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1. A framework for community curation of interspecies interactions literature

Author

Cuzick, A., Seager, J., Wood, V., Urban, M., Rutherford, K., and Hammond-Kosack, K. E.

Subjects
Curation, Pathogen species, Pathogen-host interactions, Phenotype database, Host species, PHI-base
Abstract

The quantity and complexity of data being generated and published in biology has increased substantially, but few methods exist for capturing knowledge about phenotypes derived from molecular interactions between diverse groups of species, in such a way that is amenable to data-driven biology and research. To improve access to this knowledge, we have constructed a framework for the curation of the scientific literature studying interspecies interactions, using data curated for the Pathogen-Host Interactions Database (PHI-base) as a case study. The framework provides a curation tool, phenotype ontology and controlled vocabularies to curate pathogen-host interaction data (at the level of the host, pathogen, strain, gene and genotype). The concept of a multispecies genotype, the ‘metagenotype’, is introduced to facilitate capturing changes in the pathogens’ disease-causing abilities, and host resistance or susceptibility observed by gene alterations. We report on this framework and describe PHI-Canto, a community curation tool for use by publication authors.

Published
2022

2. P748: SINGLE CELL GENOTYPING OF MATCHED BONE MARROW AND PERIPHERAL BLOOD CELLS IN TREATMENT NAIVE AND AZA-TREATED MDS AND CMML

Author

Schnegg-Kaufmann, A., primary, Thoms, J., additional, Bhuyan, G. S., additional, Henry, H., additional, Vaughan, L., additional, Rutherford, K., additional, Kakadia, P., additional, Johansson, E., additional, Failes, T., additional, Greg, A., additional, Koval, J., additional, Lindeman, R., additional, Warburton, P., additional, Rodriguez-Meira, A., additional, Mead, A., additional, Unnikrishnan, A., additional, Bohlander, S., additional, Pappaemmanuil, E., additional, Faridani, O., additional, Jolly, C., additional, Zanini, F., additional, and Pimanda, J., additional

Published
2022
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3. Evaluating untimed and timed abridged versions of Raven's Advanced Progressive Matrices

Author

Poulton, A, Rutherford, K, Boothe, S, Brygel, M, Crole, A, Dali, G, Bruns, LR, Sinnott, RO, Hester, R, Poulton, A, Rutherford, K, Boothe, S, Brygel, M, Crole, A, Dali, G, Bruns, LR, Sinnott, RO, and Hester, R

Abstract

INTRODUCTION: Raven's Advanced Progressive Matrices (APM) are frequently utilized in clinical and experimental settings to index intellectual capacity. As the APM is a relatively long assessment, abridged versions of the test have been proposed. The psychometric properties of an untimed 12-item APM have received some consideration in the literature, but validity explorations have been limited. Moreover, both reliability and validity of a timed 12-item APM have not previously been examined. METHOD: We considered the psychometric properties of untimed (Study 1; N = 608; Mage = 27.89, SD = 11.68) and timed (Study 2; N = 479; Mage = 20.93, SD = 3.12) versions of a brief online 12-item form of the APM. RESULTS: Confirmatory factor analyses established both versions of the tests are unidimensional. Item response theory analyses revealed that, in each case, the 12 items are characterized by distinct differences in difficulty, discrimination, and guessing. Differential item functioning showed few male/female or native English/non-native English performance differences. Test-retest reliability was .65 (Study 1) to .69 (Study 2). Both tests had medium-to-large correlations with the Wechsler Abbreviated Scale of Intelligence (2nd ed.) Perceptual Reasoning Index (r = .50, Study 1; r = .56, Study 2) and Full-Scale IQ (r = .34, Study 1; r = .41, Study 2). CONCLUSION: In sum, results suggest both untimed and timed online versions of the brief APM are psychometrically sound. As test duration was found to be highly variable for the untimed version, the timed form might be a more suitable choice when it is likely to form part of a longer battery of tests. Nonetheless, classical test and item response theory analyses, plus validity considerations, suggest the untimed version might be the superior abridged form.

Published
2022

5. The Gene Ontology resource: enriching a GOld mine

Author

Carbon, S, Douglass, E, Good, Bm, Unni, Dr, Harris, Nl, Mungall, Cj, Basu, S, Chisholm, Rl, Dodson, Rj, Hartline, E, Fey, P, Thomas, Pd, Albou, Lp, Ebert, D, Kesling, Mj, Mi, Hy, Muruganujan, A, Huang, Xs, Mushayahama, T, Labonte, Sa, Siegele, Da, Antonazzo, G, Attrill, H, Brown, Nh, Garapati, P, Marygold, Sj, Trovisco, V, Dos Santos, G, Falls, K, Tabone, C, Zhou, Pl, Goodman, Jl, Strelets, Vb, Thurmond, J, Garmiri, P, Ishtiaq, R, Rodriguez-Lopez, M, Acencio, Ml, Kuiper, M, Laegreid, A, Logie, C, Lovering, Rc, Kramarz, B, Saverimuttu, Scc, Pinheiro, Sm, Gunn, H, Su, Rz, Thurlow, Ke, Chibucos, M, Giglio, M, Nadendla, S, Munro, J, Jackson, R, Duesbury, Mj, Del-Toro, N, Meldal, Bhm, Paneerselvam, K, Perfetto, L, Porras, P, Orchard, S, Shrivastava, A, Chang, Hy, Finn, Rd, Mitchell, Al, Rawlings, Nd, Richardson, L, Sangrador-Vegas, A, Blake, Ja, Christie, Kr, Dolan, Me, Drabkin, Hj, Hill, Dp, Ni, L, Sitnikov, Dm, Harris, Ma, Oliver, Sg, Rutherford, K, Wood, V, Hayles, J, Bahler, J, Bolton, Er, De Pons JL, Dwinell, Mr, Hayman, Gt, Kaldunski, Ml, Kwitek, Ae, Laulederkind, Sjf, Plasterer, C, Tutaj, Ma, Vedi, M, Wang, Sj, D'Eustachio, P, Matthews, L, Balhoff, Jp, Aleksander, Sa, Alexander, Mj, Cherry, Jm, Engel, Sr, Gondwe, F, Karra, K, Miyasato, Sr, Nash, Rs, Simison, M, Skrzypek, Ms, Weng, S, Wong, Ed, Feuermann, M, Gaudet, P, Morgat, A, Bakker, E, Berardini, Tz, Reiser, L, Subramaniam, S, Huala, E, Arighi, Cn, Auchincloss, A, Axelsen, K, Argoud-Puy, G, Bateman, A, Blatter, Mc, Boutet, E, Bowler, E, Breuza, L, Bridge, A, Britto, R, Bye-A-Jee, H, Casas, Cc, Coudert, E, Denny, P, Estreicher, A, Famiglietti, Ml, Georghiou, G, Gos, A, Gruaz-Gumowski, N, Hatton-Ellis, E, Hulo, C, Ignatchenko, A, Jungo, F, Laiho, K, Le Mercier, P, Lieberherr, D, Lock, A, Lussi, Y, Macdougall, A, Magrane, M, Martin, Mj, Masson, P, Natale, Da, Hyka-Nouspikel, N, Pedruzzi, I, Pourcel, L, Poux, S, Pundir, S, Rivoire, C, Speretta, E, Sundaram, S, Tyagi, N, Warner, K, Zaru, R, Wu, Ch, Diehl, Ad, Chan, Jn, Grove, C, Lee, Ryn, Muller, Hm, Raciti, D, Van Auken, K, Sternberg, Pw, Berriman, M, Paulini, M, Howe, K, Gao, S, Wright, A, Stein, L, Howe, Dg, Toro, S, Westerfield, M, Jaiswal, P, Cooper, L, and Elser, J

