), Bouvier, J.-C. (Jean-Charles), Burgess, M. D. (Malcolm D.), Charmantier, A. (Anne), Cusimano, C. (Camillo), Doligez, B. (Blandine), Drobniak, S. M. (Szymon M.), Dubiec, A. (Anna), Eens, M. (Marcel), Eeva, T. (Tapio), Ferns, P. N. (Peter N.), Goodenough, A. E. (Anne E.), Hartley, I. R. (Ian R.), Hinsley, S. A. (Shelley A.), Ivankina, E. (Elena), Juskaitis, R. (Rimvydas), Kempenaers, B. (Bart), Kerimov, A. B. (Anvar B.), Lavigne, C. (Claire), Leivits, A. (Agu), Mainwaring, M. C. (Mark C.), Matthysen, E. (Erik), Nilsson, J.-A. (Jan-Ake), Orell, M. (Markku), Rytkönen, S. (Seppo), Carlos Senar, J. (Juan), Sheldon, B. C. (Ben C.), Sorace, A. (Alberto), Stenning, M. J. (Martyn J.), Torok, J. (Janos), van Oers, K. (Kees), Vatka, E. (Emma), Vriend, S. J. (Stefan J. G.), Visser, M. E. (Marcel E.), Bailey, L. D. (Liam D.), van de Pol, M. (Martijn), Adriaensen, F. (Frank), Arct, A. (Aneta), Barba, E. (Emilio), Bellamy, P. E. (Paul E.), Bonamour, S. (Suzanne), Bouvier, J.-C. (Jean-Charles), Burgess, M. D. (Malcolm D.), Charmantier, A. (Anne), Cusimano, C. (Camillo), Doligez, B. (Blandine), Drobniak, S. M. (Szymon M.), Dubiec, A. (Anna), Eens, M. (Marcel), Eeva, T. (Tapio), Ferns, P. N. (Peter N.), Goodenough, A. E. (Anne E.), Hartley, I. R. (Ian R.), Hinsley, S. A. (Shelley A.), Ivankina, E. (Elena), Juskaitis, R. (Rimvydas), Kempenaers, B. (Bart), Kerimov, A. B. (Anvar B.), Lavigne, C. (Claire), Leivits, A. (Agu), Mainwaring, M. C. (Mark C.), Matthysen, E. (Erik), Nilsson, J.-A. (Jan-Ake), Orell, M. (Markku), Rytkönen, S. (Seppo), Carlos Senar, J. (Juan), Sheldon, B. C. (Ben C.), Sorace, A. (Alberto), Stenning, M. J. (Martyn J.), Torok, J. (Janos), van Oers, K. (Kees), Vatka, E. (Emma), Vriend, S. J. (Stefan J. G.), and Visser, M. E. (Marcel E.)

Abstract

The phenology of many species shows strong sensitivity to climate change; however, with few large scale intra-specific studies it is unclear how such sensitivity varies over a species’ range. We document large intra-specific variation in phenological sensitivity to temperature using laying date information from 67 populations of two co-familial European songbirds, the great tit (Parus major) and blue tit (Cyanistes caeruleus), covering a large part of their breeding range. Populations inhabiting deciduous habitats showed stronger phenological sensitivity than those in evergreen and mixed habitats. However, populations with higher sensitivity tended to have experienced less rapid change in climate over the past decades, such that populations with high phenological sensitivity will not necessarily exhibit the strongest phenological advancement. Our results show that to effectively assess the impact of climate change on phenology across a species’ range it will be necessary to account for intra-specific variation in phenological sensitivity, climate change exposure, and the ecological characteristics of a population.

