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Hafeez S, Warren-Oseni K, Jones K, Mohammed K, El-Ghzal A, Dearnaley D, Harris V, Khan A, Kumar P, Lalondrelle S, McDonald F, Tan M, Thomas K, Thompson A, McNair HA, Hansen VN, Huddart R. Bladder tumour focused adaptive radiotherapy: Clinical outcomes of a phase I dose escalation study. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)03137-7. [PMID: 39069239 DOI: 10.1016/j.ijrobp.2024.07.2317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/22/2024] [Accepted: 07/04/2024] [Indexed: 07/30/2024]
Abstract
PURPOSE/OBJECTIVES We determine the maximum tolerated tumour focused dose (MTD) for the radical treatment of muscle invasive bladder cancer (MIBC) enabled by image guided adaptive radiotherapy (IGART) and long-term clinical outcomes. MATERIALS/METHODS Fifty-nine patients with T2-T4aN0M0 unifocal urothelial MIBC suitable for daily radical radiotherapy were recruited prospectively to an ethics approved protocol (XX). The uninvolved bladder (PTVbladder) was planned to 52Gy in 32 fractions (f). The bladder tumour (PTVtumour) was planned to an assigned dose level of 68, 70, 72, or 74Gy. If organ at risk (OAR) dose constraints were violated, then PTVtumour was planned to 64Gy. Dose level allocation was determined by concurrent toxicity assessment of all previous patients recruited. Acute toxicity was evaluated using CTCAE v3.0; late toxicity was evaluated using RTOG criteria. The MTD was predefined as the highest dose level with estimated probability of ≤ 15% ≥G3 late toxicity and observed rate <50% acute G3 and <10% acute G4 toxicity. RESULTS Twenty-six patients were assigned to 68Gy, of whom 6 were planned to 64Gy; 29 patients were assigned to 70Gy of whom 1 was planned to 68Gy, 2 patients were assigned and planned to 72Gy; no patients were assigned to 74Gy. Three patients did not complete treatment as planned, of whom only 1 patient stopped treatment because dose limiting toxicity occurred. The MTD was 70Gy. Acute genitourinary (GU) and gastrointestinal (GI) G3 acute toxicity was seen in 19% and 7% patients respectively. No grade 4 GU or GI toxicity was seen. Late toxicity (any) G3 and G4 was seen in 14% and 2% patients respectively. The 5-year overall survival was 58% (95% CI 44-71%). The bladder preservation rate was 89% (95% CI, 88 to 96%) with 6 patients not retaining native bladder function. CONCLUSION Bladder tumour focused dose escalation to 70Gy using IGART is feasible with acceptable toxicity. This dose level has been evaluated in a phase II randomised control trial (XXXXX).
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Batt NM, Rodrigues B, Bloom S, Sawhney R, George ES, Hodge A, Vootukuru N, McCrae C, Sood S, Roberts SK, Dev A, Bell S, Thompson A, Ryan MC, Kemp W, Gow PJ, Sood S, Nicoll AJ. Metabolic-associated fatty liver disease and hepatocellular carcinoma: a prospective study of characteristics and response to therapy. J Gastroenterol Hepatol 2024; 39:1048-1056. [PMID: 38369382 DOI: 10.1111/jgh.16501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/31/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND AND AIM The rising incidence of hepatocellular carcinoma (HCC) in Australia is related to increasing rates of metabolic-associated fatty liver disease (MAFLD). This study aimed to prospectively characterize the metabolic profile, lifestyle, biometric features, and response to treatment of HCC patients in an Australian population. METHOD Multicenter prospective cohort analysis of newly diagnosed HCC patients at six multidisciplinary team meetings over a 2-year period. RESULTS Three hundred and thirteen (313) newly diagnosed HCC patients with MAFLD (n = 77), MAFLD plus other liver disease (n = 57) (the "mixed" group), and non-MAFLD (n = 179) were included in the study. Alcohol-associated liver disease (ALD) (43%) and MAFLD (43%) were the most common underlying liver diseases. MAFLD-HCC patients were older (73 years vs 67 years vs 63 years), more likely to be female (40% vs 14% vs 20%), less likely to have cirrhosis (69% vs 88% vs 85%), showed higher ECOG, and were less likely to be identified by screening (29% vs 53% vs 45%). Metabolic syndrome was more prevalent in the MAFLD and mixed groups. The severity of underlying liver disease and HCC characteristics were the same across groups. While the MAFLD population self-reported more sedentary lifestyles, reported dietary patterns were no different across the groups. Dyslipidemia was associated with tumor size, and those taking statins had a lower recurrence rate. CONCLUSION Equal to ALD, MAFLD is now the most common underlying liver disease seen in HCC patients in Australia. Future HCC prevention screening and treatment strategies need to take this important group of patients into consideration.
