Best practice data life cycle approaches for the life sciences
- Griffin, Philippa, Khadake, Jyoti, LeMay, Kate, Lewis, Suzanna, Orchard, Sandra, Pask, Andrew, Pope, Bernard, Roessner, Ute, Russell, Keith, Seemann, Torsten, Treloar, Andrew, Tyagi, Sonika, Christiansen, Jeffrey, Dayalan, Saravanan, Gladman, Simon, Hangartner, Sandra, Hayden, Helen, Ho, William, Keeble-Gagnère, Gabriel, Korhonen, Pasi, Neish, Peter, Prestes, Priscilla, Richardson, Mark, Watson-Haigh, Nathan, Wyres, Kelly, Young, Neil, Schneider, Maria
- Authors: Griffin, Philippa , Khadake, Jyoti , LeMay, Kate , Lewis, Suzanna , Orchard, Sandra , Pask, Andrew , Pope, Bernard , Roessner, Ute , Russell, Keith , Seemann, Torsten , Treloar, Andrew , Tyagi, Sonika , Christiansen, Jeffrey , Dayalan, Saravanan , Gladman, Simon , Hangartner, Sandra , Hayden, Helen , Ho, William , Keeble-Gagnère, Gabriel , Korhonen, Pasi , Neish, Peter , Prestes, Priscilla , Richardson, Mark , Watson-Haigh, Nathan , Wyres, Kelly , Young, Neil , Schneider, Maria
- Date: 2018
- Type: Text , Journal article
- Relation: F1000 Research Vol. 6, no. (2018), p. 1-28
- Full Text:
- Reviewed:
- Description: Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices. © 2018 Griffin PC et al.
- Authors: Griffin, Philippa , Khadake, Jyoti , LeMay, Kate , Lewis, Suzanna , Orchard, Sandra , Pask, Andrew , Pope, Bernard , Roessner, Ute , Russell, Keith , Seemann, Torsten , Treloar, Andrew , Tyagi, Sonika , Christiansen, Jeffrey , Dayalan, Saravanan , Gladman, Simon , Hangartner, Sandra , Hayden, Helen , Ho, William , Keeble-Gagnère, Gabriel , Korhonen, Pasi , Neish, Peter , Prestes, Priscilla , Richardson, Mark , Watson-Haigh, Nathan , Wyres, Kelly , Young, Neil , Schneider, Maria
- Date: 2018
- Type: Text , Journal article
- Relation: F1000 Research Vol. 6, no. (2018), p. 1-28
- Full Text:
- Reviewed:
- Description: Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices. © 2018 Griffin PC et al.
Caucasian and south Asian men show equivalent improvements in surrogate biomarkers of cardiovascular and metabolic health following 6-weeks of supervised resistance training
- Knox, Allan, Sculthorpe, Nicholas, Grace, Fergal
- Authors: Knox, Allan , Sculthorpe, Nicholas , Grace, Fergal
- Date: 2018
- Type: Text , Journal article
- Relation: F1000Research Vol. 7, no. (2018), p. 1-16
- Full Text:
- Reviewed:
- Description: Background: The South Asian population have greater cardiovascular risk than their age-matched Caucasian counterparts, characterized by unfavorable biomarkers. South Asians may also be partially resistant to the pleiotropic benefits of physical activity on cardiovascular health. There is a current absence of studies that compare markers of cardio-metabolic health between Caucasians and South Asians employing resistance exercise. This study set out to compare the response in biomarkers of cardio-metabolic health in Caucasians and South Asians in response to resistance exercise. Methods: Caucasian (n=15, 25.5 ± 4.8 yrs) and South Asian (n=13, 25.4 ± 7.0 yrs) males completed a 6-week progressive resistance exercise protocol. Fasting blood glucose, insulin, and their product insulin resistance (HOMA-IR), triglycerides (TRIGS), low density lipoprotein (LDL), high density lipoprotein (HDL), total cholesterol (TC), vascular endothelial growth factor (VEGF), asymmetric dimythylarginine (ADMA), L-arginine (L-ARG) and C-reactive protein (CRP) were established at baseline and following resistance exercise. Results: There were significant improvements in fasting glucose, TC, LDL, HDL and VEGF in both groups following resistance exercise ( p<0.05, for all). No change was observed in insulin, HOMA-IR, TRIGS, ADMA, L-ARG following resistance exercise ( p>0.05, in both groups). CRP increased in the South Asian group ( p<0.05) but not the Caucasian group ( p>0.05) Conclusions: The cardio-metabolic response to resistance exercise is comparable in young Caucasian and South Asian males though inflammatory response to exercise may be prolonged in South Asians.