Published
2022

12. Interaction of climate change with effects of conspecific and heterospecific density on reproduction

Author

Moller, A. P. (Anders Pape), Balbontin, J. (Javier), Dhondt, A. A. (Andre A.), Adriaensen, F. (Frank), Artemyev, A. (Alexandr), Banbura, J. (Jerzy), Barba, E. (Emilio), Biard, C. (Clotilde), Blondel, J. (Jacques), Bouvier, J.-C. (Jean-Charles), Camprodon, J. (Jordi), Cecere, F. (Francesco), Charter, M. (Motti), Cichon, M. (Mariusz), Cusimano, C. (Camillo), Dubiec, A. (Anna), Eens, M. (Marcel), Eeva, T. (Tapio), Ferns, P. N. (Peter N.), Forsman, J. T. (Jukka T.), Goldshtein, A. (Aya), Goodenough, A. E. (Anne E.), Gosler, A. G. (Andrew G.), Gustafsson, L. (Lars), Harnist, I. (Iga), Hartley, I. R. (Ian R.), Heeb, P. (Philipp), Hinsley, S. A. (Shelley A.), Jacob, S. (Staffan), Jarvinen, A. (Antero), Juskaitis, R. (Rimvydas), Korpimaki, E. (Erkki), Krams, I. (Indrikis), Laaksonen, T. (Toni), Leclercq, B. (Bernard), Lehikoinen, E. (Esa), Loukola, O. (Olli), Mainwaring, M. C. (Mark C.), Mand, R. (Raivo), Massa, B. (Bruno), Matthysen, E. (Erik), Mazgajski, T. D. (Tomasz D.), Merino, S. (Santiago), Mitrus, C. (Cezary), Monkkonen, M. (Mikko), Nager, R. G. (Ruedi G.), Nilsson, J.-a. (Jan-ake), Nilsson, S. G. (Sven G.), Norte, A. C. (Ana C.), von Numers, M. (Mikael), Orell, M. (Markku), Pimentel, C. S. (Carla S.), Pinxten, R. (Rianne), Priedniece, I. (Ilze), Remes, V. (Vladimir), Richner, H. (Heinz), Robles, H. (Hugo), Rytkonen, S. (Seppo), Senar, J. C. (Juan Carlos), Seppanen, J. T. (Janne T.), da Silva, L. P. (Luis P.), Slagsvold, T. (Tore), Solonen, T. (Tapio), Sorace, A. (Alberto), Stenning, M. J. (Martyn J.), Torok, J. (Janos), Tryjanowski, P. (Piotr), van Noordwijk, A. J. (Arie J.), Walankiewicz, W. (Wieslaw), Lambrechts, M. M. (Marcel M.), Moller, A. P. (Anders Pape), Balbontin, J. (Javier), Dhondt, A. A. (Andre A.), Adriaensen, F. (Frank), Artemyev, A. (Alexandr), Banbura, J. (Jerzy), Barba, E. (Emilio), Biard, C. (Clotilde), Blondel, J. (Jacques), Bouvier, J.-C. (Jean-Charles), Camprodon, J. (Jordi), Cecere, F. (Francesco), Charter, M. (Motti), Cichon, M. (Mariusz), Cusimano, C. (Camillo), Dubiec, A. (Anna), Eens, M. (Marcel), Eeva, T. (Tapio), Ferns, P. N. (Peter N.), Forsman, J. T. (Jukka T.), Goldshtein, A. (Aya), Goodenough, A. E. (Anne E.), Gosler, A. G. (Andrew G.), Gustafsson, L. (Lars), Harnist, I. (Iga), Hartley, I. R. (Ian R.), Heeb, P. (Philipp), Hinsley, S. A. (Shelley A.), Jacob, S. (Staffan), Jarvinen, A. (Antero), Juskaitis, R. (Rimvydas), Korpimaki, E. (Erkki), Krams, I. (Indrikis), Laaksonen, T. (Toni), Leclercq, B. (Bernard), Lehikoinen, E. (Esa), Loukola, O. (Olli), Mainwaring, M. C. (Mark C.), Mand, R. (Raivo), Massa, B. (Bruno), Matthysen, E. (Erik), Mazgajski, T. D. (Tomasz D.), Merino, S. (Santiago), Mitrus, C. (Cezary), Monkkonen, M. (Mikko), Nager, R. G. (Ruedi G.), Nilsson, J.-a. (Jan-ake), Nilsson, S. G. (Sven G.), Norte, A. C. (Ana C.), von Numers, M. (Mikael), Orell, M. (Markku), Pimentel, C. S. (Carla S.), Pinxten, R. (Rianne), Priedniece, I. (Ilze), Remes, V. (Vladimir), Richner, H. (Heinz), Robles, H. (Hugo), Rytkonen, S. (Seppo), Senar, J. C. (Juan Carlos), Seppanen, J. T. (Janne T.), da Silva, L. P. (Luis P.), Slagsvold, T. (Tore), Solonen, T. (Tapio), Sorace, A. (Alberto), Stenning, M. J. (Martyn J.), Torok, J. (Janos), Tryjanowski, P. (Piotr), van Noordwijk, A. J. (Arie J.), Walankiewicz, W. (Wieslaw), and Lambrechts, M. M. (Marcel M.)