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Ying S, Webster B, Gomez-Cano L, Shivaiah KK, Wang Q, Newton L, Grotewold E, Thompson A, Lundquist PK. Multiscale physiological responses to nitrogen supplementation of maize hybrids. PLANT PHYSIOLOGY 2024; 195:879-899. [PMID: 37925649 PMCID: PMC11060684 DOI: 10.1093/plphys/kiad583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/15/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
Maize (Zea mays) production systems are heavily reliant on the provision of managed inputs such as fertilizers to maximize growth and yield. Hence, the effective use of nitrogen (N) fertilizer is crucial to minimize the associated financial and environmental costs, as well as maximize yield. However, how to effectively utilize N inputs for increased grain yields remains a substantial challenge for maize growers that requires a deeper understanding of the underlying physiological responses to N fertilizer application. We report a multiscale investigation of five field-grown maize hybrids under low or high N supplementation regimes that includes the quantification of phenolic and prenyl-lipid compounds, cellular ultrastructural features, and gene expression traits at three developmental stages of growth. Our results reveal that maize perceives the lack of supplemented N as a stress and, when provided with additional N, will prolong vegetative growth. However, the manifestation of the stress and responses to N supplementation are highly hybrid-specific. Eight genes were differentially expressed in leaves in response to N supplementation in all tested hybrids and at all developmental stages. These genes represent potential biomarkers of N status and include two isoforms of Thiamine Thiazole Synthase involved in vitamin B1 biosynthesis. Our results uncover a detailed view of the physiological responses of maize hybrids to N supplementation in field conditions that provides insight into the interactions between management practices and the genetic diversity within maize.
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Lopez-Cruz M, Aguate FM, Washburn JD, de Leon N, Kaeppler SM, Lima DC, Tan R, Thompson A, De La Bretonne LW, de Los Campos G. Leveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America. Nat Commun 2023; 14:6904. [PMID: 37903778 PMCID: PMC10616096 DOI: 10.1038/s41467-023-42687-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Genotype-by-environment (G×E) interactions can significantly affect crop performance and stability. Investigating G×E requires extensive data sets with diverse cultivars tested over multiple locations and years. The Genomes-to-Fields (G2F) Initiative has tested maize hybrids in more than 130 year-locations in North America since 2014. Here, we curate and expand this data set by generating environmental covariates (using a crop model) for each of the trials. The resulting data set includes DNA genotypes and environmental data linked to more than 70,000 phenotypic records of grain yield and flowering traits for more than 4000 hybrids. We show how this valuable data set can serve as a benchmark in agricultural modeling and prediction, paving the way for countless G×E investigations in maize. We use multivariate analyses to characterize the data set's genetic and environmental structure, study the association of key environmental factors with traits, and provide benchmarks using genomic prediction models.
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El-Hage D, Gao CX, Bedi G, Guerin A, Francey S, Stavely H, Rickwood D, Telford N, McGorry P, Thompson A, Brown E. Correlates of substance use in a large naturalistic cohort of young people with early and emerging psychosis. Soc Psychiatry Psychiatr Epidemiol 2023; 58:1447-1456. [PMID: 36808500 PMCID: PMC10460356 DOI: 10.1007/s00127-023-02436-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Substance use remains a barrier to recovery for young people accessing early intervention services for psychosis. While correlates of use have been explored in populations experiencing a first episode of psychosis (FEP), sample sizes have been small and less research assesses cohorts at ultrahigh risk of psychosis (UHR). METHODS This study uses data from a naturalistic cohort including UHR and FEP participants (N = 1252) to elucidate clinical correlates of use in the past 3 months of any illicit substance, amphetamine-type stimulants (ATS), cannabis, and tobacco. Moreover, network analysis based on use of these substances and additionally alcohol, cocaine, hallucinogens, sedatives, inhalants, and opioids was completed. RESULTS Young people with FEP used substances at significantly higher rates than those at UHR. High concurrence of use was seen between substances. In the FEP group, participants who had used any illicit substance, ATS, and/or tobacco had increased positive symptoms and decreased negative symptoms. Young people with FEP who used cannabis had increased positive symptoms. In the UHR group, participants who had used any illicit substance, ATS, and/or cannabis in the past 3 months showed decreased negative symptoms compared to those who had not. CONCLUSION A distinct clinical picture of more florid positive symptoms and alleviated negative symptoms seen in those who use substances in the FEP group appears muted in the UHR cohort. Treating young people at UHR in early intervention services represents the earliest opportunity to address substance use early to improve outcomes.