- Authors: Knox, Allan , Sculthorpe, Nicholas , Grace, Fergal
- Date: 2018
- Type: Text , Journal article
- Relation: F1000Research Vol. 7, no. (2018), p. 1-16
- Full Text:
- Reviewed:
- Description: Background: The South Asian population have greater cardiovascular risk than their age-matched Caucasian counterparts, characterized by unfavorable biomarkers. South Asians may also be partially resistant to the pleiotropic benefits of physical activity on cardiovascular health. There is a current absence of studies that compare markers of cardio-metabolic health between Caucasians and South Asians employing resistance exercise. This study set out to compare the response in biomarkers of cardio-metabolic health in Caucasians and South Asians in response to resistance exercise. Methods: Caucasian (n=15, 25.5 ± 4.8 yrs) and South Asian (n=13, 25.4 ± 7.0 yrs) males completed a 6-week progressive resistance exercise protocol. Fasting blood glucose, insulin, and their product insulin resistance (HOMA-IR), triglycerides (TRIGS), low density lipoprotein (LDL), high density lipoprotein (HDL), total cholesterol (TC), vascular endothelial growth factor (VEGF), asymmetric dimythylarginine (ADMA), L-arginine (L-ARG) and C-reactive protein (CRP) were established at baseline and following resistance exercise. Results: There were significant improvements in fasting glucose, TC, LDL, HDL and VEGF in both groups following resistance exercise ( p<0.05, for all). No change was observed in insulin, HOMA-IR, TRIGS, ADMA, L-ARG following resistance exercise ( p>0.05, in both groups). CRP increased in the South Asian group ( p<0.05) but not the Caucasian group ( p>0.05) Conclusions: The cardio-metabolic response to resistance exercise is comparable in young Caucasian and South Asian males though inflammatory response to exercise may be prolonged in South Asians.
Comparative effectiveness of three exercise types to treat clinical depression in older adults : a systematic review and network meta-analysis of randomised controlled trials
- Miller, Kyle, Gonçalves-Bradley, Daniela, Areerob, Pinyadapat, Hennessy, Declan, Mesagno, Christopher, Grace, Fergal
- Authors: Miller, Kyle , Gonçalves-Bradley, Daniela , Areerob, Pinyadapat , Hennessy, Declan , Mesagno, Christopher , Grace, Fergal
- Date: 2020
- Type: Text , Journal article , Review
- Relation: Ageing Research Reviews Vol. 58 (2020).