Abstract

We studied the relationship between temperature and the coexistence of great tit Parus major and blue tit Cyanistes caeruleus, breeding in 75 study plots across Europe and North Africa. We expected an advance in laying date and a reduction in clutch size during warmer springs as a general response to climate warming and a delay in laying date and a reduction in clutch size during warmer winters due to density‐dependent effects. As expected, as spring temperature increases laying date advances and as winter temperature increases clutch size is reduced in both species. Density of great tit affected the relationship between winter temperature and laying date in great and blue tit. Specifically, as density of great tit increased and temperature in winter increased both species started to reproduce later. Density of blue tit affected the relationship between spring temperature and blue and great tit laying date. Thus, both species start to reproduce earlier with increasing spring temperature as density of blue tit increases, which was not an expected outcome, since we expected that increasing spring temperature should advance laying date, while increasing density should delay it cancelling each other out. Climate warming and its interaction with density affects clutch size of great tits but not of blue tits. As predicted, great tit clutch size is reduced more with density of blue tits as temperature in winter increases. The relationship between spring temperature and density on clutch size of great tits depends on whether the increase is in density of great tit or blue tit. Therefore, an increase in temperature negatively affected the coexistence of blue and great tits differently in both species. Thus, blue tit clutch size was unaffected by the interaction effect of density with temperature, while great tit clutch size was affected in multiple ways by these interactions terms.

Published
2020

13. Differential phase-contrast microscope with a split detector for the readout system of a multilayered optical memory

Author

Kawata, Y., Juskaitis, R., Tanaka, T., Wilson, T., and Kawata, S.

Subjects
Optical storage devices -- Research, Erasable optical disk drives -- Research, Optical data processing -- Equipment and supplies, Phase microscope -- Usage, Astronomy, Physics
Abstract

A transmission differential phase-contrast microscope with a split detector is used as a readout system for a multilayered three-dimensional optical memory. The system is applicable to data recorded as refractive-index changes. The system is compact and easy to use. The three-dimensional optical transfer function for the system is derived. This shows that the spatial bandwidth of the system is the same as that of a conventional microscope with incoherent illumination but with much improved contrast. Six layers of information are recorded in a photopolymer and are read out with little cross talk and high contrast. Key words: Optical memory, photorefractive, differential phase-contrast microscope, three-dimensional optics, nonlinear optics, holographic memory.

Published
1996

14. Semiconductor laser confocal microscopy

Author

Juskaitis, R., Rea, N.P., and Wilson, T.

Subjects
Semiconductor lasers -- Research, Microscope and microscopy -- Methods, Astronomy, Physics
Abstract

A compact scanning microscope that uses a semiconductor laser both to illuminate a specimen and to detect the signal reflected from it is described. It is demonstrated that the spatial filtering performed by the laser detector ensures confocal operation. Two detection regimes, one employing a laser power monitor and the other using the diode junction voltage as a signal, are compared.

Published
1994

15. Surface profiling with scanning optical microscopes using two-mode optical fibers

Author

Juskaitis, R. and Wilson, T.