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Rieu R, Prestwich RJ, Paterson C, Vohra S, Swan A, Noble D, Srinivasan D, Dixon L, Chiu K, Scott A, Mendes R, Khan S, Pilar A, Thompson A, Nutting CM, McPartlin A. A Multicenter Study of Clinician and Patient Reported Acute and Late Toxicity after Radical (Chemo)Radiotherapy for Non-Endemic Nasopharyngeal Cancer. Int J Radiat Oncol Biol Phys 2023; 117:e619. [PMID: 37785855 DOI: 10.1016/j.ijrobp.2023.06.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Curative (chemo)radiotherapy ((CT)RT) for Nasopharyngeal cancers (NPC) achieves excellent disease control but is associated with significant late toxicities despite modern treatment delivery. Contemporary late toxicity data, including patient reported outcomes (PROs), is limited in the non-endemic population; we present a large contemporary series of toxicity outcomes and late PROs following treatment of non-endemic NPC. MATERIALS/METHODS Adult patients completing radical (CT)RT for primary NPC between February 2016 and 2020 at 7 large UK cancer centers were identified on institutional databases. Patients were excluded if they had prior head and neck cancer or prior therapeutic head and neck surgery (except neck dissection). Patients with an active other cancer were excluded from PRO assessment. Demographic, treatment, acute toxicity and outcome data were collected retrospectively from patient records. Disease-free patients were invited to complete an M.D. Anderson Dysphagia Index (MDADI) and University of Washington (UoW) Quality of Life (QoL) PROs questionnaires. RESULTS A total of 180 eligible patients were identified: 68% male, median age 54 years, 11% ≥70 years. EBV status was positive in 61% (unknown 12%). Patients had stage I (5%), II (22%), III (37%), IV (36%) disease; 95% were performance status ≤1 at baseline. Median follow-up was 31.2 months (range 0-68). A total of 54% received 70Gy in 33-35# and 43% received 65-66 Gy in 30-33#. 66% received induction and 65% received concurrent chemotherapy. 9.5% had residual disease at the first follow-up scan. Subsequent locoregional or distant recurrence occurred in 5% and 12% respectively. At last assessment, 84% patients were alive, 16% had died (of which 70% had active disease). Acute treatment toxicity included: 63% of patients required enteral support (median duration 98 days) with 9% a feeding tube at 1 year post treatment. 18% G3 dermatitis, 53% G3 mucositis. 82% requiring opioids and 40% admitted for symptom management. 90 patients completed the PROs (76% response rate) at a median of 37.8 months post treatment (Table 1). These demonstrate significant QoL detriment: 28% report significant pain, 24% require regular analgesia, and 59% report significant impact on daily activity. This was found to persist at different timepoints (not shown). CONCLUSION Excellent cancer survival outcomes are seen in a non-selected, non-endemic NPC population. However significant acute and late toxicity following radical treatment is identified which can profoundly negatively impact QoL in a relatively young cohort. This highlights the importance of ongoing efforts to reduce toxicity and supports the prospective evaluation of potential toxicity sparing technologies, such as proton beam radiotherapy.