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- Description: Background: Few studies have directly compared the effects of different exercise therapies on clinical depression in older adults. Thus, we conducted a systematic review and network meta-analysis of current evidence from randomised controlled trials (RCTs) to compare the effectiveness of three major exercise types (aerobic, resistance, and mind-body exercise) in clinically depressed older adults. Methods: We followed PRISMA-NMA guidelines and searched databases for eligible RCTs (inception – September 12th, 2019). RCTs were eligible if they included clinically depressed adults aged >65 years, implemented one or more exercise therapy arms using aerobic, resistance, or mind-body exercise, and assessed depressive symptoms at baseline and follow-up using a validated clinical questionnaire. Results: A network meta-analysis was performed on 15 eligible RCTs comprising 596 participants (321 treatment and 275 controls), including aerobic (n = 6), resistance (n = 5), and mind-body (n = 4) exercise trials. Compared with controls, mind-body exercise showed the largest improvement on depressive symptoms (g = −0.87 to −1.38), followed by aerobic exercise (g = −0.51 to −1.02), and resistance exercise (g = −0.41 to −0.92). Notably, there were no statistically significant differences between exercise types: aerobic versus resistance (g = −0.10, PrI = −2.23, 2.03), mind-body versus aerobic (g = −0.36, PrI = −2.69, 1.97), or mind-body versus resistance (g = −0.46, PrI = −2.75, 1.83). Conclusions: These findings should guide optimal exercise prescription for allied health professionals and stakeholders in clinical geriatrics. Notably, clinically depressed older adults may be encouraged to self-select their preferred exercise type in order to achieve therapeutic benefit on symptoms of depression. In coalition with high levels of compliance, these data provide encouraging evidence for the antidepressant effect of either aerobic, resistance, or mind-body exercise as effective treatment adjucts for older adults presenting with clinical depression. © 2019
- Authors: Miller, Kyle , Gonçalves-Bradley, Daniela , Areerob, Pinyadapat , Hennessy, Declan , Mesagno, Christopher , Grace, Fergal
- Date: 2020
- Type: Text , Journal article , Review
- Relation: Ageing Research Reviews Vol. 58 (2020).
- Full Text:
- Reviewed:
- Description: Background: Few studies have directly compared the effects of different exercise therapies on clinical depression in older adults. Thus, we conducted a systematic review and network meta-analysis of current evidence from randomised controlled trials (RCTs) to compare the effectiveness of three major exercise types (aerobic, resistance, and mind-body exercise) in clinically depressed older adults. Methods: We followed PRISMA-NMA guidelines and searched databases for eligible RCTs (inception – September 12th, 2019). RCTs were eligible if they included clinically depressed adults aged >65 years, implemented one or more exercise therapy arms using aerobic, resistance, or mind-body exercise, and assessed depressive symptoms at baseline and follow-up using a validated clinical questionnaire. Results: A network meta-analysis was performed on 15 eligible RCTs comprising 596 participants (321 treatment and 275 controls), including aerobic (n = 6), resistance (n = 5), and mind-body (n = 4) exercise trials. Compared with controls, mind-body exercise showed the largest improvement on depressive symptoms (g = −0.87 to −1.38), followed by aerobic exercise (g = −0.51 to −1.02), and resistance exercise (g = −0.41 to −0.92). Notably, there were no statistically significant differences between exercise types: aerobic versus resistance (g = −0.10, PrI = −2.23, 2.03), mind-body versus aerobic (g = −0.36, PrI = −2.69, 1.97), or mind-body versus resistance (g = −0.46, PrI = −2.75, 1.83). Conclusions: These findings should guide optimal exercise prescription for allied health professionals and stakeholders in clinical geriatrics. Notably, clinically depressed older adults may be encouraged to self-select their preferred exercise type in order to achieve therapeutic benefit on symptoms of depression. In coalition with high levels of compliance, these data provide encouraging evidence for the antidepressant effect of either aerobic, resistance, or mind-body exercise as effective treatment adjucts for older adults presenting with clinical depression. © 2019
Aerobic, resistance, and mind-body exercise are equivalent to mitigate symptoms of depression in older adults: A systematic review and network meta-analysis of randomised controlled trials
- Miller, Kyle, Areerob, Pinyadapat, Hennessy, Declan, Gonçalves-Bradley, Daniela, Mesagno, Christopher, Grace, Fergal
