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Boag W, Hasan A, Kim JY, Revoir M, Nichols M, Ratliff W, Gao M, Zilberstein S, Samad Z, Hoodbhoy Z, Ali M, Khan NS, Patel M, Balu S, Sendak M. The algorithm journey map: a tangible approach to implementing AI solutions in healthcare. NPJ Digit Med 2024; 7:87. [PMID: 38594344 PMCID: PMC11003994 DOI: 10.1038/s41746-024-01061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/19/2024] [Indexed: 04/11/2024] Open
Abstract
When integrating AI tools in healthcare settings, complex interactions between technologies and primary users are not always fully understood or visible. This deficient and ambiguous understanding hampers attempts by healthcare organizations to adopt AI/ML, and it also creates new challenges for researchers to identify opportunities for simplifying adoption and developing best practices for the use of AI-based solutions. Our study fills this gap by documenting the process of designing, building, and maintaining an AI solution called SepsisWatch at Duke University Health System. We conducted 20 interviews with the team of engineers and scientists that led the multi-year effort to build the tool, integrate it into practice, and maintain the solution. This "Algorithm Journey Map" enumerates all social and technical activities throughout the AI solution's procurement, development, integration, and full lifecycle management. In addition to mapping the "who?" and "what?" of the adoption of the AI tool, we also show several 'lessons learned' throughout the algorithm journey maps including modeling assumptions, stakeholder inclusion, and organizational structure. In doing so, we identify generalizable insights about how to recognize and navigate barriers to AI/ML adoption in healthcare settings. We expect that this effort will further the development of best practices for operationalizing and sustaining ethical principles-in algorithmic systems.
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Affiliation(s)
- William Boag
- Duke Institute for Health Innovation, Durham, NC, USA
| | - Alifia Hasan
- Duke Institute for Health Innovation, Durham, NC, USA
| | - Jee Young Kim
- Duke Institute for Health Innovation, Durham, NC, USA
| | - Mike Revoir
- Duke Institute for Health Innovation, Durham, NC, USA
| | | | | | - Michael Gao
- Duke Institute for Health Innovation, Durham, NC, USA
| | - Shira Zilberstein
- Duke Institute for Health Innovation, Durham, NC, USA
- Harvard University, Cambridge, MA, USA
| | | | | | | | | | - Manesh Patel
- Duke University School of Medicine, Durham, NC, USA
| | - Suresh Balu
- Duke Institute for Health Innovation, Durham, NC, USA
| | - Mark Sendak
- Duke Institute for Health Innovation, Durham, NC, USA.
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Uthappa DM, McClain MT, Nicholson BP, Park LP, Zhbannikov I, Suchindran S, Jimenez M, Constantine FJ, Nichols M, Jones DC, Hudson LL, Jaggers LB, Veldman T, Burke TW, Tsalik EL, Ginsburg GS, Woods CW. Implementation of a Prospective Index-Cluster Sampling Strategy for the Detection of Presymptomatic Viral Respiratory Infection in Undergraduate Students. Open Forum Infect Dis 2024; 11:ofae081. [PMID: 38440301 PMCID: PMC10911223 DOI: 10.1093/ofid/ofae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Background Index-cluster studies may help characterize the spread of communicable infections in the presymptomatic state. We describe a prospective index-cluster sampling strategy (ICSS) to detect presymptomatic respiratory viral illness and its implementation in a college population. Methods We enrolled an annual cohort of first-year undergraduates who completed daily electronic symptom diaries to identify index cases (ICs) with respiratory illness. Investigators then selected 5-10 potentially exposed, asymptomatic close contacts (CCs) who were geographically co-located to follow for infections. Symptoms and nasopharyngeal samples were collected for 5 days. Logistic regression model-based predictions for proportions of self-reported illness were compared graphically for the whole cohort sampling group and the CC group. Results We enrolled 1379 participants between 2009 and 2015, including 288 ICs and 882 CCs. The median number of CCs per IC was 6 (interquartile range, 3-8). Among the 882 CCs, 111 (13%) developed acute respiratory illnesses. Viral etiology testing in 246 ICs (85%) and 719 CCs (82%) identified a pathogen in 57% of ICs and 15% of CCs. Among those with detectable virus, rhinovirus was the most common (IC: 18%; CC: 6%) followed by coxsackievirus/echovirus (IC: 11%; CC: 4%). Among 106 CCs with a detected virus, only 18% had the same virus as their associated IC. Graphically, CCs did not have a higher frequency of self-reported illness relative to the whole cohort sampling group. Conclusions Establishing clusters by geographic proximity did not enrich for cases of viral transmission, suggesting that ICSS may be a less effective strategy to detect spread of respiratory infection.
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Affiliation(s)
- Diya M Uthappa
- Doctor of Medicine Program, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Micah T McClain
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | | | - Lawrence P Park
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Ilya Zhbannikov
- Bioinformatics and Clinical Analytics Team, Clinical Research Unit, Duke University Department of Medicine, Durham, North Carolina, USA
| | - Sunil Suchindran
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Monica Jimenez
- Institute for Medical Research, Durham, North Carolina, USA
| | - Florica J Constantine
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Marshall Nichols
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Daphne C Jones
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Lori L Hudson
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - L Brett Jaggers
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Timothy Veldman
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Thomas W Burke
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher W Woods
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
- Center for Infectious Disease Diagnostics and Innovation, Duke University Medical Center, Durham, North Carolina, USA
- Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
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Foote HP, Shaikh Z, Witt D, Shen T, Ratliff W, Shi H, Gao M, Nichols M, Sendak M, Balu S, Osborne K, Kumar KR, Jackson K, McCrary AW, Li JS. Development and Temporal Validation of a Machine Learning Model to Predict Clinical Deterioration. Hosp Pediatr 2024; 14:11-20. [PMID: 38053467 DOI: 10.1542/hpeds.2023-007308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
OBJECTIVES Early warning scores detecting clinical deterioration in pediatric inpatients have wide-ranging performance and use a limited number of clinical features. This study developed a machine learning model leveraging multiple static and dynamic clinical features from the electronic health record to predict the composite outcome of unplanned transfer to the ICU within 24 hours and inpatient mortality within 48 hours in hospitalized children. METHODS Using a retrospective development cohort of 17 630 encounters across 10 388 patients, 2 machine learning models (light gradient boosting machine [LGBM] and random forest) were trained on 542 features and compared with our institutional Pediatric Early Warning Score (I-PEWS). RESULTS The LGBM model significantly outperformed I-PEWS based on receiver operating characteristic curve (AUROC) for the composite outcome of ICU transfer or mortality for both internal validation and temporal validation cohorts (AUROC 0.785 95% confidence interval [0.780-0.791] vs 0.708 [0.701-0.715] for temporal validation) as well as lead-time before deterioration events (median 11 hours vs 3 hours; P = .004). However, LGBM performance as evaluated by precision recall curve was lesser in the temporal validation cohort with associated decreased positive predictive value (6% vs 29%) and increased number needed to evaluate (17 vs 3) compared with I-PEWS. CONCLUSIONS Our electronic health record based machine learning model demonstrated improved AUROC and lead-time in predicting clinical deterioration in pediatric inpatients 24 to 48 hours in advance compared with I-PEWS. Further work is needed to optimize model positive predictive value to allow for integration into clinical practice.