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Lima DC, Aviles AC, Alpers RT, Perkins A, Schoemaker DL, Costa M, Michel KJ, Kaeppler S, Ertl D, Romay MC, Gage JL, Holland J, Beissinger T, Bohn M, Buckler E, Edwards J, Flint-Garcia S, Gore MA, Hirsch CN, Knoll JE, McKay J, Minyo R, Murray SC, Schnable J, Sekhon RS, Singh MP, Sparks EE, Thomison P, Thompson A, Tuinstra M, Wallace J, Washburn JD, Weldekidan T, Xu W, de Leon N. 2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative. BMC Res Notes 2023; 16:219. [PMID: 37710302 PMCID: PMC10502993 DOI: 10.1186/s13104-023-06430-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/17/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVES This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scenarios of variable environmental patterns. Hybrids and inbreds are evaluated across multiple environments and phenotypic, genotypic, environmental, and metadata information are made publicly available. DATA DESCRIPTION The datasets include phenotypic data of the hybrids and inbreds evaluated in 30 locations across the US and one location in Germany in 2020 and 2021, soil and climatic measurements and metadata information for all environments (combination of year and location), ReadMe, and description files for each data type. A set of common hybrids is present in each environment to connect with previous evaluations. Each environment had a collaborator responsible for collecting and submitting the data, the GxE coordination team combined all the collected information and removed obvious erroneous data. Collaborators received the combined data to use, verify and declare that the data generated in their own environments was accurate. Combined data is released to the public with minimal filtering to maintain fidelity to the original data.
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Henderson DAG, Donaghy E, Dozier M, Guthrie B, Huang H, Pickersgill M, Stewart E, Thompson A, Wang HHX, Mercer SW. Understanding primary care transformation and implications for ageing populations and health inequalities: a systematic scoping review of new models of primary health care in OECD countries and China. BMC Med 2023; 21:319. [PMID: 37620865 PMCID: PMC10463288 DOI: 10.1186/s12916-023-03033-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Many countries have introduced reforms with the aim of primary care transformation (PCT). Common objectives include meeting service delivery challenges associated with ageing populations and health inequalities. To date, there has been little research comparing PCT internationally. Our aim was to examine PCT and new models of primary care by conducting a systematic scoping review of international literature in order to describe major policy changes including key 'components', impacts of new models of care, and barriers and facilitators to PCT implementation. METHODS We undertook a systematic scoping review of international literature on PCT in OECD countries and China (published protocol: https://osf.io/2afym ). Ovid [MEDLINE/Embase/Global Health], CINAHL Plus, and Global Index Medicus were searched (01/01/10 to 28/08/21). Two reviewers independently screened the titles and abstracts with data extraction by a single reviewer. A narrative synthesis of findings followed. RESULTS A total of 107 studies from 15 countries were included. The most frequently employed component of PCT was the expansion of multidisciplinary teams (MDT) (46% of studies). The most frequently measured outcome was GP views (27%), with < 20% measuring patient views or satisfaction. Only three studies evaluated the effects of PCT on ageing populations and 34 (32%) on health inequalities with ambiguous results. For the latter, PCT involving increased primary care access showed positive impacts whilst no benefits were reported for other components. Analysis of 41 studies citing barriers or facilitators to PCT implementation identified leadership, change, resources, and targets as key themes. CONCLUSIONS Countries identified in this review have used a range of approaches to PCT with marked heterogeneity in methods of evaluation and mixed findings on impacts. Only a minority of studies described the impacts of PCT on ageing populations, health inequalities, or from the patient perspective. The facilitators and barriers identified may be useful in planning and evaluating future developments in PCT.
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Lima DC, Washburn JD, Varela JI, Chen Q, Gage JL, Romay MC, Holland J, Ertl D, Lopez-Cruz M, Aguate FM, de Los Campos G, Kaeppler S, Beissinger T, Bohn M, Buckler E, Edwards J, Flint-Garcia S, Gore MA, Hirsch CN, Knoll JE, McKay J, Minyo R, Murray SC, Ortez OA, Schnable JC, Sekhon RS, Singh MP, Sparks EE, Thompson A, Tuinstra M, Wallace J, Weldekidan T, Xu W, de Leon N. Genomes to Fields 2022 Maize genotype by Environment Prediction Competition. BMC Res Notes 2023; 16:148. [PMID: 37461058 DOI: 10.1186/s13104-023-06421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
OBJECTIVES The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data. DATA DESCRIPTION This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years.
