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Mennander A, Nielsen SJ, Skyttä T, Smith ML, Martinsson A, Pivodic A, Hansson EC, Jeppsson A. Cardiac surgery and long-term risk for incident cancer: A nationwide population-based study. J Thorac Cardiovasc Surg 2024:S0022-5223(24)00690-1. [PMID: 39153716 DOI: 10.1016/j.jtcvs.2024.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/03/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
OBJECTIVE Previous studies indicate an increased long-term risk for incident cancer and cancer-specific mortality in patients undergoing cardiac surgery. We compared the risk for incident cancer and cancer-specific mortality between patients and matched control subjects from the general population. METHODS All patients (n = 127,119) undergoing first-time coronary artery or heart valve surgery in Sweden during 1997-2020 were included in a population-based observational cohort study based on individual data from the SWEDEHEART registry and 4 other mandatory national registries. The patients were compared with an age-, sex-, and place of residence-matched control population (n = 415,287) using multivariable Cox proportional hazards regression models adjusted for baseline characteristics, comorbidities, and socioeconomic factors. A propensity score-matched analysis with 81,522 well-balanced pairs was also performed. RESULTS Median follow-up was 9.2 (range, 0-24) years. A total of 31,361/127,119 patients (24.7%) and 102,959/415,287 control subjects (24.8%) developed cancer during follow-up. The crude event rates were 2.75 and 2.83 per 100 person-years, respectively. The adjusted risk for cancer and cancer-specific mortality was lower in patients (adjusted hazard ratios 0.86 [95% CI, 0.85-0.88] and 0.64 [95% CI, 0.62-0.65], respectively). The propensity score-matched analysis showed similar results (hazard ratios, 0.88 [95% CI, 0.86-0.90] and 0.65 [95% CI, 0.63-0.68], respectively). The results were consistent in subgroups based on sex, age, and comorbidities. CONCLUSIONS Patients who underwent cardiac surgery have lower risk for cancer and cancer-specific mortality than matched control subjects.
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Ghosh N, Lejonberg C, Czuba T, Dekkers K, Robinson R, Ärnlöv J, Melander O, Smith ML, Evans AM, Gidlöf O, Gerszten RE, Lind L, Engström G, Fall T, Smith JG. Analysis of plasma metabolomes from 11 309 subjects in five population-based cohorts. Sci Rep 2024; 14:8933. [PMID: 38637659 PMCID: PMC11026396 DOI: 10.1038/s41598-024-59388-7] [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: 01/23/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Plasma metabolomics holds potential for precision medicine, but limited information is available to compare the performance of such methods across multiple cohorts. We compared plasma metabolite profiles after an overnight fast in 11,309 participants of five population-based Swedish cohorts (50-80 years, 52% women). Metabolite profiles were uniformly generated at a core laboratory (Metabolon Inc.) with untargeted liquid chromatography mass spectrometry and a comprehensive reference library. Analysis of a second sample obtained one year later was conducted in a subset. Of 1629 detected metabolites, 1074 (66%) were detected in all cohorts while only 10% were unique to one cohort, most of which were xenobiotics or uncharacterized. The major classes were lipids (28%), xenobiotics (22%), amino acids (14%), and uncharacterized (19%). The most abundant plasma metabolome components were the major dietary fatty acids and amino acids, glucose, lactate and creatinine. Most metabolites displayed a log-normal distribution. Temporal variability was generally similar to clinical chemistry analytes but more pronounced for xenobiotics. Extensive metabolite-metabolite correlations were observed but mainly restricted to within each class. Metabolites were broadly associated with clinical factors, particularly body mass index, sex and renal function. Collectively, our findings inform the conduct and interpretation of metabolite association and precision medicine studies.
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van Wyngaardt WM, Bowan AHH, Clark EL, Keevers CMB, Smith ML, Zarifi M, Stopic A. Cross-validation of standardisation techniques at ANSTO using cobalt-60 and learnings from the presence and identification of non-gamma-ray emitting impurities. Appl Radiat Isot 2023; 201:111027. [PMID: 37748217 DOI: 10.1016/j.apradiso.2023.111027] [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: 05/30/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
To fulfil the technical requirements for accreditation to ISO/IEC 17025, the end-to-end validation of all processes associated with standardising 60Co, including gravimetric source dispensing, primary standardisation by the 4π(LS)β-γ coincidence and live-timed anti-coincidence extrapolation techniques, and impurity determination were performed and documented. Pure-beta-emitting impurities in a 60Co stock solution were identified. The impact of such impurities on measurement by liquid scintillation counting and comparison in the ESIR are discussed. A fresh 60Co source was produced, standardised, and compared using the SIR.
