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3. Urinalysis and culture results of free‐catch urine samples in dogs: a randomised controlled trial.

Author

Mandese, W. W., Suero, M., Reynolds, P. S., Kariyawasam, S., Beatty, S., and Griffin, F.

Subjects
URINARY tract infections, RANDOMIZED controlled trials, BACTERIURIA, BACTERIAL growth, ODDS ratio
Abstract

Objectives: To evaluate the prevalence of bacterial presence in free‐catch urine samples preceded by either a standardised prepped ("clean‐catch") protocol versus unprepped (non‐cleaned) voiding. Materials and Methods: The study was a single‐centre prospective single‐blinded randomised controlled trial. Urine samples were obtained from 100 client‐owned dogs presenting for routine evaluation. Dogs were randomly assigned to either the prepped group (preputial or peri‐vulvar area cleaned with sterile saline before collection) or the unprepped group (no preliminary cleansing) stratified by sex. Urinalysis and urine culture (blood and MacConkey agar) were performed on all samples. Significant bacterial presence on urine culture was defined as >104 colony forming units (CFU)/mL. Results: There were no statistically significant associations between prepped versus unprepped collection method or sex with a urinalysis positive for bacteriuria. However, on culture, significant bacterial growth was almost five times more likely to be associated with males relative to females (odds ratio 4.59, 95% confidence interval 1.61 to 13.10). The probability of finding a positive culture was not statistically associated with prep method (odds ratio 1.43, 95% confidence interval 0.50 to 4.08). Clinical Significance: For the majority of dogs without clinical signs of urinary tract infection, free‐catch urine collection does not result in significant bacteriuria found on analysis or culture. The presence of bacteria found in free‐catch samples may be secondary to sample contamination or subclinical bacteriuria. Sample contamination or subclinical bacteriuria may be more prevalent in male dogs. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Responses to desiccation vary among populations of an endemic freshwater isopod, Paramphisopus palustris.

Author

Emery‐Butcher, H. E., Beatty, S. J., and Robson, B. J.

Subjects
*WETLANDS, *DEHYDRATION, *FRESH water, *WATER levels, *ISOPODA
Abstract

Isopods play many important roles within freshwater ecosystems (including as shredders, prey, and detritivores), yet we know little about their responses to disturbance or whether they vary among populations. In a region undergoing severe climatic drying that is changing hydrological regimes in wetlands, we compared responses to drying (including survival) among populations of an endemic isopod Paramphisopus palustris (Amphisopidae).The survival of individuals from four isopod populations (two each from seasonal and semi‐perennial wetlands) were tested in a drying experiment with three treatments: control (permanently inundated), saturated sediment (water level maintained equal with the sediment surface), and dry (microcosms gradually raised out of the water causing sediments to dry out). Microrefuge use (three levels: no response, sought shelter or sought shelter/burrowed) was also compared among populations.As expected, isopod mortality was highest in the dry treatment for all populations. Unexpectedly, isopods from the two semi‐perennial wetlands showed higher survival in response to drying than those from seasonal wetlands. All isopods showed dormancy in response to the dry treatment and curled their bodies to limit water loss from their ventral gills. Microrefuge use differed among populations but not between the two hydroregimes. However, there was some similarity in population responses according to genetic clade.Isopods displayed some resistance to drying through dormancy behaviour and seeking microrefuges, which will increase population persistence under a drying climate. However, the reduced survival of individuals from seasonal wetland populations suggests that surviving in these wetlands is more challenging than in semi‐perennial or perennial regimes. These challenges are likely to be exacerbated as climate change further decreases hydroperiods and limits the availability of damp microrefuges. Consequently, longer‐term population persistence may be challenged as more wetlands become seasonal.The responses of endemic species are not always correctly predicted from knowledge of more widespread and commonly studied species and our results suggest that there may be variation among populations. Although P. palustris showed some innate responses to drying, their long‐term persistence (and that of other endemic species) may be threatened as environmental conditions become more extreme. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Evolutionary tracking of cancer haplotypes at single-cell resolution