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Smid CR, Ganesan K, Thompson A, Cañigueral R, Veselic S, Royer J, Kool W, Hauser TU, Bernhardt B, Steinbeis N. Neurocognitive basis of model-based decision making and its metacontrol in childhood. Dev Cogn Neurosci 2023; 62:101269. [PMID: 37352654 PMCID: PMC10329104 DOI: 10.1016/j.dcn.2023.101269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 04/16/2023] [Accepted: 06/14/2023] [Indexed: 06/25/2023] Open
Abstract
Human behavior is supported by both goal-directed (model-based) and habitual (model-free) decision-making, each differing in its flexibility, accuracy, and computational cost. The arbitration between habitual and goal-directed systems is thought to be regulated by a process known as metacontrol. However, how these systems emerge and develop remains poorly understood. Recently, we found that while children between 5 and 11 years displayed robust signatures of model-based decision-making, which increased during this developmental period, there were substantial individual differences in the display of metacontrol. Here, we inspect the neurocognitive basis of model-based decision-making and metacontrol in childhood and focus this investigation on executive functions, fluid reasoning, and brain structure. A total of 69 participants between the ages of 6-13 completed a two-step decision-making task and an extensive behavioral test battery. A subset of 44 participants also completed a structural magnetic resonance imaging scan. We find that individual differences in metacontrol are specifically associated with performance on an inhibition task and individual differences in thickness of dorsolateral prefrontal, temporal, and superior-parietal cortices. These brain regions likely reflect the involvement of cognitive processes crucial to metacontrol, such as cognitive control and contextual processing.
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Lima DC, Aviles AC, Alpers RT, McFarland BA, Kaeppler S, Ertl D, Romay MC, Gage JL, Holland J, Beissinger T, Bohn M, Buckler E, Edwards J, Flint-Garcia S, Hirsch CN, Hood E, Hooker DC, Knoll JE, Kolkman JM, Liu S, McKay J, Minyo R, Moreta DE, Murray SC, Nelson R, Schnable JC, Sekhon RS, Singh MP, Thomison P, Thompson A, Tuinstra M, Wallace J, Washburn JD, Weldekidan T, Wisser RJ, Xu W, de Leon N. 2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project. BMC Genom Data 2023; 24:29. [PMID: 37231352 DOI: 10.1186/s12863-023-01129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
OBJECTIVES This report provides information about the public release of the 2018-2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy public sources of genetic diversity to face the challenges for more sustainable agriculture in the context of variable environmental conditions. DATA DESCRIPTION Datasets include phenotypic, climatic, and soil measurements, metadata information, and inbred genotypic information for each combination of location and year. Collaborators in the G2F initiative collected data for each location and year; members of the group responsible for coordination and data processing combined all the collected information and removed obvious erroneous data. The collaborators received the data before the DOI release to verify and declare that the data generated in their own locations was accurate. ReadMe and description files are available for each dataset. Previous years of evaluation are already publicly available, with common hybrids present to connect across all locations and years evaluated since this project's inception.
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Kick DR, Wallace JG, Schnable JC, Kolkman JM, Alaca B, Beissinger TM, Edwards J, Ertl D, Flint-Garcia S, Gage JL, Hirsch CN, Knoll JE, de Leon N, Lima DC, Moreta DE, Singh MP, Thompson A, Weldekidan T, Washburn JD. Yield prediction through integration of genetic, environment, and management data through deep learning. G3 (BETHESDA, MD.) 2023; 13:jkad006. [PMID: 36625555 PMCID: PMC10085787 DOI: 10.1093/g3journal/jkad006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 07/28/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023]
Abstract
Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied toward this goal. Here we predict maize yield using deep neural networks, compare the efficacy of 2 model development methods, and contextualize model performance using conventional linear and machine learning models. We examine the usefulness of incorporating interactions between disparate data types. We find deep learning and best linear unbiased predictor (BLUP) models with interactions had the best overall performance. BLUP models achieved the lowest average error, but deep learning models performed more consistently with similar average error. Optimizing deep neural network submodules for each data type improved model performance relative to optimizing the whole model for all data types at once. Examining the effect of interactions in the best-performing model revealed that including interactions altered the model's sensitivity to weather and management features, including a reduction of the importance scores for timepoints expected to have a limited physiological basis for influencing yield-those at the extreme end of the season, nearly 200 days post planting. Based on these results, deep learning provides a promising avenue for the phenotypic prediction of complex traits in complex environments and a potential mechanism to better understand the influence of environmental and genetic factors.