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Affiliation(s)
| | - Zohaib Shaikh
- Duke Institute for Health Innovation
- Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Daniel Witt
- Duke Institute for Health Innovation
- Mayo Clinic Alix School of Medicine, Rochester, Minnesota
| | - Tong Shen
- Department of Biomedical Engineering
| | | | | | | | | | | | | | - Karen Osborne
- Duke University Health System, Duke University, Durham, North Carolina
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Miller JJ, Bohn MK, Higgins V, Nichols M, Mohammed-Ali Z, Henderson T, Selvaratnam R, Sepiashvili L, Adeli K. Pediatric reference intervals for endocrine markers in healthy children and adolescents on the Liaison XL (DiaSorin) immunoassay system. Clin Biochem 2023; 120:110644. [PMID: 37673294 DOI: 10.1016/j.clinbiochem.2023.110644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023]
Abstract
OBJECTIVES Prominent physiological changes occurring throughout childhood and adolescence necessitate the consideration of age and sex in biomarker interpretation. Critical gaps exist in pediatric reference intervals (RIs) for specialized endocrine markers, despite expected influence of growth and development. The current study aimed to establish and/or verify RIs for six specialized endocrine markers on a specialized immunoassay system. METHODS Samples were collected from healthy children and adolescents (5 to <19 years) and apparently healthy outpatients (0 to <5 years) as part of the Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER). Serum samples were analysed for aldosterone, renin (plasma), thyroglobulin, anti-thyroglobulin, growth hormone, and insulin-like growth factor-1 (IGF-1) on the Liaison XL (DiaSorin) immunoassay platform. RIs (2.5th and 97.5th percentiles) were established for aldosterone, renin, thyroglobulin, anti-thyroglobulin, and growth hormone. Manufacturer-recommended pediatric RIs for IGF-1 were verified. RESULTS Age-specific RIs were established for aldosterone, renin, and thyroglobulin, while no age-specific differences were observed for anti-thyroglobulin or growth hormone. IGF-1 was the only endocrine marker studied that demonstrated significant sex-specific differences. Manufacturer-recommended IGF-1 RIs were verified for children aged 6 to <19 years, while those for children aged 0 to <6 years did not verify. CONCLUSIONS This study marks the first time that pediatric RIs for aldosterone and renin were established in the CALIPER cohort and highlights the dynamic changes that occur in water and sodium homeostasis during the first years of life. Overall, these data will assist pediatric clinical laboratories in test result interpretation and improve clinical decision-making for patients tested using Liaison immunoassays.
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Affiliation(s)
- J J Miller
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Canada
| | - M K Bohn
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Canada; CALIPER Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - V Higgins
- DynaLIFE Medical Labs, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - M Nichols
- Department of Pathology and Laboratory Medicine, Schulich Medicine and Dentistry, Western University, London, ON, Canada
| | | | - T Henderson
- CALIPER Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - R Selvaratnam
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Canada; Laboratory Medicine Program, Division of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - L Sepiashvili
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Canada; CALIPER Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - K Adeli
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Canada; CALIPER Program, The Hospital for Sick Children, Toronto, ON, Canada.
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Higgins V, Nichols M, Gao H, Maravilla N, Liang E, Su J, Xu M, Rokhforooz F, Leung F. Defining blood gas analysis stability limits across five sample types. Clin Biochem 2022; 115:107-111. [PMID: 36126745 DOI: 10.1016/j.clinbiochem.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 11/03/2022]
Abstract
Accurate reporting of blood gas samples is dependent upon following proper preanalytical sample handling requirements though there is variation for sample acceptability criteria across institutions. We examined five common sample types (arterial, venous, umbilical arterial, umbilical venous and capillary) stored at either room temperature or on crushed ice in a time series (0, 15, 30, 45, 60, 90, 180, 240 min) and applied local regulatory and/or institutional allowable performance limits to determine the need for cold preservation and/or maximum stability time for pH, pO2, pCO2, glucose, lactate, sodium, potassium, chloride, and ionized calcium where applicable in each sample type. Although changes in sample pO2 and/or lactate values were responsible, in part or in whole, for surpassing the allowable limits in nearly all sample types analyzed, this was not uniformly observed across sample types within the typical time limits that are referenced in literature. Furthermore, we demonstrated that cold preservation may not ubiquitously provide longer stability for blood gas specimens and this is dependent on the sample type and analyte in question. Nevertheless, these results demonstrate the known instability of pO2 and lactate and suggest that it may be possible to simplify the monitoring of preanalytical conditions by first evaluating pO2 and lactate in patient blood gas samples if applicable.