- Authors: Miller, Kyle , Areerob, Pinyadapat , Hennessy, Declan , Gonçalves-Bradley, Daniela , Mesagno, Christopher , Grace, Fergal
- Date: 2020
- Type: Text , Journal article
- Relation: F1000Research Vol. 9, no. (2020), p. 1-51
- Full Text:
- Reviewed:
- Description: Background: Exercise has been identified as an allied health strategy that can support the management of depression in older adults, yet the relative effectiveness for different exercise modalities is unknown. To meet this gap in knowledge, we present a systematic review and network meta-analysis of randomised controlled trials (RCTs) to examine the head-to-head effectiveness of aerobic, resistance, and mind-body exercise to mitigate depressive symptoms in adults aged ≥ 65 years. Methods: A PRISMA-NMA compliant review was undertaken on RCTs from inception to September 12 th, 2019. PubMed, Web of Science, CINAHL, Health Source: Nursing/Academic Edition, PsycARTICLES, PsycINFO, and SPORTDiscus were systematically searched for eligible RCTs enrolling adults with a mean age ≥ 65 years, comparing one or more exercise intervention arms, and which used valid measures of depressive symptomology. Comparative effectiveness was evaluated using network meta-analysis to combine direct and indirect evidence, controlling for inherent variation in trial control groups. Results: The systematic review included 81 RCTs, with 69 meeting eligibility for the network meta-analysis ( n = 5,379 participants). Pooled analysis found each exercise type to be effective compared with controls (Hedges' g = -0.27 to -0.51). Relative head-to-head comparisons were statistically comparable between exercise types: resistance versus aerobic (Hedges' g = -0.06, PrI = -0.91, 0.79), mind-body versus aerobic (Hedges' g = -0.12, PrI = -0.95, 0.72), mind-body versus resistance (Hedges' g = -0.06, PrI = -0.90, 0.79). High levels of compliance were demonstrated for each exercise treatment. Conclusions: Aerobic, resistance, and mind-body exercise demonstrate equivalence to mitigate symptoms of depression in older adults aged ≥ 65 years, with comparably encouraging levels of compliance to exercise treatment. These findings coalesce with previous findings in clinically depressed older adults to encourage personal preference when prescribing exercise for depressive symptoms in older adults, irrespective of severity. Registration: PROSPERO CRD42018115866 (23/11/2018). © 2020 Miller KJ et al.
- Authors: Miller, Kyle , Areerob, Pinyadapat , Hennessy, Declan , Gonçalves-Bradley, Daniela , Mesagno, Christopher , Grace, Fergal
- Date: 2020
- Type: Text , Journal article
- Relation: F1000Research Vol. 9, no. (2020), p. 1-51
- Full Text:
- Reviewed:
- Description: Background: Exercise has been identified as an allied health strategy that can support the management of depression in older adults, yet the relative effectiveness for different exercise modalities is unknown. To meet this gap in knowledge, we present a systematic review and network meta-analysis of randomised controlled trials (RCTs) to examine the head-to-head effectiveness of aerobic, resistance, and mind-body exercise to mitigate depressive symptoms in adults aged ≥ 65 years. Methods: A PRISMA-NMA compliant review was undertaken on RCTs from inception to September 12 th, 2019. PubMed, Web of Science, CINAHL, Health Source: Nursing/Academic Edition, PsycARTICLES, PsycINFO, and SPORTDiscus were systematically searched for eligible RCTs enrolling adults with a mean age ≥ 65 years, comparing one or more exercise intervention arms, and which used valid measures of depressive symptomology. Comparative effectiveness was evaluated using network meta-analysis to combine direct and indirect evidence, controlling for inherent variation in trial control groups. Results: The systematic review included 81 RCTs, with 69 meeting eligibility for the network meta-analysis ( n = 5,379 participants). Pooled analysis found each exercise type to be effective compared with controls (Hedges' g = -0.27 to -0.51). Relative head-to-head comparisons were statistically comparable between exercise types: resistance versus aerobic (Hedges' g = -0.06, PrI = -0.91, 0.79), mind-body versus aerobic (Hedges' g = -0.12, PrI = -0.95, 0.72), mind-body versus resistance (Hedges' g = -0.06, PrI = -0.90, 0.79). High levels of compliance were demonstrated for each exercise treatment. Conclusions: Aerobic, resistance, and mind-body exercise demonstrate equivalence to mitigate symptoms of depression in older adults aged ≥ 65 years, with comparably encouraging levels of compliance to exercise treatment. These findings coalesce with previous findings in clinically depressed older adults to encourage personal preference when prescribing exercise for depressive symptoms in older adults, irrespective of severity. Registration: PROSPERO CRD42018115866 (23/11/2018). © 2020 Miller KJ et al.