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Green C, McGinley J, Sande C, Capone S, Makvandi-Nejad S, Vitelli A, Silva-Reyes L, Bibi S, Otasowie C, Sheerin D, Thompson A, Dold C, Klenerman P, Barnes E, Dorrell L, Rollier C, Pollard A, O’Connor D. Transcriptomic response and immunological responses to chimpanzee adenovirus- and MVA viral-vectored vaccines for RSV in healthy adults. Clin Exp Immunol 2023; 211:269-279. [PMID: 36622786 PMCID: PMC10038321 DOI: 10.1093/cei/uxad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/30/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Cohorts of healthy younger adults (18-50yrs) and healthy older adults (60-75yrs) were immunized intramuscularly or intranasally with an adenovirus-vectored RSV vaccine (PanAd3-RSV) as a prime dose and boosted with PanAd3-RSV or a poxvirus-vectored vaccine (MVA-RSV) encoding the same insert. Whole blood gene expression was measured at baseline, 3- and 7-days post vaccination. Intramuscular prime vaccination with PanAd3-RSV induced differential expression of 643 genes (DEGs, FDR < 0.05). Intranasal prime vaccination with PanAd3-RSV did not induce any differentially expressed genes (DEGs) in blood samples at 3 days post vaccination. Intranasally primed participants showed greater numbers of DEGS on boosting than intramuscularly primed participants. The most highly enriched biological processes related to DEGs after both prime and boost vaccination were type-1 interferon related pathways, lymphocytic and humoral immune responses.
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Pineda D, Bingham RE, Thompson A, Gates A, Stansfield B. Acid/base balance in fortified human milk. Am J Med Sci 2023. [DOI: 10.1016/s0002-9629(23)00653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Alsaidi Y, Thompson A, Spilchuk V, House RA, Adisesh A. Cryoglobulins and cold agglutinins for hand arm vibration syndrome. Occup Med (Lond) 2022; 72:609-613. [PMID: 36179074 DOI: 10.1093/occmed/kqac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Hand arm vibration syndrome (HAVS) is a condition caused by hand transmitted vibration from the use of hand-held vibrating tools or workpieces. The disease affects the vascular, neurological and musculoskeletal systems. The vascular component of HAVS is a form of secondary Raynaud's phenomenon. Other causes of disease must be excluded before attributing the cause to hand transmitted vibration. AIMS To evaluate the prevalence, and utility of testing for, cryoglobulins and cold agglutinins in patients with HAVS symptoms. METHODS A retrospective cohort study of 1183 patients referred for HAVS clinical assessment at St. Michael's Hospital, Toronto, Canada, between 2014 and 2020. The standard operating procedure at the clinic includes a detailed clinical and exposure history, physical examination, objective investigations and blood tests. Data were retrieved from patient chart review and laboratory investigation results for all cases with cryoglobulin and cold agglutinin testing. RESULTS A total of 1183 patients had a serum cryoglobulin measurement. Eleven patients (1%) were positive. Seven positive results were 'low titre' (1% positive) and the other four results were 2%, 6%, 9% and 18%. The patient with a 9% positive cryoglobulin titre had previously diagnosed Sjögren's syndrome. There were no positive cold agglutinin tests in the 795 patients tested. CONCLUSIONS Routine testing for cryoglobulins and cold agglutinins in patients with HAVS symptoms is not recommended because test positivity rates are negligible. Testing may be considered if the clinical history or routine blood investigations suggest evidence of underlying cryoglobulinaemia or cold agglutinin disease.