Subjects
Scanning electron microscopes -- Design and construction, Optical detectors -- Design and construction, Astronomy, Physics
Abstract

A scanning optical microscope system is proposed that uses a slightly laterally offset optical fiber. The fiber is capable of supporting two modes, and it is shown that by detecting the interference between these modes the response to surface height is linear in the focal region. This linearity permits noncontacting surface profilometry to be readily obtained for specimens of uniform reflectivity. For other specimens, a simple feedback system is introduced to obtain surface profiles as well as intensity-coded height images.

Published
1992

16. Differential confocal scanning microscope with a two-mode optical fiber

Author

Juskaitis, R. and Wilson, T.

Subjects
Microscope and microscopy -- Innovations, Scanning tunneling microscopy -- Equipment and supplies, Astronomy, Physics
Abstract

A novel technique for obtaining differential images with a scanning microscope by using a two-mode optical fiber is proposed. It is shown that both the differential amplitude and the differential phase images can be obtained by adjusting the differential phase delay between the fiber modes. The technique is demonstrated experimentally, and differential images of a specimen consisting of sharp edges in both amplitude and phase reflectivity are presented., A new method based on a double-mode optical fiber is presented for confocal scanning microscopy. The process for generating differential images improves on the split-detector technique in that it produces images with an optical branching capability and enhanced lateral resolution. It was confirmed via experiments. The study discusses how the differential amplitude and differential phase images are obtained through changing the differential phase delay between the fiber modes.

Published
1992

19. Endoscope with optical sectioning capability

Author

Giniunas, L., Juskaitis, R., and Shatalin, S.V.

Subjects
Endoscopes -- Design and construction, Scanning electron microscopes -- Usage, Astronomy, Physics
Abstract

The optical sectioning capability of a fiber-optic scanning microscope with a 9-cm-long gradient-index-rod lens probe has been demonstrated. A transverse resolution of 1.3 micrometer and a longitudinal resolution of 30 micrometer were achieved. The dimensions of the probe allow the device to be used as an endoscope.

Published
1993

20. Mitochondrial phylogeographic of the common dormouse, Muscardinus avellanarius (Rodentia: Gliridae)

Author

MOUTON, A, GRILL, A, KRYSTUFEK, B, RANDI, E, AMORI, G, JUSKAITIS, R, ALOISE, G, MORTELLITI, A, PANCHETTI, F, MICHAUX, J., SARA', Maurizio, MOUTON, A, GRILL, A, SARA’, M, KRYSTUFEK, B, RANDI, E, AMORI, G, JUSKAITIS, R, ALOISE, G, MORTELLITI, A, PANCHETTI, F, and MICHAUX, J

Subjects
Settore BIO/05 - Zoologia, Gliridae, Europe, phylogeography, Muscardinus avellanarius, Glacial refugia, Conservation
Published
2011

21. Variation in clutch size in relation to nest size in birds

Author

MØLLER, A. P., ADRIAENSEN, F., ARTEMYEV, A., BANBURA, J., BARBA, E., BIARD, C., BLONDEL, J., BOUSLAMA, Z., BOUVIER, J-C., CAMPRODON, J., CECERE, F., CHARMANTIER, A., CHARTER, M., CICHON, M., CUSIMANO, C., CZESZCZEWIK, D., DEMEYRIER, V., DOLIGEZ, B., DOUTRELANT, C., DUBIEC, A., EENS, M., EEVA, T., FAIVRE, B., FERNS, P.N., FORSMAN, J.T., GARCÍA-DEL-REY, E., GOLDSHTEIN, A., GOODENOUGH, A.E., GOSLER, A.G., GÓZDZ, I., GRÉGOIRE, A., GUSTAFSSON, L., HARTLEY, I.R., HEEB, P., HINSLEY, S.A., ISENMANN, P., JACOB, S., JÄRVINEN, A., JUSKAITIS, R., KORPIMÄKI, E., KRAMS, I., LAAKSONEN, T., LECLERCQ, B., LEHIKOINEN, E., LOUKOLA, E., LUNDBERG, A., MAINWARING, M.C., MÄND, R., MASSA, B., MAZGAJSKI, T.D., MERINO, S., MITRUS, C., MÖNKKÖNEN, M., MORALES-FERNAZ, J., MORIN, X., NAGER, R.G., NILSSON, J-A., NILSSON, S.G., NORTE, A.C., ORELL, M., PERRET, P., PIMENTEL, C.S., PINXTEN, R., PRIEDNIECE, I., QUIDOZ, M-C., REMES, V., RICHNER, H., ROBLES, H., RYTKÖNEN, S., SENAR, J.C., SEPPÄNEN, J.T., DA SILVA, L.P., SLAGSVOLD, T., SOLONEN, T., SORACE, A., STENNING, M.J., TÖRÖK, J., TRYJANOWSKI, P., VAN NOORDWIJK, A.J., VON NUMERS, M., WALANKIEWICZ, W., LAMBRECHTS, M.M.