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Affiliation(s)
- V Higgins
- DynaLIFE Medical Labs, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - M Nichols
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada; Department of Pathology and Laboratory Medicine, London Health Sciences Centre, Victoria Hospital, London, ON, Canada
| | - H Gao
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON, Canada
| | - N Maravilla
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON, Canada
| | - E Liang
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON, Canada
| | - J Su
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON, Canada
| | - M Xu
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON, Canada
| | - F Rokhforooz
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON, Canada
| | - F Leung
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
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Sendak MP, Gao M, Ratliff W, Nichols M, Bedoya A, O'Brien C, Balu S. Looking for clinician involvement under the wrong lamp post: The need for collaboration measures. J Am Med Inform Assoc 2021; 28:2541-2542. [PMID: 34498049 DOI: 10.1093/jamia/ocab129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- Mark P Sendak
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Michael Gao
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - William Ratliff
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Marshall Nichols
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Armando Bedoya
- Department of Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Cara O'Brien
- Department of Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Suresh Balu
- Duke Institute for Health Innovation, Durham, North Carolina, USA.,Duke University School of Medicine, Durham, North Carolina, USA
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7
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Sendak MP, Gao M, Ratliff W, Whalen K, Nichols M, Futoma J, Balu S. Preliminary results of a clinical research and innovation scholarship to prepare medical students to lead innovations in health care. Healthc (Amst) 2021; 9:100555. [PMID: 33957456 DOI: 10.1016/j.hjdsi.2021.100555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 04/20/2021] [Accepted: 04/24/2021] [Indexed: 12/01/2022]
Abstract
There is consensus amongst national organizations to integrate health innovation and augmented intelligence (AI) into medical education. However, there is scant evidence to guide policymakers and medical educators working to revise curricula. This study presents academic, operational, and domain understanding outcomes for the first three cohorts of participants in a clinical research and innovation scholarship program.
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Affiliation(s)
- Mark P Sendak
- Duke Institute for Health Innovation, Durham, NC, USA.
| | - Michael Gao
- Duke Institute for Health Innovation, Durham, NC, USA
| | | | - Krista Whalen
- Duke Institute for Health Innovation, Durham, NC, USA; University of Chicago, Booth School of Business, IL, USA
| | | | - Joseph Futoma
- Harvard University, John A. Paulson School of Engineering and Applied Sciences, MA, USA; Duke University, Department of Statistics, Durham, NC, USA
| | - Suresh Balu
- Duke Institute for Health Innovation, Durham, NC, USA; Duke University School of Medicine, Durham, NC, USA
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Wyche KP, Nichols M, Parfitt H, Beckett P, Gregg DJ, Smallbone KL, Monks PS. Changes in ambient air quality and atmospheric composition and reactivity in the South East of the UK as a result of the COVID-19 lockdown. Sci Total Environ 2021; 755:142526. [PMID: 33045513 PMCID: PMC7834395 DOI: 10.1016/j.scitotenv.2020.142526] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 05/19/2023]
Abstract
The COVID-19 pandemic forced governments around the world to impose restrictions on daily life to prevent the spread of the virus. This resulted in unprecedented reductions in anthropogenic activity, and reduced emissions of certain air pollutants, namely oxides of nitrogen. The UK 'lockdown' was enforced on 23/03/2020, which led to restrictions on movement, social interaction, and 'non-essential' businesses and services. This study employed an ensemble of measurement and modelling techniques to investigate changes in air quality, atmospheric composition and boundary layer reactivity in the South East of the UK post-lockdown. The techniques employed included in-situ gas- and particle-phase monitoring within central and local authority air quality monitoring networks, remote sensing by long path Differential Optical Absorption Spectroscopy and Sentinel-5P's TROPOMI, and detailed 0-D chemical box modelling. Findings showed that de-trended NO2 concentrations decreased by an average of 14-38% when compared to the mean of the same period over the preceding 5-years. We found that de-trended particulate matter concentrations had been influenced by interregional pollution episodes, and de-trended ozone concentrations had increased across most sites, by up to 15%, such that total Ox levels were roughly preserved. 0-D chemical box model simulations showed the observed increases in ozone concentrations during lockdown under the hydrocarbon-limited ozone production regime, where total NOx decreased proportionally greater than total non-methane hydrocarbons, which led to an increase in total hydroxyl, peroxy and organic peroxy radicals. These findings suggest a more complex scenario in terms of changes in air quality owing to the COVID-19 lockdown than originally reported and provide a window into the future to illustrate potential outcomes of policy interventions seeking large-scale NOx emissions reductions without due consideration of other reactive trace species.
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Affiliation(s)
- K P Wyche
- Air Environment Research, University of Brighton, Lewes Road, Brighton BN2 4GJ, UK.
| | - M Nichols
- Hydrock Consultants Ltd, Merchants House North, Wapping Road, Bristol BS1 4RW, UK
| | - H Parfitt
- Phlorum Ltd, 12 Hunns Mere Way, Brighton BN2 6AH, UK
| | - P Beckett
- Phlorum Ltd, 12 Hunns Mere Way, Brighton BN2 6AH, UK
| | - D J Gregg
- Air Environment Research, University of Brighton, Lewes Road, Brighton BN2 4GJ, UK
| | - K L Smallbone
- Air Environment Research, University of Brighton, Lewes Road, Brighton BN2 4GJ, UK
| | - P S Monks
- Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
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Abstract
Using structured elements from Electronic Health Records (EHR), we seek to: i) build predictive models to stratify patients tested for COVID-19 by their likelihood for hospitalization, ICU admission, mechanical ventilation and inpatient mortality, and ii) identify the most important EHR-based features driving the predictions. We leveraged EHR data from the Duke University Health System tested for COVID-19 or hospitalized between March 11, 2020 and August 24, 2020, to build models to predict hospital admissions within 4 weeks. Models were also created for ICU admissions, need for mechanical ventilation and mortality following admission. Models were developed on a cohort of 86,355 patients with 112,392 outpatient COVID-19 tests or any-cause hospital admissions between March 11, 2020 and June 4, 2020. The four models considered resulted in AUROC=0.838 (CI: 0.832-0.844) and AP=0.272 (CI: 0.260-0.287) for hospital admissions, AUROC=0.847 (CI: 0.839-855) and AP=0.585 (CI: 0.565-0.603) for ICU admissions, AUROC=0.858 (CI: 0.846-0.871) and AP=0.434 (CI: 0.403-0.467) for mechanical ventilation, and AUROC=0.0.856 (CI: 0.842-0.872) and AP=0.243 (CI: 0.205-0.282) for inpatient mortality. Patient history abstracted from the EHR has the potential for being used to stratify patients tested for COVID-19 in terms of utilization and mortality. The dominant EHR features for hospital admissions and inpatient outcomes are different. For the former, age, social indicators and previous utilization are the most important predictive features. For the latter, age and physiological summaries (pulse and blood pressure) are the main drivers.