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Smith ML, Sergi Z, Mignogna KM, Rodriguez NE, Tatom Z, MacLeod L, Choi KB, Philip V, Miles MF. Identification of Genetic and Genomic Influences on Progressive Ethanol Consumption in Diversity Outbred Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.554349. [PMID: 37745421 PMCID: PMC10515943 DOI: 10.1101/2023.09.15.554349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Genetic factors play a significant role in the risk for development of alcohol use disorder (AUD). Using 3-bottle choice intermittent access ethanol (IEA), we have employed the Diversity Outbred (DO) mouse panel as a model of alcohol use disorder in a genetically diverse population. Through use of gene expression network analysis techniques, in combination with expression quantitative trait loci (eQTL) mapping, we have completed an extensive analysis of the influence of genetic background on gene expression changes in the prefrontal cortex (PFC). This approach revealed that, in DO mice, genes whose expression was significantly disrupted by intermittent ethanol in the PFC also tended to be those whose expression correlated to intake. This finding is in contrast to previous studies of both mice and nonhuman primates. Importantly, these analyses identified genes involved in myelination in the PFC as significantly disrupted by IEA, correlated to ethanol intake, and having significant eQTLs. Genes that code for canonical components of the myelin sheath, such as Mbp, also emerged as key drivers of the gene expression response to intermittent ethanol drinking. Several regulators of myelination were also key drivers of gene expression, and had significant QTLs, indicating that genetic background may play an important role in regulation of brain myelination. These findings underscore the importance of disruption of normal myelination in the PFC in response to prolonged ethanol exposure, that genetic variation plays an important role in this response, and that this interaction between genetics and myelin disruption in the presence of ethanol may underlie previously observed behavioral changes under intermittent access ethanol drinking such as escalation of consumption.
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Heranudin, Smith ML, van Wyngaardt WM, Guatelli S, Li E, Rosenfeld A. Characterisation of a well-type NaI(Tl) detector by means of a Monte Carlo simulation for radionuclide metrology application. Appl Radiat Isot 2021; 176:109889. [PMID: 34375816 DOI: 10.1016/j.apradiso.2021.109889] [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: 01/31/2021] [Revised: 07/14/2021] [Accepted: 08/02/2021] [Indexed: 11/29/2022]
Abstract
A well-type NaI(Tl) detector was modelled and characterised by means of a Monte Carlo simulation, as part of a project to develop a 4πβ (Plastic Scintillator)-4πγ instrument to be used for the primary standardisation of radionuclides at ANSTO. The simulation based on GEANT4 was used to characterise the 4πγ detector in terms of potential dead layer/inactive materials, full energy peak efficiency, coincidence-summing correction, and energy resolution. An excellent agreement was obtained between the simulation results and the experimental measurements.
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Kung L, Savage RM, da Silva EB, Polukis SA, Smith ML, Johnson ACB, Miller MA. The effects of air stress during storage and low packing density on the fermentation and aerobic stability of corn silage inoculated with Lactobacillus buchneri 40788. J Dairy Sci 2021; 104:4206-4222. [PMID: 33612226 DOI: 10.3168/jds.2020-19746] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023]
Abstract
We determined if a microbial inoculant could improve the fermentation and aerobic stability of corn silage subjected to various challenges during storage that included an air stress challenge and low packing density. In Experiment 1, whole-plant corn was untreated (CTR) or treated (INO, Lactobacillus buchneri 40788 and Pediococcus pentosaceus 12455. Five individually replicated 7.5-L silos, at a density of 240 kg of dry matter (DM)/m3, for each treatment were kept sealed (NAS) for 19 wk, air stressed early (ES, 3 h/wk for wk 1-9), or air stressed late during storage (LS, 3 h/wk for wk 10-19). Inoculation increased the number of agar-culturable lactic acid bacteria regardless of air stress status, but it did not affect the relative abundance of Lactobacillus. Early, but not late air stress, resulted in silages with a higher relative abundance of Acetobacter when compared with NAS. Silages treated with INO had greater concentrations of acetic acid than CTR. Numbers of yeasts were lowest for INO regardless of air stress and CTR-LS had the most yeasts among all treatments. Silages that were not air stressed had a higher relative abundance of Candida tropicalis than air stressed silages. Monascus purpureus was detected in ES and LS but not in NAS, and its relative abundance was numerically higher in CTR-ES than in INO-ES and statistically higher in CTR-LS compared with INO-LS. Early air stress numerically reduced aerobic stability compared with NAS, and there was a statistical tendency for lower stability in LS compared with NAS. Inoculation improved aerobic stability regardless of when the air stress occurred. In Experiment 2, corn silage was prepared with the same primary treatments of CTR and INO but was packed at a low (LD; 180 kg of DM/m3) or a normal (ND; 240 kg of DM/m3) density and sealed (NAS) or air stressed (AS; 24 h on d 28, 42, and 89) for 92 d of storage. The concentration of acetic acid was greater in INO compared with CTR and in AS compared with NAS. Numbers of yeasts were lower in NAS compared with AS regardless of inoculation and they were lower in INO-AS compared with CTR-AS. Treatment with INO improved aerobic stability but the improvement was better in NAS versus AS and better in ND versus LD. Overall, our experiments corroborate past findings showing that INO markedly improves the aerobic stability of corn silage but they are the first to show that improvement can be sustained even when the silage was exposed to regular air stresses and when packed at a low density.