Subjects
Traceability, AcademicSubjects/SCI00010, Arabidopsis, Saccharomyces cerevisiae, Biology, Ontology (information science), Gene Ontology, Data curation, GO-CAMs, World Wide Web, Mice, User-Computer Interface, 03 medical and health sciences, Consistency (database systems), Annotation, 0302 clinical medicine, Documentation, Resource (project management), Schema (psychology), Schizosaccharomyces, Escherichia coli, Genetics, Database Issue, Animals, Humans, Dictyostelium, Caenorhabditis elegans, Molecular Biology, Zebrafish, 030304 developmental biology, Internet, 0303 health sciences, Molecular Sequence Annotation, File format, Rats, Drosophila melanogaster, 030217 neurology & neurosurgery
Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

Published
2021

6. Through the eyes of students: The satisfaction of remote Indigenous boarding students' with a transition support service in Queensland, Australia

Author

Redman-Maclaren, M, Benveniste, T, McCalman, J, Rutherford, K, Britton, A, Langham, E, Stewart, R, Saunders, P, Kinchin, I, Bainbridge, R, Redman-Maclaren, M, Benveniste, T, McCalman, J, Rutherford, K, Britton, A, Langham, E, Stewart, R, Saunders, P, Kinchin, I, and Bainbridge, R

Abstract

More than 4000 Indigenous Australian students enrol and take up a placement at boarding school each year. While reasons for attending boarding school vary, the impetus for many remote and very remote-dwelling students is restricted secondary educational opportunities in their home communities. A large multi-site study is being undertaken across Queensland to understand the conditions required for these students to be resilient while studying away from home. This paper reports on levels of student satisfaction with Queensland Department of Education's Transition Support Service (TSS) that provide assistance to remote-dwelling Indigenous students in the transition to boarding schools. A survey instrument administered to students included 22 close-ended questions to elicit levels of student satisfaction with TSS. Data were collected electronically using SurveyMonkey™ and analysed in SPSS v24. Descriptive statistics were calculated for variables assessing service support, student perceptions and experiences. A total of 294 primary, secondary and re-engaging students across 21 sites responded. Nearly all primary students (97%) anticipated that TSS would assist their move to boarding school. All secondary students identified that TSS had assisted their transition to boarding school. All re-engaging students agreed that TSS support had increased their capacity to cope when things go wrong. Lower scores related to students' ability to access TSS when needed. Very high levels of satisfaction with TSS were countered by constraints of distance between TSS and students, and resources available to support the work of TSS. Findings point to the need for equitable provision of transition services in Queensland that emphasise the importance of relationship between service provider and student, and can inform the design of similar transition services across Australia.

Published
2021

8. Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13

Author

Hall, N., Pain, A., Berriman, M., Churcher, C., Harris, B., Harris, D., Mungall, K., Bowman, S., Atkin, R., Baker, S., Barron, A., Brooks, K., Buckee, C. O., Burrows, C., Cherevach, I., Chillingworth, C., Chillingworth, T., Christodoulou, Z., Clark, L., Clark, R., Corton, C., Cronin, A., Davies, R., Davis, P., Dear, P., Dearden, F., Doggett, J., Feltwell, T., Goble, A., Goodhead, I., Gwilliam, R., Hamlin, N., Hance, Z., Harper, D., Hauser, H., Hornsby, T., Holroyd, S., Horrocks, P., Humphray, S., Jagels, K., James, K. D., Johnson, D., Kerhornou, A., Knights, A., Konfortov, B., Kyes, S., Larke, N., Lawson, D., Lennard, N., Line, A., Maddison, M., McLean, J., Mooney, P., Moule, S., Murphy, L., Oliver, K., Ormond, D., Price, C., Quail, M. A., Rabbinowitsch, E., Rajandream, M.-A., Rutter, S., Rutherford, K. M., Sanders, M., Simmonds, M., Seeger, K., Sharp, S., Smith, R., Squares, R., Squares, S., Stevens, K., Taylor, K., Tivey, A., Unwin, L., Whitehead, S., Woodward, J., Sulston, J. E., Craig, A., Newbold, C., and Barrell, B. G.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): N. Hall (corresponding author) [1]; A. Pain [1]; M. Berriman [1]; C. Churcher [1]; B. Harris [1]; D. Harris [1]; K. Mungall [1]; S. Bowman [1, 2]; R. Atkin [...]