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Affiliation(s)
- Connor Davis
- Duke Institute for Health Innovation, Duke University, Durham, NC 27701, USA
| | - Michael Gao
- Duke Institute for Health Innovation, Duke University, Durham, NC 27701, USA
- Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Marshall Nichols
- Duke Institute for Health Innovation, Duke University, Durham, NC 27701, USA
| | - Ricardo Henao
- Biostatistics and Bioinformatics, Duke University, Durham, NC 27710, USA
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Nichols M, Stevenson L, Koski L, Basler C, Wise M, Whitlock L, Francois Watkins L, Friedman CR, Chen J, Tagg K, Joseph L, Caidi H, Patel K, Tolar B, Hise K, Classon A, Ceric O, Reimschuessel R, Williams IT. Detecting national human enteric disease outbreaks linked to animal contact in the United States of America. REV SCI TECH OIE 2020; 39:471-480. [PMID: 33046928 DOI: 10.20506/rst.39.2.3098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Enteric pathogens, such as non-typhoidal Salmonella, Campylobacter and Escherichia coli, can reside in the intestinal tract of many animals, including livestock, companion animals, small mammals and reptiles. Often, these animals can appear healthy; nonetheless, humans can become infected after direct or indirect contact, resulting in a substantial illness burden. An estimated 14% of the 3.2 million illnesses that occur in the United States of America (USA) each year from such enteric pathogens are attributable to animal contact. Surveillance for enteric pathogens in the USA includes the compilation and interpretation of both laboratory and epidemiologic data. However, the authors feel that a collaborative, multisectoral and transdisciplinary - or One Health - approach is needed for data collection and analysis, at every level. In addition, they suggest that the future of enteric illness surveillance lies in the development of improved technologies for pathogen detection and characterisation, such as genomic sequencing and metagenomics. In particular, using whole-genome sequencing to compare genetic sequences of enteric pathogens from humans, food, animals and the environment, can help to predict antimicrobial resistance among these pathogens, determine their genetic relatedness and identify outbreaks linked to a common source. In this paper, the authors describe three recent, multi-state human enteric illness outbreaks linked to animal contact in the USA and discuss how integrated disease surveillance was essential to outbreak detection and response. Additional datasharing between public health and animal health laboratories and epidemiologists at the local, national, regional and international level may help to improve surveillance for emerging animal and human health threats and lead to new opportunities for prevention.
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McClain MT, Constantine FJ, Nicholson BP, Nichols M, Burke TW, Henao R, Jones DC, Hudson LL, Jaggers LB, Veldman T, Mazur A, Park LP, Suchindran S, Tsalik EL, Ginsburg GS, Woods CW. A blood-based host gene expression assay for early detection of respiratory viral infection: an index-cluster prospective cohort study. Lancet Infect Dis 2020; 21:396-404. [PMID: 32979932 PMCID: PMC7515566 DOI: 10.1016/s1473-3099(20)30486-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023]
Abstract
Background Early and accurate identification of individuals with viral infections is crucial for clinical management and public health interventions. We aimed to assess the ability of transcriptomic biomarkers to identify naturally acquired respiratory viral infection before typical symptoms are present. Methods In this index-cluster study, we prospectively recruited a cohort of undergraduate students (aged 18–25 years) at Duke University (Durham, NC, USA) over a period of 5 academic years. To identify index cases, we monitored students for the entire academic year, for the presence and severity of eight symptoms of respiratory tract infection using a daily web-based survey, with symptoms rated on a scale of 0–4. Index cases were defined as individuals who reported a 6-point increase in cumulative daily symptom score. Suspected index cases were visited by study staff to confirm the presence of reported symptoms of illness and to collect biospecimen samples. We then identified clusters of close contacts of index cases (ie, individuals who lived in close proximity to index cases, close friends, and partners) who were presumed to be at increased risk of developing symptomatic respiratory tract infection while under observation. We monitored each close contact for 5 days for symptoms and viral shedding and measured transcriptomic responses at each timepoint each day using a blood-based 36-gene RT-PCR assay. Findings Between Sept 1, 2009, and April 10, 2015, we enrolled 1465 participants. Of 264 index cases with respiratory tract infection symptoms, 150 (57%) had a viral cause confirmed by RT-PCR. Of their 555 close contacts, 106 (19%) developed symptomatic respiratory tract infection with a proven viral cause during the observation window, of whom 60 (57%) had the same virus as their associated index case. Nine viruses were detected in total. The transcriptomic assay accurately predicted viral infection at the time of maximum symptom severity (mean area under the receiver operating characteristic curve [AUROC] 0·94 [95% CI 0·92–0·96]), as well as at 1 day (0·87 [95% CI 0·84–0·90]), 2 days (0·85 [0·82–0·88]), and 3 days (0·74 [0·71–0·77]) before peak illness, when symptoms were minimal or absent and 22 (62%) of 35 individuals, 25 (69%) of 36 individuals, and 24 (82%) of 29 individuals, respectively, had no detectable viral shedding. Interpretation Transcriptional biomarkers accurately predict and diagnose infection across diverse viral causes and stages of disease and thus might prove useful for guiding the administration of early effective therapy, quarantine decisions, and other clinical and public health interventions in the setting of endemic and pandemic infectious diseases. Funding US Defense Advanced Research Projects Agency.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA.
