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1. Integrating knowledge-guided symbolic regression and model-based design of experiments to automate process flow diagram development

Author

Rogers, Alexander W., Lane, Amanda, Mendoza, Cesar, Watson, Simon, Kowalski, Adam, Martin, Philip, and Zhang, Dongda

Subjects
Computer Science - Machine Learning
Abstract

New products must be formulated rapidly to succeed in the global formulated product market; however, key product indicators (KPIs) can be complex, poorly understood functions of the chemical composition and processing history. Consequently, scale-up must currently undergo expensive trial-and-error campaigns. To accelerate process flow diagram (PFD) optimisation and knowledge discovery, this work proposed a novel digital framework to automatically quantify process mechanisms by integrating symbolic regression (SR) within model-based design of experiments (MBDoE). Each iteration, SR proposed a Pareto front of interpretable mechanistic expressions, and then MBDoE designed a new experiment to discriminate between them while balancing PFD optimisation. To investigate the framework's performance, a new process model capable of simulating general formulated product synthesis was constructed to generate in-silico data for different case studies. The framework could effectively discover ground-truth process mechanisms within a few iterations, indicating its great potential for use within the general chemical industry for digital manufacturing and product innovation.

Published
2024

5. Contributions of Executive Function and Cognitive Intrinsic Motivation to University Students' Reading Comprehension

Author

Cartwright, Kelly B., Lee, Sherman A., Taboada Barber, Ana, DeWyngaert, Laura U., Lane, Amanda B., and Singleton, Terrain

Abstract

Reading comprehension is an incredibly complex, purposeful activity that involves simultaneous orchestration and integration of multiple processes. However, dominant perspectives suggest that two clusters of skills, word reading and language comprehension, account for successful reading. Such two-factor models are problematic because they do not easily account for complexities in reading comprehension processes or for contributions to reading comprehension of other individual difference variables related to the purposeful nature of reading, such as executive functions (EFs) and intrinsic motivation. Further, simple models may lead to oversimplification of research questions, curricula, and instructional practices, causing researchers and educators to miss important contributors to reading comprehension necessary for students to develop into skilled readers. In this study, the authors assessed the unique contributions of EFs, both domain-general and reading-specific, and cognitive intrinsic motivation (i.e., the desire to engage in effortful cognitive activities) to reading comprehension in 122 university students beyond language comprehension and word-reading skills. Findings confirm unique contributions of cognitive intrinsic motivation and reading-specific EF to students' reading comprehension beyond established predictors and domain-general EFs. Findings also suggest complexities, such as impacts of language comprehension on word reading, as well as impacts of cognitive intrinsic motivation on both language and reading comprehension, that should be considered in theory and practice. Finally, because reading-specific EF contributed to reading comprehension directly and indirectly beyond controls, these findings underscore the importance of applying knowledge of EF to specific reading processes to better support students who struggle to understand text.

Published
2020
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9. A Model of the Factors Influencing Teaching Identity among Life Sciences Doctoral Students

Author

Lane, Amanda Kelly, Hardison, Carlton, Simon, Ariana, and Andrews, Tessa C.

Abstract

One barrier to the adoption of evidenced-based teaching practices may be that faculty do not see teaching as an important part of their identities as professionals. Graduate school is a key time for professional identity development, and currently we know little about how doctoral students develop identities as college teachers. In this qualitative study, we aim to characterize the factors that promote and hinder teaching identity among 33 life sciences doctoral students with diverse career interests at one research university. We collected data using semi-structured interviews and analyzed it using qualitative analysis closely aligned with grounded theory. Our analysis involved iteratively and collaboratively analyzing interview transcripts while considering existing literature about socialization and professional identity and remaining open to novel ideas in the data. From this analysis, we developed a mechanistic model of the factors that influenced teaching identity in our participants. Independent teaching experiences, teaching professional development, and teaching mentors contributed to salient and stable teaching identities among doctoral students. Being recognized by faculty as a teacher was also important, but rare. The professional culture that doctoral students perceived acted like a blizzard that they had to navigate through to develop a teaching identity. This culture strongly valued research over teaching, resulting in a sometimes cold and isolating environment for students interested in teaching. The culture also made it harder to see existing opportunities for teaching development and made it more challenging to move toward these opportunities, much like the deep snow and driving winds of a blizzard. The mechanistic model described in this work is an important first step in understanding how doctoral training influences teaching identity. This model serves as a hypothesis that should be tested and refined through additional empirical work across contexts.

Published
2019
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11. Complex gene expression in the dragline silk producing glands of the Western black widow (Latrodectus hesperus)

Author

Lane, Amanda, Hayashi, Cheryl Y, Whitworth, Gregg B, and Ayoub, Nadia A

Abstract

Abstract Background Orb-web and cob-web weaving spiders spin dragline silk fibers that are among the strongest materials known. Draglines are primarily composed of MaSp1 and MaSp2, two spidroins (spider fibrous proteins) expressed in the major ampullate (MA) silk glands. Prior genetic studies of dragline silk have focused mostly on determining the sequence of these spidroins, leaving other genetic aspects of silk synthesis largely uncharacterized. Results Here, we used deep sequencing to profile gene expression patterns in the Western black widow, Latrodectus hesperus. We sequenced millions of 3′-anchored “tags” of cDNAs derived either from MA glands or control tissue (cephalothorax) mRNAs, then associated the tags with genes by compiling a reference database from our newly constructed normalized L. hesperus cDNA library and published L. hesperus sequences. We were able to determine transcript abundance and alternative polyadenylation of each of three loci encoding MaSp1. The ratio of MaSp1:MaSp2 transcripts varied between individuals, but on average was similar to the estimated ratio of MaSp1:MaSp2 in dragline fibers. We also identified transcription of TuSp1 in MA glands, another spidroin family member that encodes the primary component of egg-sac silk, synthesized in tubuliform glands. In addition to the spidroin paralogs, we identified 30 genes that are more abundantly represented in MA glands than cephalothoraxes and represent new candidates for involvement in spider silk synthesis. Conclusions Modulating expression rates of MaSp1 variants as well as MaSp2 and TuSp1 could lead to differences in mechanical properties of dragline fibers. Many of the newly identified candidate genes likely encode secreted proteins, suggesting they could be incorporated into dragline fibers or assist in protein processing and fiber assembly. Our results demonstrate previously unrecognized transcript complexity in spider silk glands.