Published
2002
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9. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)

Author

Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A.-M., Challis, G. L., Thomson, N. R., James, K. D., Harris, D. E., Quail, M. A., Kieser, H., Harper, D., Bateman, A., Brown, S., Chandra, G., Chen, C. W., Collins, M., Cronin, A., Fraser, A., Goble, A., Hidalgo, J., Hornsby, T., Howarth, S., Huang, C.-H., Kieser, T., Larke, L., Murphy, L., Oliver, K., O'Neil, S., Rabbinowitsch, E., Rajandream, M.-A., Rutherford, K., Rutter, S., Seeger, K., Saunders, D., Sharp, S., Squares, R., Squares, S., Taylor, K., Warren, T., Wietzorrek, A., Woodward, J., Barrell, B. G., Parkhill, J., and Hopwood, D. A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): S. D. Bentley (corresponding author) [1]; K. F. Chater [2]; A.-M. Cerdeño-Tárraga [1]; G. L. Challis [2, 3]; N. R. Thomson [1]; K. D. James [1]; D. E. Harris [...]

Published
2002
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10. The genome sequence of Schizosaccharomyces pombe

Author

Wood, V., Gwilliam, R., Rajandream, M.-A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., Basham, D., Bowman, S., Brooks, K., Brown, D., Brown, S., Chillingworth, T., Churcher, C., Collins, M., Connor, R., Cronin, A., Davis, P., Feltwell, T., Fraser, A., Gentles, S., Goble, A., Hamlin, N., Harris, D., Hidalgo, J., Hodgson, G., Holroyd, S., Hornsby, T., Howarth, S., Huckle, E. J., Hunt, S., Jagels, K., James, K., Jones, L., Jones, M., Leather, S., McDonald, S., McLean, J., Mooney, P., Moule, S., Mungall, K., Murphy, L., Niblett, D., Odell, C., Oliver, K., O'Neil, S., Pearson, D., Quail, M. A., Rabbinowitsch, E., Rutherford, K., Rutter, S., Saunders, D., Seeger, K., Sharp, S., Skelton, J., Simmonds, M., Squares, R., Squares, S., Stevens, K., Taylor, K., Taylor, R. G., Tivey, A., Walsh, S., Warren, T., Whitehead, S., Woodward, J., Volckaert, G., Aert, R., Robben, J., Grymonprez, B., Weltjens, I., Vanstreels, E., Rieger, M., Schafer, M., Muller-Auer, S., Gabel, C., Fuchs, M., Fritzc, C., Holzer, E., Moestl, D., Hilbert, H., Borzym, K., Langer, I., Beck, A., Lehrach, H., Reinhardt, R., Pohl, T. M., Eger, P., Zimmermann, W., Wedler, H., Wambutt, R., Purnelle, B., Goffeau, A., Cadieu, E., Dreano, S., Gloux, S., Lelaure, V., Mottier, S., Galibert, F., Aves, S. J., Xiang, Z., Hunt, C., Moore, K., Hurst, S. M., Lucas, M., Rochet, M., Gaillardin, C., Tallada, V. A., Garzon, A., Thode, G., Daga, R. R., Cruzado, L., Jimenez, J., Sanchez, M., del Rey, F., Benito, J., Dominguez, A., Revuelta, J. L., Moreno, S., Armstrong, J., Forsburg, S. L., Cerrutti, L., Lowe, T., McCombie, W. R., Paulsen, I., Potashkin, J., Shpakovski, G. V., Ussery, D., Barrell, B. G., and Nurse, P.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): V. Wood [1]; R. Gwilliam [1]; M.-A. Rajandream (corresponding author) [1]; M. Lyne [1]; R. Lyne [1]; A. Stewart [2]; J. Sgouros [2]; N. Peat [3]; J. Hayles [3]; [...]

Published
2002
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11. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

Author

Parkhill, J., Dougan, G., James, K. D., Thomson, N. R., Pickard, D., Wain, J., Churcher, C., Mungall, K. L., Bentley, S. D., Holden, M. T. G., Sebaihia, M., Baker, S., Basham, D., Brooks, K., Chillingworth, T., Connerton, P., Cronin, A., Davis, P., Davies, R. M., Dowd, L., White, N., Farrar, J., Feltwell, T., Hamlin, N., Haque, A., Hien, T. T., Holroyd, S., Jagels, K., Krogh, A., Larsen, T. S., Leather, S., Moule, S., O'Gaora, P., Parry, C., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S., and Barrell, B. G.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): J. Parkhill (corresponding author) [1]; G. Dougan (corresponding author) [2]; K. D. James [1]; N. R. Thomson [1]; D. Pickard [2]; J. Wain [2]; C. Churcher [1]; K. L. [...]

Published
2001
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12. Genome sequence of Yersinia pestis, the causative agent of plague

Author

Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T. G., Prentice, M. B., Sebaihia, M., James, K. D., Churcher, C., Mungall, K. L., Baker, S., Basham, D., Bentley, S. D., Brooks, K., Cerdeno-Tarraga, A. M., Chillingworth, T., Cronin, A., Davies, R. M., Davis, P., Dougan, G., Feltwell, T., Hamlin, N., Holroyd, S., Jagels, K., Karlyshev, A. V., Leather, S., Moule, S., Oyston, P. C. F., Quail, M., Rutherford, K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S., and Barrell, B. G.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): J. Parkhill (corresponding author) [1]; B. W. Wren [2]; N. R. Thomson [1]; R. W. Titball [3]; M. T. G. Holden [1]; M. B. Prentice [4]; M. Sebaihia [1]; [...]

Published
2001
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13. Massive gene decay in the leprosy bacillus

Author

Cole, S. T., Eiglmeier, K., Parkhill, J., James, K. D., Thomson, N. R., Wheeler, P. R., Honore, N., Garnier, T., Churcher, C., Harris, D., Mungall, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R. M., Devlin, K., Duthoy, S., Feltwell, T., Fraser, A., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Lacroix, C., Maclean, J., Moule, S., Murphy, L., Oliver, K., Quail, M. A., Rajandream, M.-A., Rutherford, K. M., Rutter, S., Seeger, K., Simon, S., Simmonds, M., Skelton, J., Squares, R., Squares, S., Stevens, K., Taylor, K., Whitehead, S., Woodward, J. R., and Barrell, B. G.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): S. T. Cole [1]; K. Eiglmeier [1]; J. Parkhill [2]; K. D. James [2]; N. R. Thomson [2]; P. R. Wheeler [3]; N. Honoré [1]; T. Garnier [1]; C. [...]