| | - Florica J Constantine
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Lori L Hudson
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - L Brett Jaggers
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mazur
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lawrence P Park
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Sunil Suchindran
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
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12
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Sendak MP, Ratliff W, Sarro D, Alderton E, Futoma J, Gao M, Nichols M, Revoir M, Yashar F, Miller C, Kester K, Sandhu S, Corey K, Brajer N, Tan C, Lin A, Brown T, Engelbosch S, Anstrom K, Elish MC, Heller K, Donohoe R, Theiling J, Poon E, Balu S, Bedoya A, O'Brien C. Real-World Integration of a Sepsis Deep Learning Technology Into Routine Clinical Care: Implementation Study. JMIR Med Inform 2020; 8:e15182. [PMID: 32673244 PMCID: PMC7391165 DOI: 10.2196/15182] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/23/2019] [Accepted: 12/31/2019] [Indexed: 01/09/2023] Open
Abstract
Background Successful integrations of machine learning into routine clinical care are exceedingly rare, and barriers to its adoption are poorly characterized in the literature. Objective This study aims to report a quality improvement effort to integrate a deep learning sepsis detection and management platform, Sepsis Watch, into routine clinical care. Methods In 2016, a multidisciplinary team consisting of statisticians, data scientists, data engineers, and clinicians was assembled by the leadership of an academic health system to radically improve the detection and treatment of sepsis. This report of the quality improvement effort follows the learning health system framework to describe the problem assessment, design, development, implementation, and evaluation plan of Sepsis Watch. Results Sepsis Watch was successfully integrated into routine clinical care and reshaped how local machine learning projects are executed. Frontline clinical staff were highly engaged in the design and development of the workflow, machine learning model, and application. Novel machine learning methods were developed to detect sepsis early, and implementation of the model required robust infrastructure. Significant investment was required to align stakeholders, develop trusting relationships, define roles and responsibilities, and to train frontline staff, leading to the establishment of 3 partnerships with internal and external research groups to evaluate Sepsis Watch. Conclusions Machine learning models are commonly developed to enhance clinical decision making, but successful integrations of machine learning into routine clinical care are rare. Although there is no playbook for integrating deep learning into clinical care, learnings from the Sepsis Watch integration can inform efforts to develop machine learning technologies at other health care delivery systems.
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Affiliation(s)
- Mark P Sendak
- Duke Institute for Health Innovation, Durham, NC, United States
| | - William Ratliff
- Duke Institute for Health Innovation, Durham, NC, United States
| | - Dina Sarro
- Duke University Hospital, Durham, NC, United States
| | | | - Joseph Futoma
- Department of Statistics, Duke University, Durham, NC, United States.,John A Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Michael Gao
- Duke Institute for Health Innovation, Durham, NC, United States
| | | | - Mike Revoir
- Duke Institute for Health Innovation, Durham, NC, United States
| | - Faraz Yashar
- Department of Statistics, Duke University, Durham, NC, United States
| | | | - Kelly Kester
- Duke University Hospital, Durham, NC, United States
| | | | - Kristin Corey
- Duke Institute for Health Innovation, Durham, NC, United States.,Duke University School of Medicine, Durham, NC, United States
| | - Nathan Brajer
- Duke Institute for Health Innovation, Durham, NC, United States.,Duke University School of Medicine, Durham, NC, United States
| | - Christelle Tan
- Duke Institute for Health Innovation, Durham, NC, United States.,Duke University School of Medicine, Durham, NC, United States
| | - Anthony Lin
- Duke Institute for Health Innovation, Durham, NC, United States.,Duke University School of Medicine, Durham, NC, United States
| | - Tres Brown
- Duke Health Technology Solutions, Durham, NC, United States
| | | | - Kevin Anstrom
- Duke Clinical Research Institute, Durham, NC, United States
| | | | - Katherine Heller
- Department of Statistics, Duke University, Durham, NC, United States.,Google, Mountain View, CA, United States
| | - Rebecca Donohoe
- Division of Emergency Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Jason Theiling
- Division of Emergency Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Eric Poon
- Duke Health Technology Solutions, Durham, NC, United States.,Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Suresh Balu
- Duke Institute for Health Innovation, Durham, NC, United States.,Duke University School of Medicine, Durham, NC, United States
| | - Armando Bedoya
- Duke Health Technology Solutions, Durham, NC, United States.,Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Cara O'Brien
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
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13
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Bedoya AD, Futoma J, Clement ME, Corey K, Brajer N, Lin A, Simons MG, Gao M, Nichols M, Balu S, Heller K, Sendak M, O’Brien C. Machine learning for early detection of sepsis: an internal and temporal validation study. JAMIA Open 2020; 3:252-260. [PMID: 32734166 PMCID: PMC7382639 DOI: 10.1093/jamiaopen/ooaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 01/16/2020] [Accepted: 03/10/2020] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVE Determine if deep learning detects sepsis earlier and more accurately than other models. To evaluate model performance using implementation-oriented metrics that simulate clinical practice. MATERIALS AND METHODS We trained internally and temporally validated a deep learning model (multi-output Gaussian process and recurrent neural network [MGP-RNN]) to detect sepsis using encounters from adult hospitalized patients at a large tertiary academic center. Sepsis was defined as the presence of 2 or more systemic inflammatory response syndrome (SIRS) criteria, a blood culture order, and at least one element of end-organ failure. The training dataset included demographics, comorbidities, vital signs, medication administrations, and labs from October 1, 2014 to December 1, 2015, while the temporal validation dataset was from March 1, 2018 to August 31, 2018. Comparisons were made to 3 machine learning methods, random forest (RF), Cox regression (CR), and penalized logistic regression (PLR), and 3 clinical scores used to detect sepsis, SIRS, quick Sequential Organ Failure Assessment (qSOFA), and National Early Warning Score (NEWS). Traditional discrimination statistics such as the C-statistic as well as metrics aligned with operational implementation were assessed. RESULTS The training set and internal validation included 42 979 encounters, while the temporal validation set included 39 786 encounters. The C-statistic for predicting sepsis within 4 h of onset was 0.88 for the MGP-RNN compared to 0.836 for RF, 0.849 for CR, 0.822 for PLR, 0.756 for SIRS, 0.619 for NEWS, and 0.481 for qSOFA. MGP-RNN detected sepsis a median of 5 h in advance. Temporal validation assessment continued to show the MGP-RNN outperform all 7 clinical risk score and machine learning comparisons. CONCLUSIONS We developed and validated a novel deep learning model to detect sepsis. Using our data elements and feature set, our modeling approach outperformed other machine learning methods and clinical scores.