Published
2013

17. Flinders Island spotted fever rickettsioses caused by 'marmionii' strain of rickettsia honei, eastern Australia

Author

Unsworth, Nathan B., Stenos, John, Graves, Stephen R., Faa, Antony G., Cox, G. Erika, Dyer, John R., Boutlis, Craig S., Lane, Amanda M., Shaw, Matthew D., Robson, Jennifer, and Nissen, Michael D.

Subjects
Rickettsial diseases -- Genetic aspects, Rickettsial diseases -- Case studies, Rickettsia -- Genetic aspects, Rickettsia -- Risk factors
Abstract

Australia has 4 rickettsial diseases: murine typhus, Queensland tick typhus, Flinders Island spotted fever, and scrub typhus. We describe 7 cases of a rickettsiosis with an acute onset and symptoms [...]

Published
2007

18. Flexible mate choice: a male snake's preference for larger females is modified by the sizes of females encountered

Author

Shine, Richard, Webb, Jonathan K., Lane, Amanda, and Mason, Robert T.

Subjects
Snakes, Universities and colleges, Zoology and wildlife conservation
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.anbehav.2005.04.005 Byline: Richard Shine, Jonathan K. Webb, Amanda Lane, Robert T. Mason Abstract: Why do males exert strong mate choice in some taxa but not others? Theory suggests that mate discrimination will enhance male fitness when encounter rates with potential mates are high, when those potential mates vary in the fitness consequences likely to accrue from an attempted insemination, and when courting one female reduces the male's opportunity to court other females. One widespread form of mate choice involves a trend for males of many ectothermic species to court larger (and thus, more fecund) females. To test whether such preferences are dynamically adjusted to local conditions, we studied male preference for larger females in red-sided garter snakes, Thamnophis sirtalis parietalis, near a communal den in Manitoba, Canada. Courting a small female imposes a high opportunity cost for a male in the centre of the den, because many large and easily located females are nearby. In the surrounding woodland, in contrast, a male that neglects a small female is unlikely to encounter a larger substitute partner. In arena trials, male snakes from the den selected larger females more than did males from the surrounding woodland. Manipulating a den male's exposure to females (none, large, small) for 60min led males to adjust their criteria for courtship depending upon the sizes of females encountered. Hence, the local environment can modify courtship criteria, with male garter snakes adjusting their mate choice selectivity based upon spatial and temporal factors that affect the opportunity costs of courtship. Author Affiliation: (a) Biological Sciences A08, University of Sydney, Australia (a ) Department of Zoology, Oregon State University, U.S.A. Article History: Received 16 November 2004; Revised 20 January 2005; Accepted 29 April 2005 Article Note: (miscellaneous) MS. number: 8348R

Published
2006

21. Chapter 6

Author

West, Kim, primary, Lane, Amanda, additional, and Libby, Madison, additional

Published
2020
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24. Multiple paternity and precocial breeding in wild Tasmanian devils, Sarcophilus harrisii (Marsupialia: Dasyuridae)

Author

Russell, Tracey, Lane, Amanda, Clarke, Judy, Hogg, Carolyn, Morris, Katrina, Keeley, Tamara, Madsen, Thomas R, Ujvari, Beata, Russell, Tracey, Lane, Amanda, Clarke, Judy, Hogg, Carolyn, Morris, Katrina, Keeley, Tamara, Madsen, Thomas R, and Ujvari, Beata

Abstract

Polyandry, a common reproductive strategy in various animal species, has potential female benefits, which include enhanced offspring fitness. Benefits can be direct, such as reduced risk of male infanticide of offspring, or indirect, such as increased genetic diversity of offspring and the acquisition of 'good genes'. Multiple paternity of litters has been recorded in numerous marsupial species but has not been reported in Tasmanian devils, Sarcophilus harrisii (Boitard). We investigated whether multiple paternity occurred in litters within a wild population of Tasmanian devils. Using major histocompatibility complex-linked and neutral microsatellite markers, the paternity of nine litters was analysed. We found multiple paternity in four out of nine litters and that yearling (> 1, < 2 years old) male devils were siring offspring. This is the first record of multiple paternity and of male precocial breeding in wild Tasmanian devils. To date, there are no data relating to the subsequent survival of devils from single- vs. multiple-sired litters; therefore, we do not know whether multiple paternity increases offspring survival in the wild. These results have implications for the Tasmanian devil captive insurance programme, because group housing can lead to multiple-sired litters, making the maintenance of genetic diversity over time difficult to manage.

Published
2019

25. The Contribution of Trunk Axial Kinematics to Poststrike Ball Velocity During Maximal Instep Soccer Kicking.

Author

Fullenkamp, Adam M., Campbell, Brian M., Laurent, C. Matthew, and Paige Lane, Amanda

Subjects
BIOMECHANICS, BODY weight, STATISTICAL correlation, KINEMATICS, MOTOR ability, SOCCER, STATURE, EFFECT sizes (Statistics), TORSO, BODY movement, MOTION capture (Human mechanics), DATA analysis software, DESCRIPTIVE statistics, ONE-way analysis of variance
Abstract

To date, biomechanical analyses of soccer kicking have focused predominantly on lower-extremity motions, with little emphasis on the trunk and upper body. The purpose of this study was to evaluate differences in trunk axial kinematics between novice (n = 10) and skilled (n = 10) participants, as well as to establish the relationship of trunk axial motion and sagittal plane thigh rotation to poststrike ball velocity. Three-dimensional body segmental motion data were captured using high-resolution motion analysis (120 Hz) while each participant completed 5 maximal instep soccer-style kicks. The results demonstrate that skilled participants use 53% greater axial trunk range of motion compared with novice participants (P < .01), as well as 62% greater peak trunk rotation velocity (P < .01). The results also show a moderate, positive correlation of peak trunk rotation velocity with poststrike ball velocity (r = .57; P < .01), and peak hip flexion velocity with poststrike ball velocity (r = .63; P < .01). The current study highlights the potential for trunk rotation-specific training to improve maximum instep kick velocity in developing soccer athletes. [ABSTRACT FROM AUTHOR]