Published
2001
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14. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491

Author

Parkhill, J., Achtman, M., James, K. D., Bentley, S. D., Churcher, C., Klee, S. R., Morelli, G., Basham, D., Brown, D., Chillingworth, T., Davies, R. M., Davis, P., Devlin, K., Feltwell, T., Hamlin, N., Holroyd, S., Jagels, K., Leather, S., Moule, S., Mungall, K., Quail, M. A., Rajandream, M.-A., Rutherford, K. M., Simmonds, M., Skelton, J., Whitehead, S., Spratt, B. G., and Barrell, B. G.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): J. Parkhill (corresponding author) [1]; M. Achtman [2]; K. D. James [1]; S. D. Bentley [1]; C. Churcher [1]; S. R. Klee [2]; G. Morelli [2]; D. Basham [1]; [...]

Published
2000
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15. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

Author

Parkhill, J., Wren, B. W., Mungall, K., Ketley, J. M., Churcher, C., Basham, D., Chillingworth, T., Davies, R. M., Feltwell, T., Holroyd, S., Jagels, K., Karlyshev, A. V., Moule, S., Pallen, M. J., Penn, C. W., Quail, M. A., Rajandream, M-A., Rutherford, K. M., van Vliet, A. H. M., Whitehead, S., and Barrell, B. G.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): J. Parkhill (corresponding author) [1]; B. W. Wren [2]; K. Mungall [1]; J. M. Ketley [3]; C. Churcher [1]; D. Basham [1]; T. Chillingworth [1]; R. M. Davies [1]; [...]

Published
2000
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17. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129

Author

Cerdeño-Tárraga, A. M., Efstratiou, A., Dover, L. G., Holden, M. T. G., Pallen, M., Bentley, S. D., Besra, G. S., Churcher, C., James, K. D., De Zoysa, A., Chillingworth, T., Cronin, A., Dowd, L., Feltwell, T., Hamlin, N., Holroyd, S., Jagels, K., Moule, S., Quail, M. A., Rabbinowitsch, E., Rutherford, K. M., Thomson, N. R., Unwin, L., Whitehead, S., Barrell, B. G., and Parkhill, J.

Published
2003

19. Expansion of the Gene Ontology knowledgebase and resources

Author

Antonazzo, G, Attrill, H, Brown, NH, Marygold, SJ, McQuilton, P, Ponting, L, Millburn, GH, Rey, AJ, Stefancsik, R, Tweedie, S, Harris, MA, Hayles, J, Oliver, SG, Rutherford, K, Wood, V, Antonazzo, Giulia [0000-0003-0086-5621], Brown, Nicholas [0000-0002-8958-7017], Marygold, Steven [0000-0003-2759-266X], Harris, Midori [0000-0003-4148-4606], Oliver, Stephen [0000-0001-6330-7526], Wood, Valerie [0000-0001-6330-7526], and Apollo - University of Cambridge Repository

Subjects
Gene Ontology, Databases, Genetic, Computational Biology, Molecular Sequence Annotation, Genomics, Web Browser, Phylogeny
Abstract

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/.

Published
2017
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20. Seasonal hydrology and permafrost disturbance impacts on dissolved organic matter composition in High Arctic headwater catchments 1

Author

Fouché, Julien, Lafrenière, M., Rutherford, K., Lamoureux, S., Laboratoire d'étude des Interactions Sol - Agrosystème - Hydrosystème (UMR LISAH), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Queen's University [Kingston, Canada], 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), Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD [ Madagascar])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), and Queen's University [Kingston]

Subjects
active layer detachments, décollements de la couche active, High Arctic, matière organique dissoute, Haut-Arctique, analyse de facteurs parallèles (« PARAFAC »), [SDE.MCG]Environmental Sciences/Global Changes, parallel factor analysis (PARAFAC), fluorescence, [SDU.STU.GL]Sciences of the Universe [physics]/Earth Sciences/Glaciology, dissolved organic matter, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology
Abstract

International audience; Arctic landscapes are experiencing intense warming and modification of precipitation regimes with climate change. Permafrost disturbances and climate change impacts on hydrology of Arctic watersheds are likely to modify the quantity and composition of exported dissolved organic matter (DOM). In July 2007, intense rainfall and active layer thickening caused widespread active layer detachments at Cape Bounty, Melville Island (Canada). This study investigates the impacts of seasonal hydrology and permafrost disturbance on DOM composition exported from High Arctic headwater catchments. In 2012, streams were sampled from three disturbed catchments and one undisturbed catchment. The composition of DOM was characterized using absorbance and fluorescence spectroscopy. DOM was mostly exported during the spring freshet. Throughout this period, the undisturbed catchment exported humified DOM with high humic-like fluorescence that likely originated from runoff through shallow organic rich soil. In contrast, DOM exported from disturbed catchments was fresher, less humified with a high proportion of low molecular weight humic acid. We demonstrate that disturbed catchments delivered likely more labile DOM derived from either thawed permafrost or enhanced microbial activity. If this labile DOM comes from an ancient pool, as indicated by other studies at this site, disturbances may strengthen the permafrost carbon feedback on climate change.; Avec le changement climatique, les paysages arctiques connaissent un réchauffe-ment intense et une modification des régimes de précipitation. Les impacts des perturbations du pergélisol et du changement climatique sur l'hydrologie des bassins hydrographiques arc-tiques vont probablement modifier la quantité et la composition de matière organique dis-soute (MOD) exportée. En juillet 2007, des averses intenses et l'épaississement de la couche active ont causé des décollements généralisés de la couche active à Cape Bounty, île Melville (Canada). Cette étude examine les impacts de l'hydrologie saisonnière et de la perturbation du pergélisol sur la composition de la MOD exportée des bassins versants d'amont du Haut-Arctique. En 2012, on a échantillonné des cours d'eau de trois bassins versants perturbés et d'un bassin versant non perturbé. La composition de la MOD a été analysée en utilisant la spectroscopie à fluorescence et l'absorptiométrie. La MOD a surtout été exportée pendant la crue printanière. Pendant cette période, le bassin versant non perturbé a exporté de la MOD humifiée à haute fluorescence telle humique qui provenait probablement de ruisselle-ment par sol riche organique mince. En revanche, la MOD exportée de bassins versants per-turbés était plus fraîche, moins humifiée avec une haute proportion d'acide humique à faible poids moléculaire. Nous démontrons que les bassins versants perturbés ont déversé de la MOD probablement plus labile provenant du pergélisol dégelé ou de l'activité microbienne améliorée. Si cette MOD labile vient d'un bassin ancien, tel que révélé par d'autres études à ce site, les perturbations peuvent renforcer la rétroaction du carbone du pergélisol sur le changement climatique.