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Affiliation(s)
- Armando D Bedoya
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University, Durham, North Carolina, USA
| | - Joseph Futoma
- Department of Statistics, Duke University, Durham, North Carolina, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Meredith E Clement
- Department of Medicine, Division of Infectious Diseases, Duke University, Durham, North Carolina, USA
| | - Kristin Corey
- Duke Institute for Health Innovation, Durham, North Carolina, USA
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Nathan Brajer
- Duke Institute for Health Innovation, Durham, North Carolina, USA
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Anthony Lin
- Duke Institute for Health Innovation, Durham, North Carolina, USA
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Morgan G Simons
- Duke Institute for Health Innovation, Durham, North Carolina, USA
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael Gao
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Marshall Nichols
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Suresh Balu
- Duke Institute for Health Innovation, Durham, North Carolina, USA
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Katherine Heller
- Department of Statistics, Duke University, Durham, North Carolina, USA
| | - Mark Sendak
- Duke Institute for Health Innovation, Durham, North Carolina, USA
| | - Cara O’Brien
- Department of Medicine, Durham, North Carolina, USA
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14
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Corey KM, Helmkamp J, Simons M, Curtis L, Marsolo K, Balu S, Gao M, Nichols M, Watson J, Mureebe L, Kirk AD, Sendak M. Assessing Quality of Surgical Real-World Data from an Automated Electronic Health Record Pipeline. J Am Coll Surg 2020; 230:295-305.e12. [DOI: 10.1016/j.jamcollsurg.2019.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 11/17/2022]
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15
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Brajer N, Cozzi B, Gao M, Nichols M, Revoir M, Balu S, Futoma J, Bae J, Setji N, Hernandez A, Sendak M. Prospective and External Evaluation of a Machine Learning Model to Predict In-Hospital Mortality of Adults at Time of Admission. JAMA Netw Open 2020; 3:e1920733. [PMID: 32031645 DOI: 10.1001/jamanetworkopen.2019.20733] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
IMPORTANCE The ability to accurately predict in-hospital mortality for patients at the time of admission could improve clinical and operational decision-making and outcomes. Few of the machine learning models that have been developed to predict in-hospital death are both broadly applicable to all adult patients across a health system and readily implementable. Similarly, few have been implemented, and none have been evaluated prospectively and externally validated. OBJECTIVES To prospectively and externally validate a machine learning model that predicts in-hospital mortality for all adult patients at the time of hospital admission and to design the model using commonly available electronic health record data and accessible computational methods. DESIGN, SETTING, AND PARTICIPANTS In this prognostic study, electronic health record data from a total of 43 180 hospitalizations representing 31 003 unique adult patients admitted to a quaternary academic hospital (hospital A) from October 1, 2014, to December 31, 2015, formed a training and validation cohort. The model was further validated in additional cohorts spanning from March 1, 2018, to August 31, 2018, using 16 122 hospitalizations representing 13 094 unique adult patients admitted to hospital A, 6586 hospitalizations representing 5613 unique adult patients admitted to hospital B, and 4086 hospitalizations representing 3428 unique adult patients admitted to hospital C. The model was integrated into the production electronic health record system and prospectively validated on a cohort of 5273 hospitalizations representing 4525 unique adult patients admitted to hospital A between February 14, 2019, and April 15, 2019. MAIN OUTCOMES AND MEASURES The main outcome was in-hospital mortality. Model performance was quantified using the area under the receiver operating characteristic curve and area under the precision recall curve. RESULTS A total of 75 247 hospital admissions (median [interquartile range] patient age, 59.5 [29.0] years; 45.9% involving male patients) were included in the study. The in-hospital mortality rates for the training validation; retrospective validations at hospitals A, B, and C; and prospective validation cohorts were 3.0%, 2.7%, 1.8%, 2.1%, and 1.6%, respectively. The area under the receiver operating characteristic curves were 0.87 (95% CI, 0.83-0.89), 0.85 (95% CI, 0.83-0.87), 0.89 (95% CI, 0.86-0.92), 0.84 (95% CI, 0.80-0.89), and 0.86 (95% CI, 0.83-0.90), respectively. The area under the precision recall curves were 0.29 (95% CI, 0.25-0.37), 0.17 (95% CI, 0.13-0.22), 0.22 (95% CI, 0.14-0.31), 0.13 (95% CI, 0.08-0.21), and 0.14 (95% CI, 0.09-0.21), respectively. CONCLUSIONS AND RELEVANCE Prospective and multisite retrospective evaluations of a machine learning model demonstrated good discrimination of in-hospital mortality for adult patients at the time of admission. The data elements, methods, and patient selection make the model implementable at a system level.
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Affiliation(s)
- Nathan Brajer
- Duke Institute for Health Innovation, Durham, North Carolina
- Duke University School of Medicine, Durham, North Carolina
| | - Brian Cozzi
- Duke Institute for Health Innovation, Durham, North Carolina
- Department of Statistical Science, Duke University, Durham, North Carolina
| | - Michael Gao
- Duke Institute for Health Innovation, Durham, North Carolina
| | | | - Mike Revoir
- Duke Institute for Health Innovation, Durham, North Carolina
| | - Suresh Balu
- Duke Institute for Health Innovation, Durham, North Carolina
- Duke University School of Medicine, Durham, North Carolina
| | - Joseph Futoma
- Department of Statistical Science, Duke University, Durham, North Carolina
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, Massachusetts
| | - Jonathan Bae
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Noppon Setji
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Adrian Hernandez
- Duke University School of Medicine, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Mark Sendak
- Duke Institute for Health Innovation, Durham, North Carolina
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16
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Lucas-Borja ME, Piton G, Nichols M, Castillo C, Yang Y, Zema DA. The use of check dams for soil restoration at watershed level: A century of history and perspectives. Sci Total Environ 2019; 692:37-38. [PMID: 31336299 DOI: 10.1016/j.scitotenv.2019.07.248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- M E Lucas-Borja
- Castilla La Mancha University, School of Advanced Agricultural and Forestry Engineering, Department of Agroforestry Technology and Science and Genetics, Campus Universitario s/n, C.P. 02071 Albacete, Spain.