Using agricultural metadata : a novel investigation of trends in sowing date in on-farm research trials using the online farm trials database
- Walters, Judi, Light, Kate, Robinson, Nathan
- Authors: Walters, Judi , Light, Kate , Robinson, Nathan
- Date: 2021
- Type: Text , Journal article
- Relation: F1000Research Vol. 9, no. (2021), p.1305-1305
- Full Text:
- Reviewed:
- Description: Background: A growing ability to collect data, together with the development and adoption of the FAIR guiding principles, has increased the amount of data available in many disciplines. This has given rise to an urgent need for robust metadata. Within the Australian grains industry, data from thousands of on-farm research trials (Trial Projects) have been made available via the Online Farm Trials (OFT) website. OFT Trial Project metadata were developed as filters to refine front-end database searches, but could also be used as a dataset to investigate trends in metadata elements. Australian grains crops are being sown earlier, but whether on-farm research trials reflect this change is currently unknown. Methods: We investigated whether OFT Trial Project metadata could be used to detect trends in sowing dates of on-farm crop research trials across Australia, testing the hypothesis that research trials are being sown earlier in line with local farming practices. The investigation included 15 autumn-sown, winter crop species listed in the database, with trial records from 1993 to 2019. Results: Our analyses showed that (i) OFT Trial Project metadata can be used as a dataset to detect trends in sowing date; and (ii) cropping research trials are being sown earlier in Victoria and Western Australia, but no trend exists within the other states. Discussion/Conclusion: Our findings show that OFT Trial Project metadata can be used to detect trends in crop sowing date, suggesting that metadata could also be used to detect trends in other elements such as harvest date. Because OFT is a national database of research trials, further assessment of metadata may uncover important agronomic, cultural or economic trends within or across the Australian cropping regions. New information could then be used to lead practice change and increase productivity within the Australian grains industry. © 2021 Walters J et al.
- Authors: Walters, Judi , Light, Kate , Robinson, Nathan
- Date: 2021
- Type: Text , Journal article
- Relation: F1000Research Vol. 9, no. (2021), p.1305-1305
- Full Text:
- Reviewed:
- Description: Background: A growing ability to collect data, together with the development and adoption of the FAIR guiding principles, has increased the amount of data available in many disciplines. This has given rise to an urgent need for robust metadata. Within the Australian grains industry, data from thousands of on-farm research trials (Trial Projects) have been made available via the Online Farm Trials (OFT) website. OFT Trial Project metadata were developed as filters to refine front-end database searches, but could also be used as a dataset to investigate trends in metadata elements. Australian grains crops are being sown earlier, but whether on-farm research trials reflect this change is currently unknown. Methods: We investigated whether OFT Trial Project metadata could be used to detect trends in sowing dates of on-farm crop research trials across Australia, testing the hypothesis that research trials are being sown earlier in line with local farming practices. The investigation included 15 autumn-sown, winter crop species listed in the database, with trial records from 1993 to 2019. Results: Our analyses showed that (i) OFT Trial Project metadata can be used as a dataset to detect trends in sowing date; and (ii) cropping research trials are being sown earlier in Victoria and Western Australia, but no trend exists within the other states. Discussion/Conclusion: Our findings show that OFT Trial Project metadata can be used to detect trends in crop sowing date, suggesting that metadata could also be used to detect trends in other elements such as harvest date. Because OFT is a national database of research trials, further assessment of metadata may uncover important agronomic, cultural or economic trends within or across the Australian cropping regions. New information could then be used to lead practice change and increase productivity within the Australian grains industry. © 2021 Walters J et al.
High CD26 and low CD94 expression identifies an IL-23 responsive Vδ2+ T Cell subset with a MAIT cell-like transcriptional profile
- Wragg, Kathleen, Tan, Hyon, Kristensen, Anne, Nguyen-Robertson, Catriona, Kelleher, Anthony, Parsons, Matthew, Wheatley, Adam, Berzins, Stuart, Pellicci, Daniel, Kent, Stephen, Juno, Jennifer
- Authors: Wragg, Kathleen , Tan, Hyon , Kristensen, Anne , Nguyen-Robertson, Catriona , Kelleher, Anthony , Parsons, Matthew , Wheatley, Adam , Berzins, Stuart , Pellicci, Daniel , Kent, Stephen , Juno, Jennifer
- Date: 2020
- Type: Text , Journal article
- Relation: Cell Reports Vol. 31, no. 11 (2020), p.