Author

Nicholas Ceglia, Diljot Grewal, Justina Biele, Weiner Ac, Brimhall J, Peter Eirew, Samuel Aparicio, Ciara H. O'Flanagan, Havasov E, Masud T, Hakwoo Lee, Beatty S, Samantha Leung, Florian Uhlitz, Abrams D, Ignacio Vázquez-García, Marc J Williams, Damian Yap, Daniel Lai, Salehi S, Sohrab P. Shah, Ting J, Wang B, Farhia Kabeer, Nicole Rusk, Bojilova, Tyler Funnell, Jenifer Pham, and Andrew McPherson

Subjects
Loss of heterozygosity, Genetics, Structural variation, medicine.anatomical_structure, Haplotype, Cell, medicine, Cancer, Biology, Allele, medicine.disease, Phenotype, Genome
Abstract

Cancer genomes exhibit extensive chromosomal copy number changes and structural variation, yet how allele specific alterations drive cancer genome evolution remains unclear. Here, through application of a new computational approach we report allele specific copy number alterations in 11,097 single cell whole genomes from genetically engineered mammary epithelial cells and 21,852 cells from high grade serous ovarian and triple negative breast cancers. Resolving single cell copy number profiles to individual alleles uncovered genomic background distributions of gains, losses and loss of heterozygosity, yielding evidence of positive selection of specific chromosomal alterations. In addition specific genomic loci in maternal and paternal alleles were commonly found to be altered in parallel with convergent phenotypic transcriptional effects. Finally we show that haplotype specific alterations trace the cyclical etiology of high level amplifications and reveal clonal haplotype decomposition of complex structures. Together, our results illuminate how allele and haplotype specific alterations, here determined across thousands of single cell cancer genomes, impact the etiology and evolution of structural variations in human tumours.

Published
2021
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22. The impact of mutational processes on structural genomic plasticity in cancer cells

Author

Beatty S, Britta Weigelt, Havasov E, Douglas Jm, Beixi Wang, Samuel Aparicio, Steven McKinney, Samantha Leung, Hakwoo Lee, Brimhall J, Marc J Williams, Yang Li, Sohrab P. Shah, Justina Biele, Jamie L. P. Lim, Funnell T, Da Cruz Paula A, Ciara H. O'Flanagan, Andrew McPherson, Damian Yap, Nicholas Ceglia, Diljot Grewal, Weiner Ac, Sarah H. Kim, Allen Zhang, Ruiz de Algara T, Lee, Cerda Llanos, Liu Yf, Peter Eirew, Jorge S. Reis-Filho, Dmitriy Zamarin, Abrams D, Tehmina Masud, Daniel Lai, Bojilova, Richard A. Moore, Xu H, Farhia Kabeer, Nicole Rusk, Florian Uhlitz, Jerome Ting, and Jenifer Pham

Subjects
Structural variation, Evolutionary biology, medicine, Aneuploidy, Cancer, Biology, Ploidy, medicine.disease, Molecular clock, Phenotype, Genome, DNA sequencing
Abstract

Structural genome alterations are determinants of cancer ontogeny and therapeutic response. While bulk genome sequencing has enabled delineation of structural variation (SV) mutational processes which generate patterns of DNA damage, we have little understanding of how these processes lead to cell-to-cell variations which underlie selection and rates of accrual of different genomic lesions. We analysed 309 high grade serous ovarian and triple negative breast cancer genomes to determine their mutational processes, selecting 22 from which we sequenced >22,000 single cell whole genomes across a spectrum of mutational processes. We show that distinct patterns of cell-to-cell variation in aneuploidy, copy number alteration (CNA) and segment length occur in homologous recombination deficiency (HRD) and fold-back inversion (FBI) phenotypes. Widespread aneuploidy through induction of HRD throughBRCA1andBRCA2inactivation was mirrored by continuous whole genome duplication in HRD tumours, contrasted with early ploidy fixation in FBI. FBI tumours exhibited copy number distributions skewed towards gains, widespread clone-specific variation in amplitude of high-level amplifications, often impacting oncogenes, and break-point variability consistent with progressive genomic diversification, which we termed serriform structural variation (SSV). SSVs were consistent with a CNA-based molecular clock reflecting a continual and distributed process across clones within tumours. These observations reveal previously obscured genome plasticity and evolutionary properties with implications for cancer evolution, therapeutic targeting and response.