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Bergeron CD, John JM, Sribhashyam M, Odonkor G, Oloruntoba O, Merianos AL, Horel S, Smith ML. County-Level Characteristics Driving Malnutrition Death Rates among Older Adults in Texas. J Nutr Health Aging 2021; 25:862-868. [PMID: 34409963 PMCID: PMC8013203 DOI: 10.1007/s12603-021-1626-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVES This study aims to identify older adult malnutrition in Texas, examine county-level characteristics associated with crude malnutrition death rates, and describe assets and opportunities available to address and improve malnutrition among the older population. DESIGN Secondary data analysis using the Centers for Disease Control and Prevention's WONDER online database, the U.S. Census 2014-2018 American Community Survey, and the U.S. Department of Agriculture's Food Access Research Atlas data. SETTING All 254 counties in the state of Texas. PARTICIPANTS Individuals aged 65 years and older. MEASUREMENT The dependent variable was the proportion of county-level malnutrition crude death rates. Independent variables included Health Provider Shortage Area designations, rurality, poverty status, food access, age, race, ethnicity, and education. RESULTS The overall malnutrition crude death rate in Texas was 65.6 deaths per 100,000 older Texans, ranging from 0 to 414.46 deaths per 100,000 depending on the county. Higher malnutrition crude death rates were associated with non-metropolitan counties (P=0.018), lower education (P=0.047), greater household poverty (P=0.010), and low food access (P<0.001). CONCLUSION Socioeconomic disadvantages at the county-level appear to be one of the root causes of malnutrition crude death rates in Texas.
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Pimpalwar N, Czuba T, Smith ML, Nilsson J, Gidlöf O, Smith JG. Methods for isolation and transcriptional profiling of individual cells from the human heart. Heliyon 2020; 6:e05810. [PMID: 33426328 PMCID: PMC7779736 DOI: 10.1016/j.heliyon.2020.e05810] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 11/12/2020] [Accepted: 12/18/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Global transcriptional profiling of individual cells represents a powerful approach to systematically survey contributions from cell-specific molecular phenotypes to human disease states but requires tissue-specific protocols. Here we sought to comprehensively evaluate protocols for single cell isolation and transcriptional profiling from heart tissue, focusing particularly on frozen tissue which is necessary for study of human hearts at scale. METHODS AND RESULTS Using flow cytometry and high-content screening, we found that enzymatic dissociation of fresh murine heart tissue resulted in a sufficient yield of intact cells while for frozen murine or human heart resulted in low-quality cell suspensions across a range of protocols. These findings were consistent across enzymatic digestion protocols and whether samples were snap-frozen or treated with RNA-stabilizing agents before freezing. In contrast, we show that isolation of cardiac nuclei from frozen hearts results in a high yield of intact nuclei, and leverage expression arrays to show that nuclear transcriptomes reliably represent the cytoplasmic and whole-cell transcriptomes of the major cardiac cell types. Furthermore, coupling of nuclear isolation to PCM1-gated flow cytometry facilitated specific cardiomyocyte depletion, expanding resolution of the cardiac transcriptome beyond bulk tissue transcriptomes which were most strongly correlated with PCM1+ transcriptomes (r = 0.8). We applied these methods to generate a transcriptional catalogue of human cardiac cells by droplet-based RNA-sequencing of 8,460 nuclei from which cellular identities were inferred. Reproducibility of identified clusters was confirmed in an independent biopsy (4,760 additional PCM1- nuclei) from the same human heart. CONCLUSION Our results confirm the validity of single-nucleus but not single-cell isolation for transcriptional profiling of individual cells from frozen heart tissue, and establishes PCM1-gating as an efficient tool for cardiomyocyte depletion. In addition, our results provide a perspective of cell types inferred from single-nucleus transcriptomes that are present in an adult human heart.
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da Silva EB, Smith ML, Savage RM, Polukis SA, Drouin P, Kung L. Effects of Lactobacillus hilgardii 4785 and Lactobacillus buchneri 40788 on the bacterial community, fermentation and aerobic stability of high-moisture corn silage. J Appl Microbiol 2020; 130:1481-1493. [PMID: 33040472 DOI: 10.1111/jam.14892] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022]
Abstract
AIMS To evaluate the capacity of Lactobacillus hilgardii and Lactobacillus buchneri on modifying the bacterial community and improving fermentation and aerobic stability of high-moisture corn (HMC). METHODS AND RESULTS High-moisture corn was untreated (CTR), treated with L. hilgardii (LH) or L. buchneri (LB) at 600 000 CFU per gram fresh weight, or with L. hilgardii and L. buchneri at 300 000 CFU per gram fresh weight each (LHLB), and stored for 10, 30 or 92 days. Compared to CTR, inoculated silages had higher Lactobacillaceae relative abundance, lower yeasts numbers and higher aerobic stability. Treatment with LHLB resulted in a higher acetic acid concentration than LH and higher 1,2 propanediol concentration than LB, such differences were numerically greater at 10 and 30 days but statistically greater at 92 days. At 10 days, all inoculated silages were more stable than CTR, but LHLB was even more stable than LB or LH. CONCLUSIONS The combination of L. hilgardii and L. buchneri had a synergistic effect on yeast inhibition, leading to greater improvements in aerobic stability as early as 10 days after ensiling. SIGNIFICANCE AND IMPACT OF THE STUDY Lactobacillus hilgardii, especially in combination with L. buchneri, can improve the aerobic stability of HMC after a very short period of ensiling.