Published
2015
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29. MHC diversity and female age underpin reproductive success in an Australian icon; the Tasmanian Devil

Author

Russell, Tracey, Lisovski, Simeon, Olsson, Mats, Brown, Gregory, Spindler, Rebecca, Lane, Amanda, Keeley, Tamara, Hibbard, Chris, Hogg, Carolyn J., Thomas, Frédéric, Belov, Katherine, Ujvari, Beata, Madsen, Thomas, Russell, Tracey, Lisovski, Simeon, Olsson, Mats, Brown, Gregory, Spindler, Rebecca, Lane, Amanda, Keeley, Tamara, Hibbard, Chris, Hogg, Carolyn J., Thomas, Frédéric, Belov, Katherine, Ujvari, Beata, and Madsen, Thomas

Abstract

Devil Facial Tumour Disease (DFTD), a highly contagious cancer, has decimated Tasmanian devil (Sarcophilus harrisii) numbers in the wild. To ensure its long-term survival, a captive breeding program was implemented but has not been as successful as envisaged at its launch in 2005. We therefore investigated the reproductive success of 65 captive devil pair combinations, of which 35 produced offspring (successful pairs) whereas the remaining 30 pairs, despite being observed mating, produced no offspring (unsuccessful pairs). The devils were screened at six MHC Class I-linked microsatellite loci. Our analyses revealed that younger females had a higher probability of being successful than older females. In the successful pairs we also observed a higher difference in total number of heterozygous loci, i.e. when one devil had a high total number of heterozygous loci, its partner had low numbers. Our results therefore suggest that devil reproductive success is subject to disruptive MHC selection, which to our knowledge has never been recorded in any vertebrate. In order to enhance the success of the captive breeding program the results from the present study show the importance of using young (2-year old) females as well as subjecting the devils to MHC genotyping.

Published
2018

32. MHC diversity and female age underpin reproductive success in an Australian icon; the Tasmanian Devil

Author

Russell, Tracey, primary, Lisovski, Simeon, additional, Olsson, Mats, additional, Brown, Gregory, additional, Spindler, Rebecca, additional, Lane, Amanda, additional, Keeley, Tamara, additional, Hibbard, Chris, additional, Hogg, Carolyn J., additional, Thomas, Frédéric, additional, Belov, Katherine, additional, Ujvari, Beata, additional, and Madsen, Thomas, additional

Published
2018
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33. Universities as sustainable communities: a prospectus for people and places

Author

Roberts, Peter and Lane, Amanda

Subjects
Universities and colleges -- United Kingdom, Universities and colleges -- Buildings and facilities, Sustainable development -- Environmental aspects, Environmental services industry
Abstract

Byline: Peter Roberts, Amanda Lane The purpose of this paper is to discuss the role of universities as sustainable communities and to identify the requirements for achieving this role. The paper outlines the evolution of sustainable development theory and practice, and then considers the desirability of introducing a spatial (or community) dimension into this field of activity. From this, attention turns to the role of universities as sustainable communities, both in their own right and as a component of wider local or regional communities. In addition, the paper examines the various internal elements of the sustainable university. From the assessment of the characteristics of a sustainable community, the paper identifies a number of areas of potential activity that would allow universities to operate in accord with sustainable community principles. Furthermore, the paper discusses the required adjustments to the learning, research and operational activities of universities. Universities display a number of opportunities that if developed and implemented would both enhance the performance of individual institutions and support local and regional programmes of sustainable development. Hitherto the spatial dimension of sustainable development has been largely ignored and little has been said about the role of universities as sustainable communities.

Published
2010

34. Host adaptation of a Wolbachia strain after long-term serial passage in mosquito cell lines

Author

McMeniman, Conor J., Lane, Amanda M., Fong, Amy W.C., Voronin, Denis A., Iturbe-Ormaetxe, Inaki, Yamada, Ryuichi, McGraw, Elizabeth A., and O'Neill, Scott L.

Subjects
Aedes -- Diseases and pests, Aedes albopictus -- Diseases and pests, Drosophila -- Diseases and pests, Drosophila -- Genetic aspects, Host-parasite relationships -- Analysis, Wolbachia -- Genetic aspects, Wolbachia -- Environmental aspects, Biological sciences
Abstract

A life-shortening Wolbachia strain, wMelPop, from the fruit fly Drosophila melanogaster was transferred into a cell line derived from the mosquito Aedes albopictus to examine the process of adaptation to a novel host. The cell lines to preadapt Wolbachia to novel hosts could be applied as a possible strategy to improve the success of transinfection in novel target insect species.

Published
2008

35. Duplication and concerted evolution of MiSp-encoding genes underlie the material properties of minor ampullate silks of cobweb weaving spiders

Author

Vienneau-Hathaway, Jannelle M., primary, Brassfield, Elizabeth R., additional, Lane, Amanda Kelly, additional, Collin, Matthew A., additional, Correa-Garhwal, Sandra M., additional, Clarke, Thomas H., additional, Schwager, Evelyn E., additional, Garb, Jessica E., additional, Hayashi, Cheryl Y., additional, and Ayoub, Nadia A., additional

Published
2017
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36. Appendices.