Published
2021
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23. Irish college of ophthalmologists: Proceedings of annual meeting held in Slieve Russell Hotel, Ballyconnell, Co. Cavan on May 4th and 5th, 1995

Author

Abdulla, N., Lanigan, B., O’Keefe, M., Bowell, R., Abdulla, N., Lanigan, B., Bowell, R., O’Keefe, M., Aduriz-Lorenzo, P. M., Acheson, R. W., Aduriz-Lorenzo, P. M., Logan, P., Eustace, P., Toland, J., Beatty, S., Kheterpal, S., Eagling, E. M., O’Neill, E. C., Beatty, S., Aggarwal, R. K., David, D. B., Jones, H., Guarro, M., Pearce, J. L., Best, R. M., Bailie, J. R., Stitt, A. W., Hadden, D. R., Traub, A. I., Chakravarthy, U., Archer, D. B., Cahil, M., Acheson, R. W., Mooney, D., Peyton, K., Cassidy, L., Barry, P., Early, A., Blayney, A., Stack, S., Eustace, P., Fenton, S., Collum, A., Hurley, C., Collum, L. M. T., Foley-Nolan, A., Foley-Nolan, A., O’Keefe, M., Goggin, M., Algawi, K., Gregor, Z. J., Hedges, T. R., Hurley, C., Hillery, M., Hoh, H. B., Claoue, C., Easty, D. L., Kenna, P., Collum, L. M. T., Keenan, J. M., Kriss, A., Harris, C., Clayton, P. T., Russell-Eggitt, I. R., Kilmartin, D. J., Mooney, D., Acheson, R. W., Payne, S., Maher, E. R., Eustace, P., Kilmartin, D. J., Moore, J., Silvestri, G., Acheson, R. W., Knight-Nanan, D. M., Algawi, K., O’Keefe, M., Larkin, D. F. P., George, A. J. T., Larkin, G., Olver, J., Lund, V., Fells, P., Lee, J. P., Lewis, H., Minihan, M., Horgan, T., Cleary, P. E., Mulholland, D. A., Earley, O. T., Sharkey, J. A., Atkinson, G., Mullaney, P. B., Noble, B. A., James, T. E., O’Brannagain, D., Nelson, E. I., O’Regan, R., O’Regan, R., Power, W. J., Dutt, J. E., Foster, C. S., Saidléar, C., Gilligan, P., Robinson, E., Ennis, J., Eustace, P., Sharkey, J. A., Sinton, J. E., Jackson, J., Frazer, D. G., Stitt, A., Gardiner, W. T. A., Archer, D. B., Weiser, B., O’Brien, C., Butt, Z., Beatty, S., Murray, P. I., Beatty, S., Nischal, K., Cahill, M., O’Meara, N., Mooney, D., Acheson, R. W., Chuah, K., Lyness, R., Earley, O. T., Datta, K., Fulcher, T., O’Keefe, M., Lacey, B., Earley, O. T., Buchanan, T. A. S., Lacey, B., Best, R. M., Earley, O. T., Johnston, P. B., Archer, D. B., Moore, J., Mahon, G., Limb, G. A., Buchanan, T. A. S., Kervick, G. N., Earley, O. T., Mulholland, D. A., Sharkey, J. A., Johnston, P. B., O’Regan, R., Nelson, E., Brannagain, D. O, and Irish Diabetic Study Group

Published
1995
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30. Sediment removal in the lower Vasse River: Environmental Management Plan for Carter’s Freshwater Mussel Westralunio carteri

Author

Beatty, S., Paice, R., Cottingham, A., Lymbery, A., Beatty, S., Paice, R., Cottingham, A., and Lymbery, A.

Abstract

As part of the implementation of the Lower Vasse River Waterway Management Plan (City of Busselton, 2019), the City of Busselton proposes to remove sediment from an ~750 m reach of the Lower Vasse River in Busselton, Western Australia (WA) (hereafter primary Sediment Removal Site (‘SRS’)). An additional ~1700 m of river upstream may also be targeted for sediment removal in the future...

Published
2021

31. Survey of Carter’s Freshwater Mussel in the Lower Vasse River to inform future sediment removal

Author

Paice, R., Beatty, S., Paice, R., and Beatty, S.