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Wells QS, Gupta DK, Smith JG, Collins SP, Storrow AB, Ferguson J, Smith ML, Pulley JM, Collier S, Wang X, Roden DM, Gerszten RE, Wang TJ. Accelerating Biomarker Discovery Through Electronic Health Records, Automated Biobanking, and Proteomics. J Am Coll Cardiol 2020; 73:2195-2205. [PMID: 31047008 DOI: 10.1016/j.jacc.2019.01.074] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND Circulating biomarkers can facilitate diagnosis and risk stratification for complex conditions such as heart failure (HF). Newer molecular platforms can accelerate biomarker discovery, but they require significant resources for data and sample acquisition. OBJECTIVES The purpose of this study was to test a pragmatic biomarker discovery strategy integrating automated clinical biobanking with proteomics. METHODS Using the electronic health record, the authors identified patients with and without HF, retrieved their discarded plasma samples, and screened these specimens using a DNA aptamer-based proteomic platform (1,129 proteins). Candidate biomarkers were validated in 3 different prospective cohorts. RESULTS In an automated manner, plasma samples from 1,315 patients (31% with HF) were collected. Proteomic analysis of a 96-patient subset identified 9 candidate biomarkers (p < 4.42 × 10-5). Two proteins, angiopoietin-2 and thrombospondin-2, were associated with HF in 3 separate validation cohorts. In an emergency department-based registry of 852 dyspneic patients, the 2 biomarkers improved discrimination of acute HF compared with a clinical score (p < 0.0001) or clinical score plus B-type natriuretic peptide (p = 0.02). In a community-based cohort (n = 768), both biomarkers predicted incident HF independent of traditional risk factors and N-terminal pro-B-type natriuretic peptide (hazard ratio per SD increment: 1.35 [95% confidence interval: 1.14 to 1.61; p = 0.0007] for angiopoietin-2, and 1.37 [95% confidence interval: 1.06 to 1.79; p = 0.02] for thrombospondin-2). Among 30 advanced HF patients, concentrations of both biomarkers declined (80% to 84%) following cardiac transplant (p < 0.001 for both). CONCLUSIONS A novel strategy integrating electronic health records, discarded clinical specimens, and proteomics identified 2 biomarkers that robustly predict HF across diverse clinical settings. This approach could accelerate biomarker discovery for many diseases.
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van Wyngaardt WM, Tobin SM, Lee S, Smith ML, Jackson TW, Ilter J, Howe B, Sarbutt A. Primary standardisation of technetium-99m by liquid scintillation coincidence counting. Appl Radiat Isot 2020; 156:108935. [PMID: 31675614 DOI: 10.1016/j.apradiso.2019.108935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/26/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022]
Abstract
Technetium-99m was standardised by the 4π(LS)ce-γ coincidence extrapolation method. Sensitivity of the 4π(LS) channel to two types of radiation, namely conversion electrons and γ-rays, resulted in incorrect activity values being obtained when this was not adequately accounted for. Measurements were more robust when the LS detection efficiency was optimised, and when a γ-window setting was used that monitored the combined LS efficiency for conversion electrons and γ-rays. The primary standard was internationally compared through participation in the BIPM.RI(II)-K4.Tc99m key comparison.
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Egerstedt A, Berntsson J, Smith ML, Gidlöf O, Nilsson R, Benson M, Wells QS, Celik S, Lejonberg C, Farrell L, Sinha S, Shen D, Lundgren J, Rådegran G, Ngo D, Engström G, Yang Q, Wang TJ, Gerszten RE, Smith JG. Profiling of the plasma proteome across different stages of human heart failure. Nat Commun 2019; 10:5830. [PMID: 31862877 PMCID: PMC6925199 DOI: 10.1038/s41467-019-13306-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Heart failure (HF) is a major public health problem characterized by inability of the heart to maintain sufficient output of blood. The systematic characterization of circulating proteins across different stages of HF may provide pathophysiological insights and identify therapeutic targets. Here we report application of aptamer-based proteomics to identify proteins associated with prospective HF incidence in a population-based cohort, implicating modulation of immunological, complement, coagulation, natriuretic and matrix remodeling pathways up to two decades prior to overt disease onset. We observe further divergence of these proteins from the general population in advanced HF, and regression after heart transplantation. By leveraging coronary sinus samples and transcriptomic tools, we describe likely cardiac and specific cellular origins for several of the proteins, including Nt-proBNP, thrombospondin-2, interleukin-18 receptor, gelsolin, and activated C5. Our findings provide a broad perspective on both cardiac and systemic factors associated with HF development.