Subjects
education
Published
2014

22. Full spectrum filterless fluorescence microscopy

Author

Booth, M, Jesacher, A, Juskaitis, R, and Wilson, T

Abstract

In conventional microscopes, fluorescence emission is separated from the backscattered illumination using the Stokes shift, whereby the emission occurs at a longer wavelength to the excitation. Such separation is usually achieved through a combination of wavelength filters that divide the spectrum into mutually exclusive excitation and emission bands. It is therefore impossible in these microscopes to access the full excitation/emission spectrum of the specimen in a single image. We report on a microscope that acquired fluorescence images using illumination across the spectral range 450-680 nm; the full emission spectrum was detected simultaneously across the same range. The microscope was also combined with structured illumination optical sectioning to give three-dimensionally resolved images with improved background rejection. Full spectrum fluorescence images of biological specimens are demonstrated. As this system is more versatile than the standard fluorescence microscope, it could be of benefit in many fluorescence imaging applications.

Published
2010

27. 5-D fluorescence imaging using an all-solid-state diode-pumped laser system

Author

Elson, D.S., primary, Webb, S.E.D., additional, Siegel, J., additional, Leveque- Fort, S., additional, Parsons-Karavassilis, D., additional, Cole, M.J., additional, French, P.M.W., additional, Hopkins, M., additional, Lever, M.J., additional, Sucharov, L.O., additional, Neil, M.A.A., additional, Juskaitis, R., additional, and Wilson, T., additional

Published
2001
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37. '5-D' fluorescence microscopy

Author

Webb, Sed, Elson, Ds, Siegel, J., Leveque-Fort, S., Gu, Y., Parsons-Karavassilis, D., Cole, Mj, French, Pmw, Lever, Mj, Sucharov, Lo, Mark Neil, Juskaitis, R., Wilson, T., Anderssonengels, S., and Kaschke, Mf

39. Generation and focusing of radially polarized electric fields

Author

Wilson, T., Massoumian, F., and Juskaitis, R.

Abstract

The use of radially polarized light is known to produce, when focused by a high-numerical-aperture objective lens, a spot of light whose polarization is predominantly axial. We have generated accurately such radially polarized fields, which we have coupled into a high-numerical-aperture microscope objective so as to produce an axially polarized focal spot. © 2003 Society of Photo-Optical Instrumentation Engineers.

Published
2003
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46. Journal of Microscopy Abstracts.

Author

Neil, A., Wilsom, T., Juskaitis, R., Shishido, O., Yoshida, N., Umino, O., Cole, L., Davies, D., Hyde, G.J., and Ashford, A.E.

Subjects
*MICROSCOPY, *CELLS, *TICKS, *MEDICAL imaging systems
Abstract

Presents several abstracts of the articles published in June 2000 issue of 'Proceedings RMS,' journal. 'Iterative Thresholding for Segmentation of Cells From Noisy Images,' by H.-S. Wu, J. Barba and J. Gil; 'A Simplified Method of Cleaning Ixodid Ticks for Microscopy,' by B.R. Dixon, T.N. Petney and R.H. Andrews.