- Full Text:
- Reviewed:
- Description: Vδ2+ T cells play a critical role in immunity to micro-organisms and cancer but exhibit substantial heterogeneity in humans. Here, we demonstrate that CD26 and CD94 define transcriptionally, phenotypically, and functionally distinct Vδ2+ T cell subsets. Despite distinct antigen specificities, CD26hiCD94lo Vδ2+ cells exhibit substantial similarities to CD26hi mucosal-associated invariant T (MAIT) cells, although CD26− Vδ2+ cells exhibit cytotoxic, effector-like profiles. At birth, the Vδ2+Vγ9+ population is dominated by CD26hiCD94lo cells; during adolescence and adulthood, Vδ2+ cells acquire CD94/NKG2A expression and the relative frequency of the CD26hiCD94lo subset declines. Critically, exposure of the CD26hiCD94lo subset to phosphoantigen in the context of interleukin-23 (IL-23) and CD26 engagement drives the acquisition of a cytotoxic program and concurrent loss of the MAIT cell-like phenotype. The ability to modulate the cytotoxic potential of CD26hiCD94lo Vδ2+ cells, combined with their adenosine-binding capacity, may make them ideal targets for immunotherapeutic expansion and adoptive transfer. Wragg et al. identify a population of human gd T cells with striking similarities to MAIT cells. These cells dominate the cord blood Vd2 population and upregulate an effector-like program upon antigen and IL-23 stimulation, providing a potential mechanism by which cytotoxic Vd2 cells may accumulate during adolescence and adulthood. © 2020
- Description: National Health and Medical Research Council, NHMRC
- Authors: Wragg, Kathleen , Tan, Hyon , Kristensen, Anne , Nguyen-Robertson, Catriona , Kelleher, Anthony , Parsons, Matthew , Wheatley, Adam , Berzins, Stuart , Pellicci, Daniel , Kent, Stephen , Juno, Jennifer
- Date: 2020
- Type: Text , Journal article
- Relation: Cell Reports Vol. 31, no. 11 (2020), p.
- Full Text:
- Reviewed:
- Description: Vδ2+ T cells play a critical role in immunity to micro-organisms and cancer but exhibit substantial heterogeneity in humans. Here, we demonstrate that CD26 and CD94 define transcriptionally, phenotypically, and functionally distinct Vδ2+ T cell subsets. Despite distinct antigen specificities, CD26hiCD94lo Vδ2+ cells exhibit substantial similarities to CD26hi mucosal-associated invariant T (MAIT) cells, although CD26− Vδ2+ cells exhibit cytotoxic, effector-like profiles. At birth, the Vδ2+Vγ9+ population is dominated by CD26hiCD94lo cells; during adolescence and adulthood, Vδ2+ cells acquire CD94/NKG2A expression and the relative frequency of the CD26hiCD94lo subset declines. Critically, exposure of the CD26hiCD94lo subset to phosphoantigen in the context of interleukin-23 (IL-23) and CD26 engagement drives the acquisition of a cytotoxic program and concurrent loss of the MAIT cell-like phenotype. The ability to modulate the cytotoxic potential of CD26hiCD94lo Vδ2+ cells, combined with their adenosine-binding capacity, may make them ideal targets for immunotherapeutic expansion and adoptive transfer. Wragg et al. identify a population of human gd T cells with striking similarities to MAIT cells. These cells dominate the cord blood Vd2 population and upregulate an effector-like program upon antigen and IL-23 stimulation, providing a potential mechanism by which cytotoxic Vd2 cells may accumulate during adolescence and adulthood. © 2020
- Description: National Health and Medical Research Council, NHMRC
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