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Seneviratne D, DeWees T, Buras M, Beuerlein W, Chumsri S, Thompson A, Thorpe C, Vallow L, Pockaj B, Cronin P, Halyard M, Vern-Gross T, McGee L, Mclaughlin S, Zot P, Vargas C. Assessing the Relationship between Residual Cancer Burden and the Tumor Immune-Microenvironment in Early-Stage, Hormone Receptor-Positive Breast Cancer Following Preoperative Radiation Therapy in MC1732 Clinical Trial. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Connor C, Yap MBH, Warwick J, Birchwood M, De Valliere N, Madan J, Melvin GA, Padfeld E, Patterson P, Petrou S, Raynes K, Stewart-Brown S, Thompson A. Correction: An online parenting intervention to prevent affective disorders in high-risk adolescents: the PIPA trial protocol. Trials 2022; 23:919. [PMID: 36316757 PMCID: PMC9620662 DOI: 10.1186/s13063-022-06870-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Ridley J, Huff M, Thompson A, Masood A, Vela E. 303 Improving Obstetrical Trauma Care Using a Standardized Protocol. Ann Emerg Med 2022. [DOI: 10.1016/j.annemergmed.2022.08.331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Hafeez S, Koh M, Jones K, El Ghzal A, D'Arcy J, Kumar P, Khoo V, Lalondrelle S, McDonald F, Thompson A, Scurr E, Sohaib A, Huddart R. Assessing Bladder Radiotherapy Response With Quantitative Diffusion-Weighted Magnetic Resonance Imaging Analysis. Clin Oncol (R Coll Radiol) 2022; 34:630-641. [PMID: 35534398 DOI: 10.1016/j.clon.2022.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/13/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Abstract
AIMS Radiotherapy with radiosensitisation offers opportunity for cure with organ preservation in muscle-invasive bladder cancer (MIBC). Treatment response assessment and follow-up are reliant on regular endoscopic evaluation of the retained bladder. In this study we aim to determine the role of diffusion-weighted magnetic resonance imaging (DWI) and apparent diffusion coefficient (ADC) analysis to assess bladder radiotherapy response. MATERIALS AND METHODS Patients with T2-T4aN0-3M0 MIBC suitable for radical radiotherapy were recruited prospectively to an ethics approved protocol. Following transurethral resection of the bladder tumour and prior to any treatment, magnetic resonance imaging including DWI was performed on a 1.5T system using b values of 0, 100, 150, 250, 500, 750 s/mm2. DWI was repeated 3 months after completing radiotherapy. Cystoscopy and tumour site biopsy were undertaken following this. The response was dichotomised into response ( RESULTS Thirty-four patients were evaluated. Response was associated with a significant increase in ΔADC mean compared with poor response at ΔADCall (0.57 × 10-3 mm2/s versus -0.01 × 10-3 mm2/s; P < 0.0001) and ΔADCb100 (0.58 × 10-3 mm2/s versus -0.10 x 10-3 mm2/s; P = 0.007). A 48.50% increase in %ΔADCall mean was seen in response compared with a 1.37% decrease in poor response (P < 0.0001). This corresponded to a %ΔADCb100 mean increase of 50.34% in response versus a 7.36% decrease for poor response (P < 0.0001). Significant area under the curve (AUC) values predictive of radiotherapy response were identified at ΔADC and %ΔADC for ADCall and ADCb100 mean, 10th, 25th, 50th, 75th and 90th percentiles (AUC >0.9, P < 0.01). ΔADCall mean of 0.16 × 10-3 mm2/s and ΔADCb100 mean 0.12 × 10-3 mm2/s predicted radiotherapy response with sensitivity/specificity/positive predictive value/negative predictive value of 92.9%/100.0%/100.0%/75.0% and 89.3%/100.0%/100.0%/66.7%, respectively. CONCLUSIONS Quantitative DWI analysis can successfully provide non-invasive assessment of bladder radiotherapy response. Multicentre validation is required before prospective testing to inform MIBC radiotherapy follow-up schedules and decision making.
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Nigrovic L, Neville D, Chapman L, Kharbanda A, Balamuth F, Levas M, Thompson A, Gerstbrein D, Buchan B. 5EMF Frequency of Tick-borne Coinfections in Children With Suspected Lyme Disease. Ann Emerg Med 2022. [DOI: 10.1016/j.annemergmed.2022.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Meyer C, Zeidan A, Beshara G, Cortes J, Tibbetts C, Tracy BM, Jayaraman Muralidharan V, Sola R, Hernandez Irizarry R, Williams K, Thompson A, Todd S, Sciarretta J, Smith R. Characterizing injury patterns and outcomes in hospitalized trauma patients with non-English Language Preferences. Am J Surg 2022; 225:948-952. [DOI: 10.1016/j.amjsurg.2022.09.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/14/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022]
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22