Author

Baruch, Adele, Lane, Amanda, and Rand, Molly

Subjects
HURRICANE Katrina, 2005, MORAL courage
Abstract

Appendix A presents a further discussion of methodology as it relates to both the Courage and Moral Choice Project (CMPC) and the Zakynthos and Hurricane Katrina interviews and analyses. Appendix B contains the interview questions. Appendix C presents a curriculum map for those interested in undertaking a project similar to the CMCP. [ABSTRACT FROM AUTHOR]

Published
2019

37. Chapter 6: Essays from the Courage and Moral Choice Project.

Author

West, Kim, Lane, Amanda, and Libby, Madison

Subjects
MORAL courage, COMMUNITY-school relationships, ESSAYS, DESPAIR
Abstract

In this chapter, participants from the Courage and Moral Choice Project share personal essays about their experiences with the project. Teachers describe the ways in which they sought to connect the stories of moral courage with a deepened awareness of the needs and challenges in the school and wider community. One teacher described the stories as "reminders" that courage and goodness exist in the world, a world often filled with stories of despair. Another teacher, who was once described as an "at risk" student herself, also noted that the stories provide a perspective of hope. One student described how meaningful it was for her to hear stories about the many Danish citizens to shelter and transport their neighbors during the Nazi occupation. She notes, "I think more people need to be like that". [ABSTRACT FROM AUTHOR]

Published
2019

41. Fascinating and Forgotten: The Conservation Status of Marine Elapid Snakes

Author

Elfes, Cristiane T., Livingstone, Suzanne R., Lane, Amanda, Lukosche, Vimoksalehi, Sanders, Kate L., Courtney, Anthony J., Gatus, Joey L., Guinea, Michael, Lobo, Aaron S., Milton, David, Rasmussen, Arne R., Read, Mark, White, Mahree-Dee, Sanciangco, Jonnell, Alcala, Angel, Heatwole, Harold, Karns, Daryl R., Seminoff, Jeffrey A., Voris, Harold K., Carpenter, Kent E., et al., Elfes, Cristiane T., Livingstone, Suzanne R., Lane, Amanda, Lukosche, Vimoksalehi, Sanders, Kate L., Courtney, Anthony J., Gatus, Joey L., Guinea, Michael, Lobo, Aaron S., Milton, David, Rasmussen, Arne R., Read, Mark, White, Mahree-Dee, Sanciangco, Jonnell, Alcala, Angel, Heatwole, Harold, Karns, Daryl R., Seminoff, Jeffrey A., Voris, Harold K., Carpenter, Kent E., and et al.

Abstract

An assessment of marine elapid snakes found 9% of marine elapids are threatened with extinction, and anadditional 6% are Near Threatened. A large portion (34%) is Data Deficient. An analysis of distributions revealed thegreatest species diversity is found in Southeast Asia and northern Australia. Three of the seven threatened species occurat Ashmore and Hibernia Reefs in the Timor Sea, while the remaining threatened taxa occur in the Philippines, Niue, andSolomon Islands. The majority of Data Deficient species are found in Southeast Asia. Threats to marine snakes includeloss of coral reefs and coastal habitat, incidental bycatch in fisheries, as well as fisheries that target snakes for leather.The presence of two Critically Endangered and one Endangered species in the Timor Sea suggests the area is ofparticular conservation concern. More rigorous, long-term monitoring of populations is needed to evaluate the success of“conservation measures” for marine snake species, provide scientifically based guidance for determining harvest quotas,and to assess the populations of many Data Deficient species.