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Nawani H, Smith ML, Wheeler AL, Widjaja E. Functional Connectivity Associated with Health-Related Quality of Life in Children with Focal Epilepsy. AJNR Am J Neuroradiol 2019; 40:1213-1220. [PMID: 31221633 DOI: 10.3174/ajnr.a6106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/16/2019] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Although functional connectivity has been linked to cognitive function in epilepsy, its relationship with physical, psychological, or social dysfunction is unknown. This study aimed to assess the relationship between network architecture from resting-state fMRI and health-related quality of life in children with medically intractable focal epilepsy. MATERIALS AND METHODS Forty-seven children with nonlesional focal epilepsy were included; 22 had frontal lobe epilepsy and 15 had temporal lobe epilepsy. We computed graph metrics of functional connectivity, including network segregation (clustering coefficient and modularity) and integration (characteristic path length and participation coefficient). Health-related quality of life was measured using the Quality of Life in Childhood Epilepsy questionnaire. We examined the associations between graph metrics and the Quality of Life in Childhood Epilepsy total and domains scores, with age, sex, age at seizure onset, fMRI motion, and network density as covariates. RESULTS There was a negative relationship between the clustering coefficient and total Quality of Life in Childhood Epilepsy score [t(40) = -2.0; P = .04] and social function [t(40) = -2.9; P = .005]. There was a positive association between the mean participation coefficient and total Quality of Life in Childhood Epilepsy score [t(40) = 2.2; P = .03] and cognition [t(40) = 3.8; P = .0004]. In temporal lobe epilepsy, there was a negative relationship between the clustering coefficient and total Quality of Life in Childhood Epilepsy score [t(8) = -2.8; P = .02] and social function [t(8) = -3.6; P = .0075] and between modularity and total Quality of Life in Childhood Epilepsy score [t(8) = -2.5; P = .04] and social function [t(8) = -4.4; P = .0021]. In frontal lobe epilepsy, there was no association between network segregation and integration and Quality of Life in Childhood Epilepsy total or domain scores. CONCLUSIONS Our findings indicate that there are other higher order brain functions beyond cognition, which may be linked with functional connectivity of the brain.
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Zar G, Smith JG, Smith ML, Andersson B, Nilsson J. Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation. PLoS One 2019; 14:e0217747. [PMID: 31166960 PMCID: PMC6550412 DOI: 10.1371/journal.pone.0217747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) of heart transplant recipient- and donor-derived cardiac biopsies may facilitate organ matching, graft failure prediction, and immunotolerance research. The objective of this study was to determine the feasibility of WGS based on formalin-fixed paraffin-embedded endomyocardial biopsies. METHODS AND RESULTS The study included serial donor- and recipient samples from patients who had undergone heart transplantation at Skane University Hospital, Lund, Sweden, between 1988 and 2009. DNA extraction and WGS were conducted. Additional WGS sequencing quality metrics and coverage were obtained with the Genome Analysis Toolkit (GATK). 455 endomyocardial samples from 37 heart transplant recipients were acquired from routine rejection monitoring and stored as formalin-fixed paraffin-embedded samples. They were analyzed after 3-26 years of storage. DNA was extracted from 114 samples and WGS was run on 85 samples. DNA extraction yielded 313 ng (IQR 96-601) for all samples. A coverage of 11.3x (IQR 9.0-15.9) was recorded for all WGS samples. Three samples stored for > 25 years yielded a coverage of > 25x. Data were generated for 1.7 billion reads per sample (IQR 1.4-2.7). A Transition/Transversion (TiTv) ratio of 2.09 ± 0.05 was calculated for all WGS samples. No associations were found among storage time, DNA yield, or sequencing quality metrics. CONCLUSIONS The present study demonstrated the feasibility of whole-genome sequencing based on endomyocardial biopsies. This process could enable large-scale retrospective genomic studies using stored histopathological samples.
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Vollmer Dahlke DJ, Smith ML, Han G, Ory MG, Cohen E. Abstract P6-14-03: Metastatic breast cancer alliance's patient education and access to trials: Perceptions and actions. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p6-14-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Those living with metastatic breast cancer (MBC) have distinct and shifting concerns in regard to education and decision making in considering clinical trials as a treatment option. Clinical trials designs, are becoming increasingly complex, and many patients have concerns for biomarker requirements Aims/Research Questions
· What is the status of MBCA advocacy members' and partners' digital information, education and access to metastatic breast cancer trials?
· What plans do MBCA members/partners have for the next 6-18 months to educate and inform their constituents for the 2018 rollout of BreastCancerTrials.org's (BCT)Metastatic Trial Search (MTS) and Metastatic Trial Talk (MTT) and other trial matching systems?
· What are the top 5 barriers regarding trial enrollment?
· What are best practices for MBC trial education?
Research Methodology and Design
A comprehensive analysis was conducted comprising both secondary and primary research to inform these specific aims. Secondary research was conducted using previous capture of MBCA online digital resources and strengthened to include additional research on MBCA members and partners online resources including pages specifically devoted to clinical trials and metastatic clinical trials.
Mixed methods approaches include:
1) An assessment of MBCA members' and partners' digital media presence regarding MBC trials using a standardized form and rating system, and an analysis of MBCA members 2017 use of MTS using BCT secondary data;
2) Structured, recorded interviews with selected MBCA members/ partners, sharing the results of the assessments and querying them regarding their future plans and perceived barriers; and
3) Mixed methods analyses of the interview recordings using DeDoose to assess and articulate key trends and perceptions.