Published
2000

47. Evolutionary history and species delimitations:a case study of the hazel dormouse, Muscardinus avellanarius

Author

Alessio Mortelliti, M. Dorenbosch, Roger Trout, Morten Elmeros, Johan Michaux, S. Mazzoti, Ferhat Matur, S. Ehlers, Giovanni Amori, Andrea Grill, F. Poitevin, Johannes Lang, Maurizio Sarà, Gaetano Aloise, Alice Latinne, Rimvydas Juškaitis, Björn Schulz, Ettore Randi, Peter Adamík, Goedele Verbeylen, Boris Kryštufek, Sven Büchner, Alice Mouton, Zonguldak Bülent Ecevit Üniversitesi, Mouton, A, Mortelliti, A, Grill, A, Sarà, M, Krystufek, B, Juskaitis, R, Latinne, A, Amori, G, Randi, E, Buchner, S, Schulz, B, Ehlers, S, Lang, J, Adamik, P, Verbeylen, G, Dorenbosch, M, Trout, R, Elmeros, M, Aloise, G, Mazzoti, S, Matur, F, Poitevin, F, and Michaux, JR

Subjects
0106 biological sciences, 0301 basic medicine, Species complex, Range (biology), Muscardinus avellanarius, Settore BIO/05 - Zoologia, Endangered species, Zoology, Muscardinus, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Evolutionary history, biology.animal, Genetics, Species delimitation, Dormouse, Ecology, Evolution, Behavior and Systematics, Evolutionary significant unit, Evolutionary significant unit, biology.organism_classification, Genetic divergence, 030104 developmental biology, Phylogenetic Pattern, Threatened species, Keywords Muscardinus avellanariu
Abstract

Robust identification of species and significant evolutionary units (ESUs) is essential to implement appropriate conservation strategies for endangered species. However, definitions of species or ESUs are numerous and sometimes controversial, which might lead to biased conclusions, with serious consequences for the management of endangered species. The hazel dormouse, an arboreal rodent of conservation concern throughout Europe is an ideal model species to investigate the relevance of species identification for conservation purposes. This species is a member of the Gliridae family, which is protected in Europe and seriously threatened in the northern part of its range. We assessed the extent of genetic subdivision in the hazel dormouse by sequencing one mitochondrial gene (cytb) and two nuclear genes (BFIBR, APOB) and genotyping 10 autosomal microsatellites. These data were analysed using a combination of phylogenetic analyses and species delimitation methods. Multilocus analyses revealed the presence of two genetically distinct lineages (approximately 11 % cytb genetic divergence, no nuclear alleles shared) for the hazel dormouse in Europe, which presumably diverged during the Late Miocene. The phylogenetic patterns suggests that Muscardinus avellanarius populations could be split into two cryptic species respectively distributed in western and central-eastern Europe and Anatolia. However, the comparison of several species definitions and methods estimated the number of species between 1 and 10. Our results revealed the difficulty in choosing and applying an appropriate criterion and markers to identify species and highlight the fact that consensus guidelines are essential for species delimitation in the future. In addition, this study contributes to a better knowledge about the evolutionary history of the species. © 2016, Springer Science+Business Media Dordrecht.

Published
2017
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48. Evidence of a complex phylogeographic structure in the common dormouse, Muscardinus avellanarius (Rodentia: Gliridae)

Author

Mouton, Alice, Grill, Andrea, Sara, Maurizio, Krystufek, Boris, Randi, Etorre, Amori, Giovanni, Juškaitis, Rimvydas, Aloise, Gaetano, Mortelliti, Alessio, Manchetti, Fabiana, Michaux, Johan, Institut de Botanique, Université de Liège, University of Vienna [Vienna], Dipartimento Biologia Ambientale e Biodiversità, Laboratorio di Zoogeografia ed Ecologia Animale, Partenaires INRAE, University of Primorska, Istituto Nazionale per la Fauna Selvatica, Institute of Ecosystem Studies, Box AB, Institute of Ecology of Nature Research Centre, Museo di Storia Naturale della Calabria e Orto Botanico, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Università degli Studi di Roma, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Mouton, A, Grill, A, Sara', M, Krystufek, B, Randi, E, Amori, G, Juskaitis, R, Aloise, G, Mortelliti, A, Panchetti, F, and Michaux, J