Published
2013

42. The conservation status of the world’s reptiles

Author

Böhm, Monika, Collen, Ben, Baillie, Jonathan E. M., Bowles, Philip, Chanson, Janice, Cox, Neil, Hammerson, Geoffrey, Hoffmann, Michael, Livingstone, Suzanne R., Ram, Mala, Rhodin, Anders G. J., Stuart, Simon N., van Dijk, Peter Paul, Young, Bruce E., Afuang, Leticia E., Aghasyan, Aram, García, Andrés, Aguilar, César, Ajtic, Rastko, Akarsu, Ferdi, Alencar, Laura R. V., Allison, Allen, Ananjeva, Natalia, Anderson, Steve, Andrén, Claes, Ariano-Sánchez, Daniel, Arredondo, Juan Camilo, Auliya, Mark, Austin, Christopher C., Avci, Aziz, Baker, Patrick J., Barreto-Lima, André F., Barrio-Amorós, César L., Basu, Dhruvayothi, Bates, Michael F., Batistella, Alexandre, Bauer, Aaron, Bennett, Daniel, Böhme, Wolfgang, Broadley, Don, Brown, Rafe, Burgess, Joseph, Captain, Ashok, Carreira, Santiago, Castañeda, Maria del Rosario, Castro, Fernando, Catenazzi, Alessandro, Cedeño-Vázquez, José R., Chapple, David G., Cheylan, Marc, Cisneros-Heredia, Diego F., Cogalniceanu, Dan, Cogger, Hal, Corti, Claudia, Costa, Gabriel C., Couper, Patrick J., Courtney, Tony, Crnobrnja-Isailovic, Jelka, Crochet, Pierre-André, Crother, Brian, Cruz, Felix, Daltry, Jennifer C., Daniels, R. J. Ranjit, Das, Indraneil, de Silva, Anslem, Diesmos, Arvin C., Dirksen, Lutz, Doan, Tiffany M., Dodd Jr, C. Kenneth, Doody, J. Sean, Dorcas, Michael E., Duarte de Barros Filho, Jose, Egan, Vincent T., El Mouden, El Hassan, Embert, Dirk, Espinoza, Robert E., Fallabrino, Alejandro, Feng, Xie, Feng, Zhao-Jun, Fitzgerald, Lee, Flores-Villela, Oscar, França, Frederico G. R., Frost, Darrell, Gadsden, Hector, Gamble, Tony, Ganesh, S. R., Garcia, Miguel A., García-Pérez, Juan E., Gatus, Joey, Gaulke, Maren, Geniez, Philippe, Georges, Arthur, Gerlach, Justin, Goldberg, Stephen, Gonzalez, Juan-Carlos T., Gower, David J., Grant, Tandora, Greenbaum, Eli, Grieco, Cristina, Guo, Peng, Hamilton, Alison M., Hare, Kelly, Hedges, S. Blair, Heideman, Neil, Hilton-Taylor, Craig, Hitchmough, Rod, Hollingsworth, Bradford, Hutchinson, Mark, Ineich, Ivan, Iverson, John, Jaksic, Fabian M., Jenkins, Richard, Joger, Ulrich, Jose, Reizl, Kaska, Yakup, Kaya, Uğur, Keogh, J. Scott, Köhler, Gunther, Kuchling, Gerald, Kumlutaş, Yusuf, Kwet, Axel, La Marca, Enrique, Lamar, William, Lane, Amanda, Lardner, Bjorn, Latta, Craig, Latta, Gabrielle, Lau, Michael, Lavin, Pablo, Lawson, Dwight, LeBreton, Matthew, Lehr, Edgar, Limpus, Duncan, Lipczynski, Nicola, Lobo, Aaron S., López-Luna, Marco A., Luiselli, Luca, Lukoschek, Vimoksalehi, Lundberg, Mikael, Lymberakis, Petros, Macey, Robert, Magnusson, William E., Mahler, D. Luke, Malhotra, Anita, Mariaux, Jean, Maritz, Bryan, Marques, Otavio A. V., Márquez, Rafael, Martins, Marcio, Masterson, Gavin, Mateo, José A., Mathew, Rosamma, Mathews, Nixon, Mayer, Gregory, McCranie, James R., Measey, G. John, Mendoza-Quijano, Fernando, Menegon, Michele, Métrailler, Sébastien, Milton, David A., Montgomery, Chad, Morato, Sérgio A. A., Mott, Tami, Muñoz-Alonso, Antonio, Murphy, John, Nguyen, Truong Q., Nilson, Göran, Nogueira, Cristiano, Núñez, Herman, Orlov, Nikolai, Ota, Hidetoshi, Ottenwalder, José, Papenfuss, Theodore, Pasachnik, Stesha, Passos, Paulo, Pauwels, Olivier S. G., Pérez-Buitrago, Néstor, Pérez-Mellado, Valentín, Pianka, Eric R., Pleguezuelos, Juan, Pollock, Caroline, Ponce-Campos, Paulino, Powell, Robert, Pupin, Fabio, Quintero Díaz, Gustavo E., Radder, Raju, Ramer, Jan, Rasmussen, Arne R., Raxworthy, Chris, Reynolds, Robert, Richman, Nadia, Rico, Edmund L., Riservato, Elisa, Rivas, Gilson, da Rocha, Pedro L. B., Rödel, Mark-Oliver, Rodríguez Schettino, Lourdes, Roosenburg, Willem M., Ross, James P., Sadek, Riyad, Sanders, Kate, Santos-Barrera, Georgina, Schleich, Hermann H., Schmidt, Benedikt R., Schmitz, Andreas, Sharifi, Mozafar, Shea, Glenn, Shi, Hai-Tao, Shine, Richard, Sindaco, Roberto, Slimani, Tahar, Somaweera, Ruchira, Spawls, Steve, Stafford, Peter, Stuebing, Rob, Sweet, Sam, Sy, Emerson, Temple, Helen J., Tognelli, Marcelo F., Tolley, Krystal, Tolson, Peter J., Tuniyev, Boris, Tuniyev, Sako, Üzüm, Nazan, van Buurt, Gerard, Van Sluys, Monique, Velasco, Alvaro, Vences, Miguel, Veselý, Milan, Vinke, Sabine, Vinke, Thomas, Vogel, Gernot, Vogrin, Milan, Vogt, Richard C., Wearn, Oliver R., Werner, Yehudah L., Whiting, Martin J., Wiewandt, Thomas, Wilkinson, John, Wilson, Byron, Wren, Sally, Zamin, Tara, Zhou, Kaiya, Zug, George, Böhm, Monika, Collen, Ben, Baillie, Jonathan E. M., Bowles, Philip, Chanson, Janice, Cox, Neil, Hammerson, Geoffrey, Hoffmann, Michael, Livingstone, Suzanne R., Ram, Mala, Rhodin, Anders G. J., Stuart, Simon N., van Dijk, Peter Paul, Young, Bruce E., Afuang, Leticia E., Aghasyan, Aram, García, Andrés, Aguilar, César, Ajtic, Rastko, Akarsu, Ferdi, Alencar, Laura R. V., Allison, Allen, Ananjeva, Natalia, Anderson, Steve, Andrén, Claes, Ariano-Sánchez, Daniel, Arredondo, Juan Camilo, Auliya, Mark, Austin, Christopher C., Avci, Aziz, Baker, Patrick J., Barreto-Lima, André F., Barrio-Amorós, César L., Basu, Dhruvayothi, Bates, Michael F., Batistella, Alexandre, Bauer, Aaron, Bennett, Daniel, Böhme, Wolfgang, Broadley, Don, Brown, Rafe, Burgess, Joseph, Captain, Ashok, Carreira, Santiago, Castañeda, Maria del Rosario, Castro, Fernando, Catenazzi, Alessandro, Cedeño-Vázquez, José R., Chapple, David G., Cheylan, Marc, Cisneros-Heredia, Diego F., Cogalniceanu, Dan, Cogger, Hal, Corti, Claudia, Costa, Gabriel C., Couper, Patrick J., Courtney, Tony, Crnobrnja-Isailovic, Jelka, Crochet, Pierre-André, Crother, Brian, Cruz, Felix, Daltry, Jennifer C., Daniels, R. J. Ranjit, Das, Indraneil, de Silva, Anslem, Diesmos, Arvin C., Dirksen, Lutz, Doan, Tiffany M., Dodd Jr, C. Kenneth, Doody, J. Sean, Dorcas, Michael E., Duarte de Barros Filho, Jose, Egan, Vincent T., El Mouden, El Hassan, Embert, Dirk, Espinoza, Robert E., Fallabrino, Alejandro, Feng, Xie, Feng, Zhao-Jun, Fitzgerald, Lee, Flores-Villela, Oscar, França, Frederico G. R., Frost, Darrell, Gadsden, Hector, Gamble, Tony, Ganesh, S. R., Garcia, Miguel A., García-Pérez, Juan E., Gatus, Joey, Gaulke, Maren, Geniez, Philippe, Georges, Arthur, Gerlach, Justin, Goldberg, Stephen, Gonzalez, Juan-Carlos T., Gower, David J., Grant, Tandora, Greenbaum, Eli, Grieco, Cristina, Guo, Peng, Hamilton, Alison M., Hare, Kelly, Hedges, S. Blair, Heideman, Neil, Hilton-Taylor, Craig, Hitchmough, Rod, Hollingsworth, Bradford, Hutchinson, Mark, Ineich, Ivan, Iverson, John, Jaksic, Fabian M., Jenkins, Richard, Joger, Ulrich, Jose, Reizl, Kaska, Yakup, Kaya, Uğur, Keogh, J. Scott, Köhler, Gunther, Kuchling, Gerald, Kumlutaş, Yusuf, Kwet, Axel, La Marca, Enrique, Lamar, William, Lane, Amanda, Lardner, Bjorn, Latta, Craig, Latta, Gabrielle, Lau, Michael, Lavin, Pablo, Lawson, Dwight, LeBreton, Matthew, Lehr, Edgar, Limpus, Duncan, Lipczynski, Nicola, Lobo, Aaron S., López-Luna, Marco A., Luiselli, Luca, Lukoschek, Vimoksalehi, Lundberg, Mikael, Lymberakis, Petros, Macey, Robert, Magnusson, William E., Mahler, D. Luke, Malhotra, Anita, Mariaux, Jean, Maritz, Bryan, Marques, Otavio A. V., Márquez, Rafael, Martins, Marcio, Masterson, Gavin, Mateo, José A., Mathew, Rosamma, Mathews, Nixon, Mayer, Gregory, McCranie, James R., Measey, G. John, Mendoza-Quijano, Fernando, Menegon, Michele, Métrailler, Sébastien, Milton, David A., Montgomery, Chad, Morato, Sérgio A. A., Mott, Tami, Muñoz-Alonso, Antonio, Murphy, John, Nguyen, Truong Q., Nilson, Göran, Nogueira, Cristiano, Núñez, Herman, Orlov, Nikolai, Ota, Hidetoshi, Ottenwalder, José, Papenfuss, Theodore, Pasachnik, Stesha, Passos, Paulo, Pauwels, Olivier S. G., Pérez-Buitrago, Néstor, Pérez-Mellado, Valentín, Pianka, Eric R., Pleguezuelos, Juan, Pollock, Caroline, Ponce-Campos, Paulino, Powell, Robert, Pupin, Fabio, Quintero Díaz, Gustavo E., Radder, Raju, Ramer, Jan, Rasmussen, Arne R., Raxworthy, Chris, Reynolds, Robert, Richman, Nadia, Rico, Edmund L., Riservato, Elisa, Rivas, Gilson, da Rocha, Pedro L. B., Rödel, Mark-Oliver, Rodríguez Schettino, Lourdes, Roosenburg, Willem M., Ross, James P., Sadek, Riyad, Sanders, Kate, Santos-Barrera, Georgina, Schleich, Hermann H., Schmidt, Benedikt R., Schmitz, Andreas, Sharifi, Mozafar, Shea, Glenn, Shi, Hai-Tao, Shine, Richard, Sindaco, Roberto, Slimani, Tahar, Somaweera, Ruchira, Spawls, Steve, Stafford, Peter, Stuebing, Rob, Sweet, Sam, Sy, Emerson, Temple, Helen J., Tognelli, Marcelo F., Tolley, Krystal, Tolson, Peter J., Tuniyev, Boris, Tuniyev, Sako, Üzüm, Nazan, van Buurt, Gerard, Van Sluys, Monique, Velasco, Alvaro, Vences, Miguel, Veselý, Milan, Vinke, Sabine, Vinke, Thomas, Vogel, Gernot, Vogrin, Milan, Vogt, Richard C., Wearn, Oliver R., Werner, Yehudah L., Whiting, Martin J., Wiewandt, Thomas, Wilkinson, John, Wilson, Byron, Wren, Sally, Zamin, Tara, Zhou, Kaiya, and Zug, George