Published
2017

25. Review: Assessment of completeness of reporting in intervention studies using livestock: an example from pain mitigation interventions in neonatal piglets

Author

O’Connor, A., primary, Anthony, R., additional, Bergamasco, L., additional, Coetzee, J.F., additional, Dzikamunhenga, R.S., additional, Johnson, A.K., additional, Karriker, L.A., additional, Marchant, J.N., additional, Martineau, G.P., additional, Millman, S.T., additional, Pajor, E.A., additional, Rutherford, K., additional, Sprague, M., additional, Sutherland, M.A., additional, von Borell, E., additional, and Webb, S.R., additional

Published
2016
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26. BOARD INVITED REVIEW: The importance of the gestation period for welfare of calves: Maternal stressors and difficult births

Author

Arnott, G., Roberts, D., Rooke, J. A., Turner, S. P., Lawrence, A. B., and Rutherford, K. M. D.

Subjects
DAIRY CALVES, offspring welfare, dystocia, NEONATAL BEEF-CALVES, CONGENITAL CHONDRODYSTROPHY, DEVELOPMENTAL ORIGINS, NEW-YORK-STATE, NEWBORN CALF, PRENATAL STRESS, gestation, cattle, CALF MORTALITY, REPRODUCTIVE-PERFORMANCE, SOUTH-EASTERN AUSTRALIA
Abstract

The prenatal period is of critical importance in defining how individuals respond to their environment throughout life. Stress experienced by pregnant females has been shown to have detrimental effects on offspring biology in humans and a variety of other species. It also is becoming increasingly apparent that prenatal events can have important consequences for the behavior, health, and productivity of offspring in farmed species. Pregnant cattle may experience many potentially important stressors, for instance, relating to their social environment, housing system and physical environment, interactions with humans and husbandry procedures, and their state of health. We examined the available literature to provide a review of the implications of prenatal stress for offspring welfare in cattle. The long-term effects of dystocia on cattle offspring also are reviewed. To ensure a transparent and repeatable selection process, a systematic review approach was adopted. The research literature clearly demonstrates that prenatal stress and difficult births in beef and dairy cattle both have implications for offspring welfare and performance. Common husbandry practices, such as transport, were shown to influence offspring biology and the importance of environmental variables, including thermal stress and drought, also were highlighted. Maternal disease during pregnancy was shown to negatively impact offspring welfare. Moreover, dystocia-affected calves suffer increased mortality and morbidity, decreased transfer of passive immunity, and important physiological and behavioral changes. This review also identified considerable gaps in our knowledge and understanding of the effects of prenatal stress in cattle.

Published
2012

28. Behaviour of dairy cows on organic and non-organic farms

Author

Langford, F, Rutherford, K, Sherwood, L, Jack, M, Haskell, M, Atkinson, C, Ball, B, Davies, D H K, Rees, R, Russell, G, Stockdale, E A, Watson, C A, Walker, R, and Younie, D

Subjects
animal diseases, Feeding and growth, food and beverages, Dairy cattle, Health and welfare
Abstract

There is an increasing number of organic dairy farms in the UK. The aim of this study is to compare behaviour of dairy cows on organic and non-organic farms. Twenty organic and 20 non-organic farms throughout the UK were visited over two winters (2004/05 and 2005/06). Organic and non-organic farms were paired for housing type, herd size, milk production traits and location. The number of cows feeding was counted every fifteen minutes for 4.5 h after new feed was available post morning milking. Behaviour at the feed-face was recorded for 60 minutes and aggressive interactions between cows were quantified. Farm type had no effect on numbers of cows feeding. There were more interactions between cows feeding at open feed-faces compared to head-bale barriers. At open feed-faces, there were more interactions on organic farms than non-organic. It is possible that organic cows were hungrier than non-organic cows after the arrival of new feed.

Published
2006

29. The genome sequence of Schizosaccharomyces pombe (vol 415, pg 871, 2002)

Author

Wood, V, Gwilliam, R, Rajandream, MA, Lyne, M, Lyne, R, Stewart, A, Sgouros, J, Peat, N, Hayles, J, Baker, S, Basham, D, Bowman, S, Brooks, K, Brown, D, Brown, S, Chillingworth, T, Churcher, C, Collins, M, Connor, R, Cronin, A, Davis, P, Feltwell, T, Fraser, A, Gentles, S, Goble, A, Hamlin, N, Harris, D, Hidalgo, J, Hodgson, G, Holroyd, S, Hornsby, T, Howarth, S, Huckle, EJ, Hunt, S, Jagels, K, James, K, Jones, L, Jones, M, Leather, S, McDonald, S, McLean, J, Mooney, P, Moule, S, Mungall, K, Murphy, L, Niblett, D, Odell, C, Oliver, K, O'Neil, S, Pearson, D, Quail, MA, Rabbinowitsch, E, Rutherford, K, Rutter, S, Saunders, D, Seeger, K, Sharp, S, Skelton, J, Simmonds, M, Squares, R, Squares, S, Stevens, K, Taylor, K, Taylor, RG, Tivey, A, Walsh, S, Warren, T, Whitehead, S, Woodward, J, Volckaert, G, Aert, R, Robben, J, Grymonprez, B, Weltjens, I, Vanstreels, E, Rieger, M, Schafer, M, Muller-Auer, S, Gabel, C, Fuchs, M, Dusterhoft, A, Fritzc, C, Holzer, E, Moestl, D, Hilbert, H, Borzym, K, Langer, I, Beck, A, Lehrach, H, Reinhardt, R, Pohl, TM, Eger, P, Zimmermann, W, Wedler, H, Wambutt, R, Purnelle, B, Goffeau, A, Cadieu, E, Dreano, S, Gloux, S, Lelaure, V, Mottier, S, Galibert, F, Aves, SJ, Xiang, Z, Hunt, C, Moore, K, Hurst, SM, Lucas, M, Rochet, M, Gaillardin, C, Tallada, VA, Garzon, A, Thode, G, Daga, RR, Cruzado, L, Jimenez, J, Sanchez, M, del Rey, F, Benito, J, Dominguez, A, Revuelta, JL, Moreno, S, Armstrong, J, Forsburg, SL, Cerutti, L, Lowe, T, McCombie, WR, Paulsen, I, Potashkin, J, Shpakovski, GV, Ussery, D, Barrell, BG, and Nurse, P

Published
2003

30. Review: Assessment of completeness of reporting in intervention studies using livestock: an example from pain mitigation interventions in neonatal piglets.