Abstract

This report presents the outcomes of a survey of Carter’s Freshwater Mussel (Westralunio carteri) in the Lower Vasse River, Busselton, to provide information for planning of sediment removal in the river. The City of Busselton proposes to undertake sediment removal from the river and is required to minimise potential impacts of these works on mussels in the river. The Lower Vasse River is degraded with a long history of seasonal algal blooms and the purpose of sediment removal is to provide benefits to water quality, habitat and public amenity...

Published
2021

35. Macular pigment levels following successful macular hole surgery

Author

Neelam, K., O'Gorman, N., Nolan, J., O'Donovan, O., Au Eong, K.G., and Beatty, S.

Subjects
Macula lutea -- Physiological aspects, Photoreceptors -- Physiological aspects, Eye -- Surgery, Eye -- Complications and side effects, Health
Published
2005

39. Review of pulsed power-driven high energy density physics research on Z at Sandia

Author

Sinars, D. B., primary, Sweeney, M. A., additional, Alexander, C. S., additional, Ampleford, D. J., additional, Ao, T., additional, Apruzese, J. P., additional, Aragon, C., additional, Armstrong, D. J., additional, Austin, K. N., additional, Awe, T. J., additional, Baczewski, A. D., additional, Bailey, J. E., additional, Baker, K. L., additional, Ball, C. R., additional, Barclay, H. T., additional, Beatty, S., additional, Beckwith, K., additional, Bell, K. S., additional, Benage, J. F., additional, Bennett, N. L., additional, Blaha, K., additional, Bliss, D. E., additional, Boerner, J. J., additional, Bourdon, C. J., additional, Branch, B. A., additional, Brown, J. L., additional, Campbell, E. M., additional, Campbell, R. B., additional, Chacon, D. G., additional, Chandler, G. A., additional, Chandler, K., additional, Christenson, P. J., additional, Christison, M. D., additional, Christner, E. B., additional, Clay, R. C., additional, Cochrane, K. R., additional, Colombo, A. P., additional, Cook, B. M., additional, Coverdale, C. A., additional, Cuneo, M. E., additional, Custer, J. S., additional, Dasgupta, A., additional, Davis, J.-P., additional, Desjarlais, M. P., additional, Dolan, D. H., additional, Douglass, J. D., additional, Dunham, G. S., additional, Duwal, S., additional, Edens, A. D., additional, Edwards, M. J., additional, Evstatiev, E. G., additional, Farfan, B. G., additional, Fein, J. R., additional, Field, E. S., additional, Fisher, J. A., additional, Flanagan, T. M., additional, Flicker, D. G., additional, Furnish, M. D., additional, Galloway, B. R., additional, Gard, P. D., additional, Gardiner, T. A., additional, Geissel, M., additional, Giuliani, J. L., additional, Glinsky, M. E., additional, Gomez, M. R., additional, Gomez, T., additional, Grim, G. P., additional, Hahn, K. D., additional, Haill, T. A., additional, Hamlin, N. D., additional, Hammer, J. H., additional, Hansen, S. B., additional, Hanshaw, H. L., additional, Harding, E. C., additional, Harvey-Thompson, A. J., additional, Headley, D., additional, Herrmann, M. C., additional, Hess, M. H., additional, Highstrete, C., additional, Hurricane, O. A., additional, Hutsel, B. T., additional, Jennings, C. A., additional, Johns, O. M., additional, Johnson, D., additional, Johnston, M. D., additional, Jones, B. M., additional, Jones, M. C., additional, Jones, P. A., additional, Kalita, P. E., additional, Kamm, R. J., additional, Kellogg, J. W., additional, Kiefer, M. L., additional, Kimmel, M. W., additional, Knapp, P. F., additional, Knudson, M. D., additional, Kreft, A., additional, Laity, G. R., additional, Lake, P. W., additional, Lamppa, D. C., additional, Langston, W. L., additional, Lash, J. S., additional, LeChien, K. R., additional, Leckbee, J. J., additional, Leeper, R. J., additional, Leifeste, G. T., additional, Lemke, R. W., additional, Lewis, W., additional, Lewis, S. A., additional, Loisel, G. P., additional, Looker, Q. M., additional, Lopez, A. J., additional, Lucero, D. J., additional, MacLaren, S. A., additional, Magyar, R. J., additional, Mangan, M. A., additional, Martin, M. R., additional, Mattsson, T. R., additional, Matzen, M. K., additional, Maurer, A. J., additional, Mazarakis, M. G., additional, McBride, R. D., additional, McLean, H. S., additional, McCoy, C. A., additional, McKee, G. R., additional, McKenney, J. L., additional, Miles, A. R., additional, Mills, J. A., additional, Mitchell, M. D., additional, Moore, N. W., additional, Myers, C. E., additional, Nagayama, T., additional, Natoni, G., additional, Owen, A. C., additional, Patel, S., additional, Peterson, K. J., additional, Pointon, T. D., additional, Porter, J. L., additional, Porwitzky, A. J., additional, Radovich, S., additional, Raman, K. S., additional, Rambo, P. K., additional, Reinhart, W. D., additional, Robertson, G. K., additional, Rochau, G. A., additional, Root, S., additional, Rose, D. V., additional, Rovang, D. C., additional, Ruiz, C. L., additional, Ruiz, D. E., additional, Sandoval, D., additional, Savage, M. E., additional, Sceiford, M. E., additional, Schaeuble, M. A., additional, Schmit, P. F., additional, Schollmeier, M. S., additional, Schwarz, J., additional, Seagle, C. T., additional, Sefkow, A. B., additional, Seidel, D. B., additional, Shipley, G. A., additional, Shores, J., additional, Shulenburger, L., additional, Simpson, S. C., additional, Slutz, S. A., additional, Smith, I. C., additional, Speas, C. S., additional, Specht, P. E., additional, Speir, M. J., additional, Spencer, D. C., additional, Springer, P. T., additional, Steiner, A. M., additional, Stoltzfus, B. S., additional, Stygar, W. A., additional, Ward Thornhill, J., additional, Torres, J. A., additional, Townsend, J. P., additional, Tyler, C., additional, Vesey, R. A., additional, Wakeland, P. E., additional, Webb, T. J., additional, Weinbrecht, E. A., additional, Weis, M. R., additional, Welch, D. R., additional, Wise, J. L., additional, Wu, M., additional, Yager-Elorriaga, D. A., additional, Yu, A., additional, and Yu, E. P., additional