Statistical Methods
Simple frequency percentages and means were used in the assessment rankings of the MBCA members. DeDoose was used to provide mixed method analyses of the MBCA member and partner interviews. Results
Analysis of the MBCA members and partners websites and digital media showed that, increasingly, both groups use the full variety of digital media to educate their constituents regarding MBC clinical trials. The 13 MBCA advocacy members providing online access to BreastCancerTrials' MTS in 2017 provided 97% of the traffic to the MTS trial matching service. System types accessing the MTS widget were 57.3% desktops, 28.6% mobile devices and 14% tablets. Table 1 shows assessment totals of 5 categories of the 13 MBCA advocacy group members' websites using MTS as compared to the 19 MBCA members not using the widget. Table 2 shows the 2017 usage of BCT's MTS with 97% of the page views coming from MBCA members.
Table 1.Assessment Ratings of MBCA Advocacy Partners on Metastatic Trial Education/AccessAwareness of Trials (e.g. explains trial Phases)Knowledge SharingInterest in Metastatic Breast CancerAction Potential for clinical trial access or enrollmentTotal (0-100)13 MBCA Advocate Members with MTS widget22.1523.0024.3124.1593.6219 MBCA Members without MTS widget13.2113.9513.5311.9552.16
Table 2.2017 Use Of Metastatic Trial SearchBCT's Metastatic Trial Search (MTS) Results2017Annual Page views33,360Unique Sessions14,295Show Trials8,100Show Trials by month675Average Time on Site (minutes)3:34Total Engagement Events5,006
Citation Format: Vollmer Dahlke DJ, Smith ML, Han G, Ory MG, Cohen E. Metastatic breast cancer alliance's patient education and access to trials: Perceptions and actions [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-14-03.
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Washington TR, Hilliard TS, Mingo CA, Hall RK, Smith ML, Lea JI. ORGANIZATIONAL READINESS TO IMPLEMENT HEALTH PROMOTION PROGRAMS IN HEALTHCARE. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.1493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Law N, Smith ML, Widjaja E. Thalamocortical Connections and Executive Function in Pediatric Temporal and Frontal Lobe Epilepsy. AJNR Am J Neuroradiol 2018; 39:1523-1529. [PMID: 29880477 DOI: 10.3174/ajnr.a5691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 04/11/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Largely accepted in the literature is the role the interconnections between the thalamus and cortex play in generalized epilepsy. However, thalamocortical involvement is less understood in focal epilepsy in terms of the effect of seizures on thalamocortical circuitry in the developing brain and subsequent cognitive outcome. We investigated thalamocortical pathway microstructure in pediatric frontal lobe epilepsy and temporal lobe epilepsy and examined the associations between pathway microstructure and measures of executive function. MATERIALS AND METHODS We examined thalamocortical connections in 24 children with frontal lobe epilepsy, 17 patients with temporal lobe epilepsy, and 25 healthy children using DTI. We investigated several executive function measures in patients and controls, which were distilled into latent executive function components to compare among groups, and the associations between measures of thalamocortical microstructure and executive function. RESULTS We found no differences in thalamocortical pathway microstructure between the groups, but aspects of executive function (mental flexibility/inhibition/shifting) were impaired in the frontal lobe epilepsy group compared with controls. In patients with frontal lobe epilepsy, younger age at seizure onset and a greater number of antiepileptic drugs were associated with DTI indices indicative of damaged/less developed thalamocortical pathways. In patients with temporal lobe epilepsy, poorer performance on all measures of executive function was associated with DTI indices reflective of damaged/less developed pathways. CONCLUSIONS Our results give insight into vulnerable neural networks in pediatric focal epilepsy and suggest thalamocortical pathway damage as a potential mechanism of executive function impairment in temporal lobe epilepsy but not frontal lobe epilepsy. Identifying structure-function relations can help inform how we measure functional and cognitive/behavioral outcomes in these populations.
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Hansen MF, Smith ML, Smith LN, Abdul Jabbar K, Forbes D. Automated monitoring of dairy cow body condition, mobility and weight using a single 3D video capture device. COMPUT IND 2018; 98:14-22. [PMID: 29997403 PMCID: PMC6034442 DOI: 10.1016/j.compind.2018.02.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we propose a low-cost automated system for the unobtrusive and continuous welfare monitoring of dairy cattle on the farm. We argue that effective and regular monitoring of multiple condition traits is not currently practicable and go on to propose 3D imaging technology able to acquire differing forms of related animal condition data (body condition, lameness and weight), concurrently using a single device. Results obtained under farm conditions in continuous operation are shown to be comparable or better than manual scoring of the herd. We also consider inherent limitations of using scoring and argue that sensitivity to relative change over successive observations offers greater benefit than the use of what may be considered abstract and arbitrary scoring systems.