Abstract

Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed in order to highlight urgent conservation cases and inform environmental policy with appropriate biodiversity information in a timely manner. We present the first ever global analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16% of all currently known species). To our knowledge, our results provide the first analysis of the global conservation status and distribution patterns of reptiles and the threats affecting them, highlighting conservation priorities and knowledge gaps which need to be addressed urgently to ensure the continued survival of the world’s reptiles. Nearly one in five reptilian species are threatened with extinction, with another one in five species classed as Data Deficient. The proportion of threatened reptile species is highest in freshwater environments, tropical regions and on oceanic islands, while data deficiency was highest in tropical areas, such as Central Africa and Southeast Asia, and among fossorial reptiles. Our results emphasise the need for research attention to be focussed on tropical areas which are experiencing the most dramatic rates of habitat loss, on fossorial reptiles for which there is a chronic lack of data, and on certain taxa such as snakes for which extinction risk may currently be underestimated due to lack of population information. Conservation actions specifically need to mitigate the effects of human-induced habitat loss and harvesting, which are the predominant threats to reptiles.

Published
2013

43. New insights into the role of MHC diversity in devil facial tumour disease

Author

Lane, Amanda, Cheng, Yuanyuan, Wright, Belinda, Hamede, Rodrigo, Levan, Laura, Jones, Menna, Ujvari, Beata, Belov, Katherine, Lane, Amanda, Cheng, Yuanyuan, Wright, Belinda, Hamede, Rodrigo, Levan, Laura, Jones, Menna, Ujvari, Beata, and Belov, Katherine

Abstract

Devil facial tumour disease (DFTD) is a fatal contagious cancer that has decimated Tasmanian devil populations. The tumour has spread without invoking immune responses, possibly due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils. Animals from a region in north-western Tasmania have lower infection rates than those in the east of the state. This area is a genetic transition zone between sub-populations, with individuals from north-western Tasmania displaying greater diversity than eastern devils at MHC genes, primarily through MHC class I gene copy number variation. Here we test the hypothesis that animals that remain healthy and tumour free show predictable differences at MHC loci compared to animals that develop the disease.

Published
2012

44. Interactive Exploration of Ingredient Mixtures Using Multiple Coordinated Views

Author

Johansson, Sara, Knaving, Kristina, Lane, Amanda, Jern, Mikael, Johansson, Jimmy, Johansson, Sara, Knaving, Kristina, Lane, Amanda, Jern, Mikael, and Johansson, Jimmy

Abstract

The complex nature of multivariate data sets calls forhigh interactive performance and intuitive metaphors. Aspecific type of multivariate data is where the variables sum up to a constant, here defined as multicomponent data.This application paper presents an interactive applicationfor analysis of modelled multicomponent data. The aim isto find high performance variable combinations that fulfil some requested properties. The application is basedon coordinated views that include parallel coordinates, a ternary diagram, a 2D scatter plot and a line plot. It supports numerous interaction techniques enabling fast analysisof complex patterns in multicomponent data sets. The application is developed in collaboration with researchers within the fields of statistics and chemistry. An informal usability evaluation indicates that the interactive nature ofthe application clearly facilitates the analysis process.