| | - G Piton
- Univ. Grenoble Alpes, Irstea, Grenoble Center, UR ETNA, Grenoble, France
| | - M Nichols
- United States Department of Agriculture - Agricultural Research Service - Southwest Watershed Research Center, Tucson, AZ 85719, USA
| | - C Castillo
- University of Cordoba, Dept. of Rural Engineering, Campus Rabanales, Leonardo Da Vinci Building, 14071 Cordoba, Spain
| | - Y Yang
- Department of Sediment Research, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - D A Zema
- Mediterranean University of Reggio Calabria, Department AGRARIA, Reggio Calabria, Italy
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17
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Poore GD, Ko ER, Valente A, Henao R, Sumner K, Hong C, Burke TW, Nichols M, McClain MT, Huang ES, Ginsburg GS, Woods CW, Tsalik EL. A miRNA Host Response Signature Accurately Discriminates Acute Respiratory Infection Etiologies. Front Microbiol 2018; 9:2957. [PMID: 30619110 PMCID: PMC6298190 DOI: 10.3389/fmicb.2018.02957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Acute respiratory infections (ARIs) are the leading indication for antibacterial prescriptions despite a viral etiology in the majority of cases. The lack of available diagnostics to discriminate viral and bacterial etiologies contributes to this discordance. Recent efforts have focused on the host response as a source for novel diagnostic targets although none have explored the ability of host-derived microRNAs (miRNA) to discriminate between these etiologies. Methods: In this study, we compared host-derived miRNAs and mRNAs from human H3N2 influenza challenge subjects to those from patients with Streptococcus pneumoniae pneumonia. Sparse logistic regression models were used to generate miRNA signatures diagnostic of ARI etiologies. Generalized linear modeling of mRNAs to identify differentially expressed (DE) genes allowed analysis of potential miRNA:mRNA relationships. High likelihood miRNA:mRNA interactions were examined using binding target prediction and negative correlation to further explore potential changes in pathway regulation in response to infection. Results: The resultant miRNA signatures were highly accurate in discriminating ARI etiologies. Mean accuracy was 100% [88.8-100; 95% Confidence Interval (CI)] in discriminating the healthy state from S. pneumoniae pneumonia and 91.3% (72.0-98.9; 95% CI) in discriminating S. pneumoniae pneumonia from influenza infection. Subsequent differential mRNA gene expression analysis revealed alterations in regulatory networks consistent with known biology including immune cell activation and host response to viral infection. Negative correlation network analysis of miRNA:mRNA interactions revealed connections to pathways with known immunobiology such as interferon regulation and MAP kinase signaling. Conclusion: We have developed novel human host-response miRNA signatures for bacterial and viral ARI etiologies. miRNA host response signatures reveal accurate discrimination between S. pneumoniae pneumonia and influenza etiologies for ARI and integrated analyses of the host-pathogen interface are consistent with expected biology. These results highlight the differential miRNA host response to bacterial and viral etiologies of ARI, offering new opportunities to distinguish these entities.
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Affiliation(s)
- Gregory D. Poore
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Emily R. Ko
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Department of Hospital Medicine, Duke Regional Hospital, Durham, NC, United States
| | - Ashlee Valente
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Kelsey Sumner
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Christopher Hong
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, United States
- Medicine Service, Durham VA Medical Center, Durham, NC, United States
| | - Erich S. Huang
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States
- Duke Clinical and Translational Science Institute, Durham, NC, United States
| | - Geoffrey S. Ginsburg
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, United States
- Medicine Service, Durham VA Medical Center, Durham, NC, United States
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, United States
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, United States
- Emergency Medicine Service, Durham VA Health Care System, Durham, NC, United States
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18
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Alston L, Allender S, Jacobs J, Nichols M. PO471 Public Health Recommendations and the Differences In Ischaemic Heart Disease Mortality In Rural and Metropolitan Australia- the Best Case Scenario. Glob Heart 2018. [DOI: 10.1016/j.gheart.2018.09.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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19
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Gambino-Shirley K, Stevenson L, Concepción-Acevedo J, Trees E, Wagner D, Whitlock L, Roberts J, Garrett N, Van Duyne S, McAllister G, Schick B, Schlater L, Peralta V, Reporter R, Li L, Waechter H, Gomez T, Fernández Ordenes J, Ulloa S, Ragimbeau C, Mossong J, Nichols M. Flea market finds and global exports: Four multistate outbreaks of human Salmonella infections linked to small turtles, United States-2015. Zoonoses Public Health 2018; 65:560-568. [PMID: 29577654 DOI: 10.1111/zph.12466] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Indexed: 11/28/2022]
Abstract
Zoonotic transmission of Salmonella infections causes an estimated 11% of salmonellosis annually in the United States. This report describes the epidemiologic, traceback and laboratory investigations conducted in the United States as part of four multistate outbreaks of Salmonella infections linked to small turtles. Salmonella isolates indistinguishable from the outbreak strains were isolated from a total of 143 ill people in the United States, pet turtles, and pond water samples collected from turtle farm A, as well as ill people from Chile and Luxembourg. Almost half (45%) of infections occurred in children aged <5 years, underscoring the importance of the Centers for Disease Control and Prevention recommendation to keep pet turtles and other reptiles out of homes and childcare settings with young children. Although only 43% of the ill people who reported turtle exposure provided purchase information, most small turtles were purchased from flea markets or street vendors, which made it difficult to locate the vendor, trace the turtles to a farm of origin, provide education and enforce the United States federal ban on the sale and distribution of small turtles. These outbreaks highlight the importance of improving public awareness and education about the risk of Salmonella from small turtles not only in the United States but also worldwide.