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van Wyngaardt WM, Smith ML, Jackson TW, Howe B, Tobin SM, Reinhard MI. Development of the Australian Standard for Germanium-68 by two Liquid Scintillation Counting methods. Appl Radiat Isot 2018; 134:79-84. [PMID: 29102160 DOI: 10.1016/j.apradiso.2017.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 09/04/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
Abstract
In response to the increasing application of 68Ge/68Ga and 68Ga in nuclear medicine, an international comparison of activity measurement of 68Ge in equilibrium with 68Ga was organised. ANSTO standardised the comparison solution by the 4π(LS)β+-γ coincidence extrapolation and TDCR efficiency calculation methods, with excellent agreement between the two results. The primary standard was transferred to the ANSTO Secondary Standard Ionisation Chamber. Internationally traceable Australian Certified Reference Materials (ACRMs) of 68Ge/68Ga can now be prepared in various measurement geometries applied in nuclear medicine.
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Frank ES, Basila D, Collyar D, Pinto D, Smith ML, Geirisch J, Lynch T, Hwang S. Abstract P5-17-04: Changing the DCIS conversation: Development of an alternative discourse by patient stakeholders in the COMET study. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p5-17-04] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The conversation about ductal carcinoma in situ (DCIS) is structured and influenced by traditional oncology values and beliefs, resulting in current standards of guideline concordant care (GCC). It is now widely known that DCIS is a heterogeneous condition requiring a tailored treatment approach based on characteristics of the specific lesion. Further, “low-risk” DCIS—defined as low grade, hormone-receptor positive condition—may be a subset with lower likelihood of progression to invasive breast cancer. Yet, most women diagnosed with any type of DCIS are encouraged to undergo the same immediate, aggressive treatments that women diagnosed with invasive breast cancer receive. Emerging evidence suggests that surgery may not increase overall survival compared to no surgery in many women diagnosed with low-risk DCIS.
The COMET (Comparison of Operative to Monitoring and Endocrine Therapy) study is a new randomized, prospective clinical trial funded by the Patient-Centered Outcomes Research Institute that aims to determine whether active surveillance is a safe and reasonable alternative to GCC for patients with low-risk DCIS. COMET also seeks to change the way patients, providers, and other key stakeholders view DCIS management options. Thus, COMET governance integrates patient collaborators into every aspect of planning and development via a Patient Leadership Team (PLT) and an independent external multi-stakeholder advisory board (SAB). The PLT is a fully integrated, yet autonomous part of the COMET study governance and is comprised of 4 patient advocates who meet independently and with COMET Principal Investigators (PIs). The SAB is a fully external and independent body of clinicians, content experts, payers, patients and patient advocates, and policymaker advisors.
To facilitate the cultural shift, the PLT developed communication materials with language and terminology that aims to communicate a diagnosis of DCIS without increasing unnecessary fear and anxiety that often accompanies a diagnosis of invasive cancer. In collaboration with study team PI's and the SAB, PLT also has developed content for a newly established website (www.DCISoptions.org), which includes patient-centered materials that aim to help newly diagnosed patients understand that a majority of DCIS is low-risk and that they have time to make informed decisions about their care.
The PLT contends that managing DCIS is as much a cultural phenomenon as a scientific one. As such, changing the conversation about DCIS between medical providers and patients is essential for generating a cultural shift in understanding the condition, correcting risk perception, and enabling improvement in patient experience. The novel approach of a stand-alone PLT that is also integrated throughout the trial's stakeholder structure ensures patient-centered involvement across all aspects of the study. The unique talents of each stakeholder group are leveraged in a unified effort to educate the DCIS community about low-risk DCIS, with the overarching goal of enabling a patient to choose the treatment approach that best reflects her risk profile and personal preferences, thus minimizing potential physical, emotional, and financial harms.
Citation Format: Frank ES, Basila D, Collyar D, Pinto D, Smith ML, Geirisch J, Lynch T, Hwang S. Changing the DCIS conversation: Development of an alternative discourse by patient stakeholders in the COMET study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-17-04.
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Patel AB, Mangold AR, Costello CM, Nagel TH, Smith ML, Hayden RE, Sekulic A. Frequent loss of inositol polyphosphate-5-phosphatase in oropharyngeal squamous cell carcinoma. J Eur Acad Dermatol Venereol 2017; 32:e36-e37. [PMID: 28696004 DOI: 10.1111/jdv.14462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Meng L, Robinson KT, Smith ML. Factors associated with sickness absence among employees with chronic conditions. Occup Med (Lond) 2017; 67:296-300. [PMID: 28339972 DOI: 10.1093/occmed/kqx028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background The growing prevalence of chronic conditions in the ageing workforce has been shown to have a negative impact in terms of optimal work performance and quality of life. It is therefore important to understand the factors associated with sickness absence due to health problems. Aims To examine the socio-demographics, health status indicators, barriers to self-care and social support associated with working adults missing work because of chronic conditions. Methods We analysed data from working adults in the USA with one or more chronic conditions who completed the National Council on Aging (NCOA) Chronic Care Survey. Analyses were performed using SPSS version 22; independent sample t-tests and chi-squared tests were used to compare sample characteristics and logistic regression was used to assess factors associated with missed work as a dichotomous outcome variable. Results Among the 250 study subjects, employees who reported poorer general health status [odd ratio (OR) = 1.62, P < 0.05], more physician visits (OR = 1.45, P < 0.01), not having enough money for their health (OR = 3.69, P < 0.01) and a higher reliance on their co-workers (OR = 1.71, P < 0.05) were significantly more likely to report sickness absence due to their chronic conditions. Conclusions To reduce absences among employees with chronic conditions, employers need to understand the importance of factors such as employee income, resources and knowledge of disease self-care. US employers should explore opportunities for employees to offset health care costs, apply appropriate time-flexible work policies and encourage employees' participation in health knowledge enhancing interventions.