Published
2020
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50. Big trouble for little fish: Identifying Australian freshwater fishes in imminent risk of extinction

Author

Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z., Garnett, S.T., Lintermans, M., Geyle, H.M., Beatty, S., Brown, C., Ebner, B.C., Freeman, R., Hammer, M.P., Humphreys, W.F., Kennard, M.J., Kern, P., Martin, K., Morgan, D.L., Raadik, T.A., Unmack, P.J., Wager, R., Woinarski, J.C.Z., and Garnett, S.T.

Abstract

Globally, freshwater fishes are declining at an alarming rate. Despite much evidence of catastrophic declines, few Australian species are listed as threatened under national legislation. We aim to help redress this by identifying the Australian freshwater fishes that are in the most immediate risk of extinction. For 22 freshwater fishes (identified as highly threatened by experts), we used structured expert elicitation to estimate the probability of extinction in the next ~20 years, and to identify key threats and priority management needs. All but one of the 22 species are small (<150 mm total length), 12 have been formally described only in the last decade, with seven awaiting description. Over 90% of these species were assessed to have a >50% probability of extinction in the next ~20 years. Collectively, the biggest factor contributing to the likelihood of extinction of the freshwater fishes considered is that they occur in small (distributions ≤44 km2), geographically isolated populations, and are threatened by a mix of processes (particularly alien fishes and climate change). Nineteen of these species are unlisted on national legislation, so legislative drivers for recovery actions are largely absent. Research has provided strong direction on how to manage ~35% of known threats to the species considered, and, of these, ~36% of threats have some management underway (although virtually none are at the stage where intervention is no longer required). Increased resourcing, management intervention and social attitudinal change is urgently needed to avert the impending extinction of Australia’s most imperilled freshwater fishes.

Published
2020

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