Subjects
Europe, LOIR, cytochrome b, refuges glaciaires, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], conservation, cytochrome b, Europe, glacial refugia, conservation, Settore BIO/05 - Zoologia, glacial refugia, GENETIQUE DES POPULATIONS
Abstract

Contact: amouton@ulg.ac.be; International audience; This is the first mitochondrial phylogeography of the common dormouse, Muscardinus avellanarius (Linnaeus, 1758), a hibernating rodent strictly protected in Europe (Habitat Directive, annex IV; Bern Convention, annex III). The 84 individuals of M. avellanarius, sampled throughout the distributional range of the species, have been sequenced at the mitochondrial DNA gene (cytochrome b, 704 base pairs). The results revealed two highly divergent lineages, with an ancient separation around 7.7 Mya and a genetic divergence of 7.7%. Lineage 1 occurs in Western Europe (France, Belgium, and Switzerland) and Italy, and lineage 2 occurs in CentralNorthern Europe (Poland, Germany, Latvia, and Lithuania), on the Balkan Peninsula, and in Turkey. Furthermore, these two lineages are subdivided into five sublineages genetically isolated with a strong geographical association. Therefore, lineage 1 branches into two further sublineages (Western European and Italian), whereas lineage 2 contained three sublineages (CentralNorthern European, Turkish, and Balkan). We observed low genetic diversity within the sublineages, in contrast to the significant level of genetic differentiation between them. The understanding of genetic population structure is essential for identifying units to be conserved. Therefore, these results may have important implications for M. avellanarius conservation.

Published
2012
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49. Real-time slit scanning microscopy in the meridional plane.

Author

Botcherby EJ, Booth MJ, Juskaitis R, and Wilson T

Subjects
Fluorescence, Microscopy, Confocal instrumentation, Pollen cytology, Time Factors, Microscopy, Confocal methods
Abstract

The standard microscope architecture around which confocal microscopes are built imposes fundamental restrictions on the speed with which images (three-dimensional data sets) can be obtained. Commercially available slit scanning confocal microscopes are able to produce optically sectioned images at frame rates well in excess of 100 Hz. However only the focal (x-y) plane can be imaged at this speed. To image a volume specimen it is necessary to physically change the distance between the objective lens and the specimen. This refocusing process is often necessarily slow and represents a bottleneck to the speed of image acquisition. We describe the construction of a slit scanning confocal microscope based on what we know to be a novel microscope architecture, which permits images of other planes and, particular, the meridional (x-z) plane to be acquired in real time.

Published
2009
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50. Real-time extended depth of field microscopy.

Author

Botcherby EJ, Booth MJ, Juskaitis R, and Wilson T

Subjects
Algorithms, Animals, Equipment Design, Image Processing, Computer-Assisted, Imaging, Three-Dimensional instrumentation, Mice, Microscopy methods, Microscopy, Confocal instrumentation, Microscopy, Fluorescence methods, Optical Devices, Optical Fibers, Video Recording methods, Image Enhancement methods, Imaging, Three-Dimensional methods, Microscopy, Confocal methods
Abstract

We describe an optical microscope system whose focal setting can be changed quickly without moving the objective lens or specimen. Using this system, diffraction limited images can be acquired from a wide range of focal settings without introducing optical aberrations that degrade image quality. We combine this system with a real time Nipkow disc based confocal microscope so as to permit the acquisition of extended depth of field images directly in a single frame of the CCD camera. We also demonstrate a simple modification that enables extended depth of field images to be acquired from different angles of perspective, where the angle can be changed over a continuous range by the user in real-time.

Published
2008
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