Author

O'Connor, A., Anthony, R., Bergamasco, L., Coetzee, J.F., Dzikamunhenga, R.S., Johnson, A.K., Karriker, L.A., Marchant, J.N., Martineau, G.P., Millman, S.T., Pajor, E.A., Rutherford, K., Sprague, M., Sutherland, M.A., von Borell, E., and Webb, S.R.

Abstract

Accurate and complete reporting of study methods, results and interpretation are essential components for any scientific process, allowing end-users to evaluate the internal and external validity of a study. When animals are used in research, excellence in reporting is expected as a matter of continued ethical acceptability of animal use in the sciences. Our primary objective was to assess completeness of reporting for a series of studies relevant to mitigation of pain in neonatal piglets undergoing routine management procedures. Our second objective was to illustrate how authors can report the items in the Reporting guidElines For randomized controLled trials for livEstoCk and food safety (REFLECT) statement using examples from the animal welfare science literature. A total of 52 studies from 40 articles were evaluated using a modified REFLECT statement. No single study reported all REFLECT checklist items. Seven studies reported specific objectives with testable hypotheses. Six studies identified primary or secondary outcomes. Randomization and blinding were considered to be partially reported in 21 and 18 studies, respectively. No studies reported the rationale for sample sizes. Several studies failed to report key design features such as units for measurement, means, standard deviations, standard errors for continuous outcomes or comparative characteristics for categorical outcomes expressed as either rates or proportions. In the discipline of animal welfare science, authors, reviewers and editors are encouraged to use available reporting guidelines to ensure that scientific methods and results are adequately described and free of misrepresentations and inaccuracies. Complete and accurate reporting increases the ability to apply the results of studies to the decision-making process and prevent wastage of financial and animal resources. [ABSTRACT FROM AUTHOR]

Published
2016
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31. Behaviour of dairy cows on organic and non-organic farms

Author

Atkinson, C, Ball, B, Davies, D H K, Rees, R, Russell, G, Stockdale, E A, Watson, C A, Walker, R, Younie, D, Langford, F, Rutherford, K, Sherwood, L, Jack, M, Haskell, M, Atkinson, C, Ball, B, Davies, D H K, Rees, R, Russell, G, Stockdale, E A, Watson, C A, Walker, R, Younie, D, Langford, F, Rutherford, K, Sherwood, L, Jack, M, and Haskell, M

Abstract

There is an increasing number of organic dairy farms in the UK. The aim of this study is to compare behaviour of dairy cows on organic and non-organic farms. Twenty organic and 20 non-organic farms throughout the UK were visited over two winters (2004/05 and 2005/06). Organic and non-organic farms were paired for housing type, herd size, milk production traits and location. The number of cows feeding was counted every fifteen minutes for 4.5 h after new feed was available post morning milking. Behaviour at the feed-face was recorded for 60 minutes and aggressive interactions between cows were quantified. Farm type had no effect on numbers of cows feeding. There were more interactions between cows feeding at open feed-faces compared to head-bale barriers. At open feed-faces, there were more interactions on organic farms than non-organic. It is possible that organic cows were hungrier than non-organic cows after the arrival of new feed.

Published
2006

33. The Use of SMS Text Messaging to Improve the Hospital-to-Community Transition in Patients With Acute Coronary Syndrome (Txt2Prevent): Results From a Pilot Randomized Controlled Trial

Author

Ross, Emily S, Sakakibara, Brodie M, Mackay, Martha H, Whitehurst, David G T, Singer, Joel, Toma, Mustafa, Corbett, Kitty K, Van Spall, Harriette G C, Rutherford, Kimberly, Gheorghiu, Bobby, Code, Jillianne, and Lear, Scott A

Subjects
Information technology, T58.5-58.64, Public aspects of medicine, RA1-1270
Abstract

BackgroundAcute coronary syndrome (ACS) is a leading cause of hospital admission in North America. Many patients with ACS experience challenges after discharge that impact their clinical outcomes and psychosocial well-being. SMS text messaging has the potential to provide support to patients during this postdischarge period. ObjectiveThis study pilot tested a 60-day SMS text messaging intervention (Txt2Prevent) for patients with ACS. The primary objective was to compare self-management domains between usual care and usual care plus Txt2Prevent. The secondary objectives were to compare medication adherence, health-related quality of life, self-efficacy, and health care resource use between groups. The third objective was to assess the feasibility of the study protocol and the acceptability of the intervention. MethodsThis was a randomized controlled trial with blinding of outcome assessors. We recruited 76 patients with ACS from St. Paul’s Hospital in Vancouver, Canada, and randomized them to 1 of 2 groups within 7 days of discharge. The Txt2Prevent program included automated 1-way SMS text messages about follow-up care, self-management, and healthy living. Data were collected during the index admission and at 60 days after randomization. The primary outcome was measured with the Health Education Impact Questionnaire (heiQ). Other outcomes included the EQ-5D-5L, EQ-5D-5L Visual Analog Scale, a modified Sullivan Cardiac Self-Efficacy Scale, and Morisky Medication Adherence Scale scores, and self-reported health care resource use. Analyses of covariance were used to test the effect of group assignment on follow-up scores (controlling for baseline) and were considered exploratory in nature. Feasibility was assessed with descriptive characteristics of the study protocol. Acceptability was assessed with 2 survey questions and semistructured interviews. ResultsThere were no statistically significant differences between the groups for the heiQ domains (adjusted mean difference [Txt2Prevent minus usual care] for each domain—Health-directed activity: –0.13, 95% CI –0.39 to 0.13, P=.31; Positive and active engagement in life: 0.03, 95% CI –0.19 to 0.25, P=.76; Emotional distress: 0.04, 95% CI –0.22 to 0.29, P=.77; Self-monitoring and insight: –0.14, 95% CI –0.33 to 0.05, P=.15; Constructive attitudes and approaches: –0.10, 95% CI –0.36 to 0.17, P=.47; Skill technique and acquisition: 0.05, 95% CI –0.18 to 0.27, P=.69; Social integration and support: –0.12, 95% CI –0.34 to 0.10, P=.27; and Health services navigation: –0.05, 95% CI –0.29 to 0.19, P=.69). For the secondary outcomes, there were no statistically significant differences in adjusted analyses except in 1 self-efficacy domain (Total plus), where the Txt2Prevent group had lower scores (mean difference –0.36, 95% CI –0.66 to –0.50, P=.03). The study protocol was feasible, but recruitment took longer than expected. Over 90% (29/31 [94%]) of participants reported they were satisfied with the program. ConclusionsThe Txt2Prevent study was feasible to implement; however, although exploratory, there were no differences between the 2 groups in adjusted analyses except for 1 self-efficacy domain. As the intervention appeared acceptable, there is potential in using SMS text messages in this context. The design of the intervention may need to be reconsidered to have more impact on outcome measures. Trial RegistrationClinicalTrials.gov NCT02336919; https://clinicaltrials.gov/ct2/show/NCT02336919 International Registered Report Identifier (IRRID)RR2-10.2196/resprot.6968