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Mullan K, Ferris K, Thompson A, Loughran C. ALLERGIC CONTACT DERMATITIS TO A COMMON TOPICAL ACNE TREATMENT - AN UNFAMILIAR MIMIC OF ANGIOEDEMA. THE ULSTER MEDICAL JOURNAL 2022; 91:167-169. [PMID: 36474842 PMCID: PMC9720594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Thompson A, Chavas L, Isabet T, Jamme F, Montaville P, Perez J, Pineau B, Susini J, Lassalle B, Eric L, Pierre-Damien C. New opportunities for integrated structural biology at fourth-generation synchrotron sources. ACTA CRYSTALLOGRAPHICA SECTION A FOUNDATIONS AND ADVANCES 2022. [DOI: 10.1107/s2053273322093159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Connor C, Mbh Y, Warwick J, Birchwood M, De Valliere N, Madan J, Melvin GA, Padfield E, Patterson P, Petrou S, Raynes K, Stewart-Brown S, Thompson A. An online parenting intervention to prevent affective disorders in high-risk adolescents: the PIPA trial protocol. Trials 2022; 23:655. [PMID: 35971178 PMCID: PMC9376903 DOI: 10.1186/s13063-022-06563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adolescent depression can place a young person at high risk of recurrence and a range of psychosocial and vocational impairments in adult life, highlighting the importance of early recognition and prevention. Parents/carers are well placed to notice changes in their child's emotional wellbeing which may indicate risk, and there is increasing evidence that modifiable factors exist within the family system that may help reduce the risk of depression and anxiety in an adolescent. A randomised controlled trial (RCT) of the online personalised 'Partners in Parenting' programme developed in Australia, focused on improving parenting skills, knowledge and awareness, showed that it helped reduce depressive symptoms in adolescents who had elevated symptom levels at baseline. We have adapted this programme and will conduct an RCT in a UK setting. METHODS In total, 433 family dyads (parents/carers and children aged 11-15) will be recruited through schools, social media and parenting/family groups in the UK. Following completion of screening measures of their adolescent's depressive symptoms, parents/carers of those with elevated scores will be randomised to receive either the online personalised parenting programme or a series of online factsheets about adolescent development and wellbeing. The primary objective will be to test whether the personalised parenting intervention reduces depressive symptoms in adolescents deemed at high risk, using the parent-reported Short Mood & Feelings Questionnaire. Follow-up assessments will be undertaken at 6 and 15 months and a process evaluation will examine context, implementation and impact of the intervention. An economic evaluation will also be incorporated with cost-effectiveness of the parenting intervention expressed in terms of incremental cost per quality-adjusted life year gained. DISCUSSION Half of mental health problems emerge before mid-adolescence and approximately three-quarters by mid-20s, highlighting the need for effective preventative strategies. However, few early interventions are family focused and delivered online. We aim to conduct a National Institute for Health and Care Research (NIHR) funded RCT of the online personalised 'Partners in Parenting' programme, proven effective in Australia, targeting adolescents at risk of depression to evaluate its effectiveness, cost-effectiveness and usability in a UK setting. TRIAL REGISTRATION {2A}: ISRCTN63358736 . Registered 18 September 2019.
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Papaluca T, Craigie A, McDonald L, Edwards A, Winter R, Hoang A, Pappas A, Waldron A, McCoy K, Stoove M, Doyle J, Hellard M, Holmes J, MacIsaac M, Desmond P, Iser D, Thompson A. Care navigation increases initiation of hepatitis C treatment following release from prison in a prospective randomised controlled trial: The C-LINK Study. Open Forum Infect Dis 2022; 9:ofac350. [PMID: 35949401 PMCID: PMC9356682 DOI: 10.1093/ofid/ofac350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background Prison-based hepatitis C treatment is safe and effective; however, many individuals are released untreated due to time or resource constraints. On community re-entry, individuals face a number of immediate competing priorities, and in this context, linkage to hepatitis C care is low. Interventions targeted at improving healthcare continuity after prison release have yielded positive outcomes for other health diagnoses; however, data regarding hepatitis C transitional care are limited. Methods We conducted a prospective randomized controlled trial comparing a hepatitis C care navigator intervention with standard of care for individuals released from prison with untreated hepatitis C infection. The primary outcome was prescription of hepatitis C direct-acting antivirals (DAA) within 6 months of release. Results Forty-six participants were randomized. The median age was 36 years and 59% were male. Ninety percent (n = 36 of 40) had injected drugs within 6 months before incarceration. Twenty-two were randomized to care navigation and 24 were randomized to standard of care. Individuals randomized to the intervention were more likely to commence hepatitis C DAAs within 6 months of release (73%, n = 16 of 22 vs 33% n = 8 of 24, P < .01), and the median time between re-entry and DAA prescription was significantly shorter (21 days [interquartile range {IQR}, 11–42] vs 82 days [IQR, 44–99], P = .049). Conclusions Care navigation increased hepatitis C treatment uptake among untreated individuals released from prison. Public policy should support similar models of care to promote treatment in this high-risk population. Such an approach will help achieve hepatitis C elimination as a public health threat.
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