Published
2009
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45. Genomic Evolution of the Pathogenic Wolbachia Strain, wMelPop

Author

Woolfit, Megan, primary, Iturbe-Ormaetxe, Iñaki, additional, Brownlie, Jeremy C., additional, Walker, Thomas, additional, Riegler, Markus, additional, Seleznev, Andrei, additional, Popovici, Jean, additional, Rancès, Edwige, additional, Wee, Bryan A., additional, Pavlides, Jennifer, additional, Sullivan, Mitchell J., additional, Beatson, Scott A., additional, Lane, Amanda, additional, Sidhu, Manpreet, additional, McMeniman, Conor J., additional, McGraw, Elizabeth A., additional, and O’Neill, Scott L., additional

Published
2013
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46. The conservation status of the world’s reptiles

Author

Böhm, Monika, primary, Collen, Ben, additional, Baillie, Jonathan E.M., additional, Bowles, Philip, additional, Chanson, Janice, additional, Cox, Neil, additional, Hammerson, Geoffrey, additional, Hoffmann, Michael, additional, Livingstone, Suzanne R., additional, Ram, Mala, additional, Rhodin, Anders G.J., additional, Stuart, Simon N., additional, van Dijk, Peter Paul, additional, Young, Bruce E., additional, Afuang, Leticia E., additional, Aghasyan, Aram, additional, García, Andrés, additional, Aguilar, César, additional, Ajtic, Rastko, additional, Akarsu, Ferdi, additional, Alencar, Laura R.V., additional, Allison, Allen, additional, Ananjeva, Natalia, additional, Anderson, Steve, additional, Andrén, Claes, additional, Ariano-Sánchez, Daniel, additional, Arredondo, Juan Camilo, additional, Auliya, Mark, additional, Austin, Christopher C., additional, Avci, Aziz, additional, Baker, Patrick J., additional, Barreto-Lima, André F., additional, Barrio-Amorós, César L., additional, Basu, Dhruvayothi, additional, Bates, Michael F., additional, Batistella, Alexandre, additional, Bauer, Aaron, additional, Bennett, Daniel, additional, Böhme, Wolfgang, additional, Broadley, Don, additional, Brown, Rafe, additional, Burgess, Joseph, additional, Captain, Ashok, additional, Carreira, Santiago, additional, Castañeda, Maria del Rosario, additional, Castro, Fernando, additional, Catenazzi, Alessandro, additional, Cedeño-Vázquez, José R., additional, Chapple, David G., additional, Cheylan, Marc, additional, Cisneros-Heredia, Diego F., additional, Cogalniceanu, Dan, additional, Cogger, Hal, additional, Corti, Claudia, additional, Costa, Gabriel C., additional, Couper, Patrick J., additional, Courtney, Tony, additional, Crnobrnja-Isailovic, Jelka, additional, Crochet, Pierre-André, additional, Crother, Brian, additional, Cruz, Felix, additional, Daltry, Jennifer C., additional, Daniels, R.J. Ranjit, additional, Das, Indraneil, additional, de Silva, Anslem, additional, Diesmos, Arvin C., additional, Dirksen, Lutz, additional, Doan, Tiffany M., additional, Dodd, C. Kenneth, additional, Doody, J. Sean, additional, Dorcas, Michael E., additional, Duarte de Barros Filho, Jose, additional, Egan, Vincent T., additional, El Mouden, El Hassan, additional, Embert, Dirk, additional, Espinoza, Robert E., additional, Fallabrino, Alejandro, additional, Feng, Xie, additional, Feng, Zhao-Jun, additional, Fitzgerald, Lee, additional, Flores-Villela, Oscar, additional, França, Frederico G.R., additional, Frost, Darrell, additional, Gadsden, Hector, additional, Gamble, Tony, additional, Ganesh, S.R., additional, Garcia, Miguel A., additional, García-Pérez, Juan E., additional, Gatus, Joey, additional, Gaulke, Maren, additional, Geniez, Philippe, additional, Georges, Arthur, additional, Gerlach, Justin, additional, Goldberg, Stephen, additional, Gonzalez, Juan-Carlos T., additional, Gower, David J., additional, Grant, Tandora, additional, Greenbaum, Eli, additional, Grieco, Cristina, additional, Guo, Peng, additional, Hamilton, Alison M., additional, Hare, Kelly, additional, Hedges, S. Blair, additional, Heideman, Neil, additional, Hilton-Taylor, Craig, additional, Hitchmough, Rod, additional, Hollingsworth, Bradford, additional, Hutchinson, Mark, additional, Ineich, Ivan, additional, Iverson, John, additional, Jaksic, Fabian M., additional, Jenkins, Richard, additional, Joger, Ulrich, additional, Jose, Reizl, additional, Kaska, Yakup, additional, Kaya, Uğur, additional, Keogh, J. Scott, additional, Köhler, Gunther, additional, Kuchling, Gerald, additional, Kumlutaş, Yusuf, additional, Kwet, Axel, additional, La Marca, Enrique, additional, Lamar, William, additional, Lane, Amanda, additional, Lardner, Bjorn, additional, Latta, Craig, additional, Latta, Gabrielle, additional, Lau, Michael, additional, Lavin, Pablo, additional, Lawson, Dwight, additional, LeBreton, Matthew, additional, Lehr, Edgar, additional, Limpus, Duncan, additional, Lipczynski, Nicola, additional, Lobo, Aaron S., additional, López-Luna, Marco A., additional, Luiselli, Luca, additional, Lukoschek, Vimoksalehi, additional, Lundberg, Mikael, additional, Lymberakis, Petros, additional, Macey, Robert, additional, Magnusson, William E., additional, Mahler, D. Luke, additional, Malhotra, Anita, additional, Mariaux, Jean, additional, Maritz, Bryan, additional, Marques, Otavio A.V., additional, Márquez, Rafael, additional, Martins, Marcio, additional, Masterson, Gavin, additional, Mateo, José A., additional, Mathew, Rosamma, additional, Mathews, Nixon, additional, Mayer, Gregory, additional, McCranie, James R., additional, Measey, G. John, additional, Mendoza-Quijano, Fernando, additional, Menegon, Michele, additional, Métrailler, Sébastien, additional, Milton, David A., additional, Montgomery, Chad, additional, Morato, Sérgio A.A., additional, Mott, Tami, additional, Muñoz-Alonso, Antonio, additional, Murphy, John, additional, Nguyen, Truong Q., additional, Nilson, Göran, additional, Nogueira, Cristiano, additional, Núñez, Herman, additional, Orlov, Nikolai, additional, Ota, Hidetoshi, additional, Ottenwalder, José, additional, Papenfuss, Theodore, additional, Pasachnik, Stesha, additional, Passos, Paulo, additional, Pauwels, Olivier S.G., additional, Pérez-Buitrago, Néstor, additional, Pérez-Mellado, Valentín, additional, Pianka, Eric R., additional, Pleguezuelos, Juan, additional, Pollock, Caroline, additional, Ponce-Campos, Paulino, additional, Powell, Robert, additional, Pupin, Fabio, additional, Quintero Díaz, Gustavo E., additional, Radder, Raju, additional, Ramer, Jan, additional, Rasmussen, Arne R., additional, Raxworthy, Chris, additional, Reynolds, Robert, additional, Richman, Nadia, additional, Rico, Edmund L., additional, Riservato, Elisa, additional, Rivas, Gilson, additional, da Rocha, Pedro L.B., additional, Rödel, Mark-Oliver, additional, Rodríguez Schettino, Lourdes, additional, Roosenburg, Willem M., additional, Ross, James P., additional, Sadek, Riyad, additional, Sanders, Kate, additional, Santos-Barrera, Georgina, additional, Schleich, Hermann H., additional, Schmidt, Benedikt R., additional, Schmitz, Andreas, additional, Sharifi, Mozafar, additional, Shea, Glenn, additional, Shi, Hai-Tao, additional, Shine, Richard, additional, Sindaco, Roberto, additional, Slimani, Tahar, additional, Somaweera, Ruchira, additional, Spawls, Steve, additional, Stafford, Peter, additional, Stuebing, Rob, additional, Sweet, Sam, additional, Sy, Emerson, additional, Temple, Helen J., additional, Tognelli, Marcelo F., additional, Tolley, Krystal, additional, Tolson, Peter J., additional, Tuniyev, Boris, additional, Tuniyev, Sako, additional, Üzüm, Nazan, additional, van Buurt, Gerard, additional, Van Sluys, Monique, additional, Velasco, Alvaro, additional, Vences, Miguel, additional, Veselý, Milan, additional, Vinke, Sabine, additional, Vinke, Thomas, additional, Vogel, Gernot, additional, Vogrin, Milan, additional, Vogt, Richard C., additional, Wearn, Oliver R., additional, Werner, Yehudah L., additional, Whiting, Martin J., additional, Wiewandt, Thomas, additional, Wilkinson, John, additional, Wilson, Byron, additional, Wren, Sally, additional, Zamin, Tara, additional, Zhou, Kaiya, additional, and Zug, George, additional