Published
2021
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34. modMine: flexible access to modENCODE data

Author

Contrino, S., primary, Smith, R. N., additional, Butano, D., additional, Carr, A., additional, Hu, F., additional, Lyne, R., additional, Rutherford, K., additional, Kalderimis, A., additional, Sullivan, J., additional, Carbon, S., additional, Kephart, E. T., additional, Lloyd, P., additional, Stinson, E. O., additional, Washington, N. L., additional, Perry, M. D., additional, Ruzanov, P., additional, Zha, Z., additional, Lewis, S. E., additional, Stein, L. D., additional, and Micklem, G., additional

Published
2011
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35. PomBase: a comprehensive online resource for fission yeast

Author

Wood, V., primary, Harris, M. A., additional, McDowall, M. D., additional, Rutherford, K., additional, Vaughan, B. W., additional, Staines, D. M., additional, Aslett, M., additional, Lock, A., additional, Bahler, J., additional, Kersey, P. J., additional, and Oliver, S. G., additional

Published
2011
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37. ACT: the Artemis comparison tool

Author

Carver, T. J., primary, Rutherford, K. M., additional, Berriman, M., additional, Rajandream, M.-A., additional, Barrell, B. G., additional, and Parkhill, J., additional

Published
2005
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38. corrigendum: The genome sequence of Schizosaccharomyces pombe

Author

Wood, V., Gwilliam, R., Rajandream, M.-A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J., Baker, S., Basham, D., Bowman, S., Brooks, K., Brown, D., Brown, S., Chillingworth, T., Churcher, C., Collins, M., Connor, R., Cronin, A., Davis, P., Feltwell, T., Fraser, A., Gentles, S., Goble, A., Hamlin, N., Harris, D., Hidalgo, J., Hodgson, G., Holroyd, S., Hornsby, T., Howarth, S., Huckle, E. J., Hunt, S., Jagels, K., James, K., Jones, L., Jones, M., Leather, S., McDonald, S., McLean, J., Mooney, P., Moule, S., Mungall, K., Murphy, L., Niblett, D., Odell, C., Oliver, K., O'Neil, S., Pearson, D., Quail, M. A., Rabbinowitsch, E., Rutherford, K., Rutter, S., Saunders, D., Seeger, K., Sharp, S., Skelton, J., Simmonds, M., Squares, R., Squares, S., Stevens, K., Taylor, K., Taylor, R. G., Tivey, A., Walsh, S., Warren, T., Whitehead, S., Woodward, J., Volckaert, G., Aert, R., Robben, J., Grymonprez, B., Weltjens, I., Vanstreels, E., Rieger, M., Schafer, M., Muller-Auer, S., Gabel, C., Fuchs, M., Dusterhoft, A., Fritzc, C., Holzer, E., Moestl, D., Hilbert, H., Borzym, K., Langer, I., Beck, A., Lehrach, H., Reinhardt, R., Pohl, T. M., Eger, P., Zimmermann, W., Wedler, H., Wambutt, R., Purnelle, B., Goffeau, A., Cadieu, E., Dreano, S., Gloux, S., Lelaure, V., Mottier, S., Galibert, F., Aves, S. J., Xiang, Z., Hunt, C., Moore, K., Hurst, S. M., Lucas, M., Rochet, M., Gaillardin, C., Tallada, V. A., Garzon, A., Thode, G., Daga, R. R., Cruzado, L., Jimenez, J., Sanchez, M., del Rey, F., Benito, J., Dominguez, A., Revuelta, J. L., Moreno, S., Armstrong, J., Forsburg, S. L., Cerutti, L., Lowe, T., McCombie, W. R., Paulsen, I., Potashkin, J., Shpakovski, G. V., Ussery, D., Barrell, B. G., and Nurse, P.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): V. Wood; R. Gwilliam; M.-A. Rajandream; M. Lyne; R. Lyne; A. Stewart; J. Sgouros; N. Peat; J. Hayles; S. Baker; D. Basham; S. Bowman; K. Brooks; D. Brown; S. [...]

Published
2003
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39. Erratum: corrigendum: The genome sequence of Schizosaccharomyces pombe