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Smith ML, McGuinness J, O'Reilly MK, Nolke L, Murray JG, Jones JFX. The role of 3D printing in preoperative planning for heart transplantation in complex congenital heart disease. Ir J Med Sci 2017; 186:753-756. [PMID: 28124282 DOI: 10.1007/s11845-017-1564-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/16/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The presence of a structural cardiac defect in the setting of dextrocardia is extremely rare. Graspable models allow enhanced appreciation of aberrant structures and vascular relations, particularly in rare and complex cases. This is the first case report of the use of a replica of a patients' anatomy to plan the surgical strategy in the setting of dextrocardia. AIMS We intend to demonstrate the benefit of three-dimensional printing to enhance preoperative planning in complex congenital heart disease undergoing heart transplantation. The anomalous structures encountered include situs inversus dextrocardia, transposition of the great vessels, a single atrium and a dilated double-outlet single right ventricle. METHODS Computed Tomography acquisition was performed with the use of ECG multiphase gating technology and contrast enhancement. The structures of interest were segmented and the generated 3D mesh was exported as a stereolithographic (STL) file. The model was printed on a Z-Corp 250 binder jetting printer. Post processing techniques were used to enhance model strength. RESULTS Pre-operative 3D visualisation of the patients' anatomy allowed for a more comprehensive surgical strategy to be planned, thus reducing the intra-operative duration and cross-clamp time which are recognised to correlate with reduced patient morbidity. CONCLUSION The ongoing advances in medical image procurement and 3D processing software and printing technology will continue to enhance preoperative planning and thereby improve patient care. We demonstrate the pivotal role played by such technologies in advancing spatial comprehension of complex aberrant anatomy.
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Giardino WJ, Rodriguez ED, Smith ML, Ford MM, Galili D, Mitchell SH, Chen A, Ryabinin AE. Control of chronic excessive alcohol drinking by genetic manipulation of the Edinger-Westphal nucleus urocortin-1 neuropeptide system. Transl Psychiatry 2017; 7:e1021. [PMID: 28140406 PMCID: PMC5299395 DOI: 10.1038/tp.2016.293] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/25/2016] [Accepted: 12/15/2016] [Indexed: 11/23/2022] Open
Abstract
Midbrain neurons of the centrally projecting Edinger-Westphal nucleus (EWcp) are activated by alcohol, and enriched with stress-responsive neuropeptide modulators (including the paralog of corticotropin-releasing factor, urocortin-1). Evidence suggests that EWcp neurons promote behavioral processes for alcohol-seeking and consumption, but a definitive role for these cells remains elusive. Here we combined targeted viral manipulations and gene array profiling of EWcp neurons with mass behavioral phenotyping in C57BL/6 J mice to directly define the links between EWcp-specific urocortin-1 expression and voluntary binge alcohol intake, demonstrating a specific importance for EWcp urocortin-1 activity in escalation of alcohol intake.
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Heilman RL, Mathur A, Smith ML, Kaplan B, Reddy KS. Increasing the Use of Kidneys From Unconventional and High-Risk Deceased Donors. Am J Transplant 2016; 16:3086-3092. [PMID: 27172238 DOI: 10.1111/ajt.13867] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/19/2016] [Accepted: 05/03/2016] [Indexed: 01/25/2023]
Abstract
In this paper, we have reviewed the literature and report on kidney donors that are currently used at relatively low rates. Kidneys from donors with acute kidney injury (AKI) seem to have outcomes equivalent to those from donors without AKI, provided one can rule out significant cortical necrosis. Kidneys from donors with preexisting diabetes or hypertension may have marginally lower aggregate survival but still provide patients with a significant benefit over remaining on the wait list. The Kidney Donor Profile Index derives only an aggregate association with survival with a very modest C statistic; therefore, the data indicated that this index should not be the sole reason to discard a kidney, except perhaps in patients with extremely low estimated posttransplant survival scores. It is important to note that the Scientific Registry of Transplant Recipients models of risk adjustment should allay concerns regarding regulatory issues for observed outcomes falling below expectations. The successful utilization of kidneys from donation after cardiac death over the past decade shows how expanding our thinking can translate into more patients benefiting from transplantation. Given the growing number of patients on the wait list, broadening our approach to kidney acceptance could have an important impact on the population with end-stage renal disease. Many lives could be prolonged by carefully considering use of kidneys that are often discarded.
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