Published
2013
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50. Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia

Author

Luck, Naomi L., primary, Thomas, Kristen C., additional, Morin-Adeline, Victoria E., additional, Barwick, Sophie, additional, Chong, Amanda Y., additional, Carpenter, Eliza L., additional, Wan, LinXiao, additional, Willet, Cali E., additional, Langford-Salisbury, Shannan M., additional, Abdelsayd, Mary, additional, Ang, Rachel A., additional, Atkinson, Sarah J., additional, Barcelo, Fabian G., additional, Booth, Melanie E., additional, Bradbury, Emma J., additional, Branighan, Thomas L., additional, Brown, Jennifer, additional, Castillo, Lesley E., additional, Chandler, Nichola D., additional, Chong, Josephine Y., additional, Collits, Kimberly J., additional, Cook, Emma, additional, Cruz, Rachel E., additional, Farrugia, Claire A., additional, Fletcher, Jessica L., additional, Fletcher, Sophie, additional, Gamaliel, Nicole S., additional, Gurr, Jessica F., additional, Hallett, Nathan J., additional, Hargreaves, Grace, additional, Harris, Teresa, additional, Hollings, Samantha, additional, Hopcroft, Ryan L., additional, Johinke, Danielle, additional, Kern, Pippa L., additional, Kiddell, Jane L., additional, Kilby, Kristen E., additional, Kragic, Borjana, additional, Kwan, Jacqueline H., additional, Lee, Joseph I., additional, Liang, Jennifer M., additional, Lillie, Mette C., additional, Lui, Belle C., additional, Luk, Sharon W., additional, Lun, Kwok H., additional, Marshall, Kate L., additional, Marzec, Jolanta A., additional, Masters, Kellie T., additional, Mazurkijevic, Laura J., additional, Medlock, Jeremy, additional, Meoli, Christopher, additional, Morris, Katrina M., additional, Noh, Yvonne H., additional, Okazaki, Hana, additional, Orourke, Tamara J., additional, Payne, Elyssa M., additional, Powell, Dean J., additional, Quinlivan, Antonia R., additional, Reeves, Thomas J., additional, Robson, Kate, additional, Robson, Kate L., additional, Royle, Leah J., additional, Stevenson, Ryan, additional, Sellens, Teigan, additional, Sun, ZiChen, additional, Sutton, Amanda L., additional, Swan, Amelia, additional, Tang, Jason M., additional, Tinker, Jarrod E., additional, Tomlinson, Suzanne C., additional, Wilkin, Tessa, additional, Wright, Amanda L., additional, Xiao, Sam T., additional, Yang, Jessica, additional, Yee, Christine, additional, Jaratlerdsiri, Weerachai, additional, Isberg, Sally R., additional, Miles, Lee, additional, Higgins, Damien, additional, Lane, Amanda, additional, and Gongora, Jaime, additional

Published
2012
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