Author

Wood, V., primary, Gwilliam, R., additional, Rajandream, M.-A., additional, Lyne, M., additional, Lyne, R., additional, Stewart, A., additional, Sgouros, J., additional, Peat, N., additional, Hayles, J., additional, Baker, S., additional, Basham, D., additional, Bowman, S., additional, Brooks, K., additional, Brown, D., additional, Brown, S., additional, Chillingworth, T., additional, Churcher, C., additional, Collins, M., additional, Connor, R., additional, Cronin, A., additional, Davis, P., additional, Feltwell, T., additional, Fraser, A., additional, Gentles, S., additional, Goble, A., additional, Hamlin, N., additional, Harris, D., additional, Hidalgo, J., additional, Hodgson, G., additional, Holroyd, S., additional, Hornsby, T., additional, Howarth, S., additional, Huckle, E. J., additional, Hunt, S., additional, Jagels, K., additional, James, K., additional, Jones, L., additional, Jones, M., additional, Leather, S., additional, McDonald, S., additional, McLean, J., additional, Mooney, P., additional, Moule, S., additional, Mungall, K., additional, Murphy, L., additional, Niblett, D., additional, Odell, C., additional, Oliver, K., additional, O'Neil, S., additional, Pearson, D., additional, Quail, M. A., additional, Rabbinowitsch, E., additional, Rutherford, K., additional, Rutter, S., additional, Saunders, D., additional, Seeger, K., additional, Sharp, S., additional, Skelton, J., additional, Simmonds, M., additional, Squares, R., additional, Squares, S., additional, Stevens, K., additional, Taylor, K., additional, Taylor, R. G., additional, Tivey, A., additional, Walsh, S., additional, Warren, T., additional, Whitehead, S., additional, Woodward, J., additional, Volckaert, G., additional, Aert, R., additional, Robben, J., additional, Grymonprez, B., additional, Weltjens, I., additional, Vanstreels, E., additional, Rieger, M., additional, Schäfer, M., additional, Müller-Auer, S., additional, Gabel, C., additional, Fuchs, M., additional, Düsterhöft, A., additional, Fritzc, C., additional, Holzer, E., additional, Moestl, D., additional, Hilbert, H., additional, Borzym, K., additional, Langer, I., additional, Beck, A., additional, Lehrach, H., additional, Reinhardt, R., additional, Pohl, T. M., additional, Eger, P., additional, Zimmermann, W., additional, Wedler, H., additional, Wambutt, R., additional, Purnelle, B., additional, Goffeau, A., additional, Cadieu, E., additional, Dréano, S., additional, Gloux, S., additional, Lelaure, V., additional, Mottier, S., additional, Galibert, F., additional, Aves, S. J., additional, Xiang, Z., additional, Hunt, C., additional, Moore, K., additional, Hurst, S. M., additional, Lucas, M., additional, Rochet, M., additional, Gaillardin, C., additional, Tallada, V. A., additional, Garzon, A., additional, Thode, G., additional, Daga, R. R., additional, Cruzado, L., additional, Jimenez, J., additional, Sánchez, M., additional, del Rey, F., additional, Benito, J., additional, Domínguez, A., additional, Revuelta, J. L., additional, Moreno, S., additional, Armstrong, J., additional, Forsburg, S. L., additional, Cerutti, L., additional, Lowe, T., additional, McCombie, W. R., additional, Paulsen, I., additional, Potashkin, J., additional, Shpakovski, G. V., additional, Ussery, D., additional, Barrell, B. G., additional, and Nurse, P., additional

Published
2003
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41. The effect of lameness prevalence on technical efficiency at the dairy farm level: An adjusted data envelopment analysis approach.

Author

Barnes, A. P., Rutherford, K. M. D., Langford, F. M., and Haskell, M. J.

Subjects
*LAMENESS in cattle, *DAIRY farms, *DAIRY farming, *MILK yield, *FARM management
Abstract

A key indicator of resource use within farming is technical efficiency, which measures the amount of physical output attainable from a given set of inputs. The social aspects, in particular the treatment of animals, have generally been ignored within these measurement schemas. In addition, animal welfare will affect the production technology under which farms operate, and some allowance for this is needed within the measurement approach. This is the first paper to apply animal welfare as a discriminating technology within a technical efficiency framework. Using results from an animal welfare monitoring study coupled with resource usage data, it presents an adjusted measure of technical efficiency applied to a sample of British dairy farms and compares differences in lameness management strategies for herds. We employ both a categorical and nondiscretionary variant of the data envelopment analysis approach to measure technical efficiencies and adjust for various degrees of lameness prevalence among these farms. This paper finds that farms with low rates of lameness (below 10% of the cattle herd) tend to have significantly higher technical efficiencies than those with lameness rates of above 10% of the herd. Farms that have levels of lameness of between 10 to 20% of the herd and higher levels of lameness (above 20% of the herd) did not differ significantly. Furthermore, low lameness farms are inefficient in terms of labor and stocking density, but this is outweighed by the gain in milk yield obtained on these farms. Consequently, we argue for a whole-farm, rather than a partial indicator, approach to assessing efficiency when noneconomic factors such as lameness are accounted for. From a policy perspective, we support programs that encourage active lameness management. [ABSTRACT FROM AUTHOR]

Published
2011
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42. Hock Injury Prevalence and Associated Risk Factors on Organic and Nonorganic Dairy Farms in the United Kingdom.

Author

Rutherford, K. M. D., Langford, F. M., Jack, M. C., Sherwood, L., Lawrence, A. B., and Haskell, M. J.

Subjects
*WOUNDS & injuries, *DAIRY cattle, *DAIRY farms, *FARM management
Abstract

The presence of hock injury was assessed in the milking herds of 80 dairy farms (40 organic, 40 nonorganic) across the United Kingdom. A wide range of information on farm management and husbandry was gathered via interview to assess the factors contributing to hock damage for all 80 farms, and a comprehensive building appraisal was conducted for 40 farms visited during the winter housing period. The prevalence of hock lesions was lower on organic compared with nonorganic farms (37.2 vs. 49.1%). Prevalence of hock damage was greater in the spring than fall (59.9 vs. 21.6%) and cows housed in free-stalls had a greater prevalence of hock lesions than those housed on straw (46.0 vs. 25.0%). Prevalence of hock damage increased with lactation number. In the analysis of fall/spring data, the age first mated, herd biosecurity, duration of summer grazing, and cow milk yield were significant factors relating to herd hock damage. Larger herds had a greater proportion of cows with hock swellings. Farms with a shorter calving interval had more cows with hock swellings. Factors relating to housing conditions that were positively associated with the prevalence of hock damage were low feed face space per cow, inferior passageway cleanliness, low total standing area per cow, and the type of bedding added to the free-stall. To assess whether free-stall versus straw-pen or organic versus nonorganic farms had different sets of risk factors, the data were reanalyzed for these types separately. For the straw-pen farms a high culling rate was associated with more hock damage. Within nonorganic farms, the length of summer grazing was significant, with longer periods meaning less hock injury. The prevalence of hock injuries on many UK farms, both organic and nonorganic, exceeded levels that are deemed acceptable for cow comfort. Efforts are needed to improve housing standards to reduce the prevalence of hock injury and consequently improve cow welfare. [ABSTRACT FROM AUTHOR]

Published
2008
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