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Affiliation(s)
- K Gambino-Shirley
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - L Stevenson
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - J Concepción-Acevedo
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - E Trees
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - D Wagner
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - L Whitlock
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - J Roberts
- Louisiana Department of Agriculture & Forestry, Office of Animal Health & Food Safety, Baton Rouge, LA, USA
| | - N Garrett
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S Van Duyne
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - G McAllister
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - B Schick
- Service Center 4, USDA, APHIS, Veterinary Services, Oklahoma City, OK, USA
| | - L Schlater
- Diagnostic Bacteriology Laboratory, National Veterinary Services Laboratories, Ames, IA, USA
| | - V Peralta
- California Department of Public Health, Richmond, CA, USA
| | - R Reporter
- Los Angeles County Department of Public Health, Los Angeles, CA, USA
| | - L Li
- New York City Department of Health & Mental Hygiene, Long Island City, NY, USA
| | - H Waechter
- New York City Department of Health & Mental Hygiene, Long Island City, NY, USA
| | - T Gomez
- USDA, APHIS, Veterinary Services Liaison to CDC, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - S Ulloa
- Instituto de Salud Pública de Chile, Santiago-Chile, Chile
| | - C Ragimbeau
- Laboratoire National de Santé, Dudelange, Luxembourg
| | - J Mossong
- Laboratoire National de Santé, Dudelange, Luxembourg
| | - M Nichols
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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20
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Curran KG, Heiman Marshall KE, Singh T, Doobovsky Z, Hensley J, Melius B, Whitlock L, Stevenson L, Leinbach J, Oltean H, Glover WA, Kunesh T, Lindquist S, Williams I, Nichols M. An outbreak of Escherichia coli O157:H7 infections following a dairy education school field trip in Washington state, 2015. Epidemiol Infect 2018; 146:442-449. [PMID: 29271327 PMCID: PMC9134535 DOI: 10.1017/s0950268817002862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/30/2017] [Accepted: 11/21/2017] [Indexed: 11/07/2022] Open
Abstract
On 27 April 2015, Washington health authorities identified Escherichia coli O157:H7 infections associated with dairy education school field trips held in a barn 20-24 April. Investigation objectives were to determine the magnitude of the outbreak, identify the source of infection, prevent secondary illness transmission and develop recommendations to prevent future outbreaks. Case-finding, hypothesis generating interviews, environmental site visits and a case-control study were conducted. Parents and children were interviewed regarding event activities. Odds ratios (OR) and 95% confidence intervals (CI) were computed. Environmental testing was conducted in the barn; isolates were compared to patient isolates using pulsed-field gel electrophoresis (PFGE). Sixty people were ill, 11 (18%) were hospitalised and six (10%) developed haemolytic uremic syndrome. Ill people ranged in age from <1 year to 47 years (median: 7), and 20 (33%) were female. Twenty-seven case-patients and 88 controls were enrolled in the case-control study. Among first-grade students, handwashing (i.e. soap and water, or hand sanitiser) before lunch was protective (adjusted OR 0.13; 95% CI 0.02-0.88, P = 0.04). Barn samples yielded E. coli O157:H7 with PFGE patterns indistinguishable from patient isolates. This investigation provided epidemiological, laboratory and environmental evidence for a large outbreak of E. coli O157:H7 infections from exposure to a contaminated barn. The investigation highlights the often overlooked risk of infection through exposure to animal environments as well as the importance of handwashing for disease prevention. Increased education and encouragement of infection prevention measures, such as handwashing, can prevent illness.
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Affiliation(s)
- K. G. Curran
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - T. Singh
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Z. Doobovsky
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - J. Hensley
- Whatcom County Health Department, Bellingham, WA, USA
| | - B. Melius
- Washington State Department of Health, Shoreline, WA, USA
| | - L. Whitlock
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - L. Stevenson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - J. Leinbach
- Whatcom County Health Department, Bellingham, WA, USA
| | - H. Oltean
- Washington State Department of Health, Shoreline, WA, USA
| | - W. A. Glover
- Washington State Public Health Laboratories, Shoreline, WA, USA
| | - T. Kunesh
- Whatcom County Health Department, Bellingham, WA, USA
| | - S. Lindquist
- Washington State Department of Health, Shoreline, WA, USA
| | - I. Williams
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M. Nichols
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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21
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Sweeney TE, Perumal TM, Henao R, Nichols M, Howrylak JA, Choi AM, Bermejo-Martin JF, Almansa R, Tamayo E, Davenport EE, Burnham KL, Hinds CJ, Knight JC, Woods CW, Kingsmore SF, Ginsburg GS, Wong HR, Parnell GP, Tang B, Moldawer LL, Moore FE, Omberg L, Khatri P, Tsalik EL, Mangravite LM, Langley RJ. A community approach to mortality prediction in sepsis via gene expression analysis. Nat Commun 2018; 9:694. [PMID: 29449546 PMCID: PMC5814463 DOI: 10.1038/s41467-018-03078-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/18/2018] [Indexed: 12/27/2022] Open
Abstract
Improved risk stratification and prognosis prediction in sepsis is a critical unmet need. Clinical severity scores and available assays such as blood lactate reflect global illness severity with suboptimal performance, and do not specifically reveal the underlying dysregulation of sepsis. Here, we present prognostic models for 30-day mortality generated independently by three scientific groups by using 12 discovery cohorts containing transcriptomic data collected from primarily community-onset sepsis patients. Predictive performance is validated in five cohorts of community-onset sepsis patients in which the models show summary AUROCs ranging from 0.765-0.89. Similar performance is observed in four cohorts of hospital-acquired sepsis. Combining the new gene-expression-based prognostic models with prior clinical severity scores leads to significant improvement in prediction of 30-day mortality as measured via AUROC and net reclassification improvement index These models provide an opportunity to develop molecular bedside tests that may improve risk stratification and mortality prediction in patients with sepsis.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Inflammatix Inc., Burlingame, CA, 94010, USA
| | | | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
| | - Judith A Howrylak
- Division of Pulmonary and Critical Care Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA, 17033, USA
| | - Augustine M Choi
- Department of Medicine, Cornell Medical Center, New York, NY, 10065, USA
| | | | - Raquel Almansa
- Hospital Clínico Universitario de Valladolid/IECSCYL, Valladolid, 47005, Spain
| | - Eduardo Tamayo
- Hospital Clínico Universitario de Valladolid/IECSCYL, Valladolid, 47005, Spain
| | - Emma E Davenport
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Partners Center for Personalized Genetic Medicine, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Katie L Burnham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Charles J Hinds
- William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University, London, EC1M 6BQ, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Durham Veteran's Affairs Health Care System, Durham, NC, 27705, USA
| | | | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, OH, 45223, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Grant P Parnell
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Benjamin Tang
- Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia, Penrith, NSW, 2751, Australia
- Nepean Genomic Research Group, Nepean Clinical School, University of Sydney, Penrith, NSW, 2751, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Westmead, NSW, 2145, Australia
| | - Lyle L Moldawer
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Frederick E Moore
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | | | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Durham Veteran's Affairs Health Care System, Durham, NC, 27705, USA
| | | | - Raymond J Langley
- Department of Pharmacology, University of South Alabama, Mobile, AL, 36688, USA.
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22
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Corcoran J, Kane G, Muruganandan M, Liebmann O, Leo M, Nichols M, Kummer T. 365 Detecting Pericardial Effusions: Is One View Enough? Ann Emerg Med 2017. [DOI: 10.1016/j.annemergmed.2017.07.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Orlando LA, Sperber NR, Voils C, Nichols M, Myers RA, Wu RR, Rakhra-Burris T, Levy KD, Levy M, Pollin TI, Guan Y, Horowitz CR, Ramos M, Kimmel SE, McDonough CW, Madden EB, Damschroder LJ. Developing a common framework for evaluating the implementation of genomic medicine interventions in clinical care: the IGNITE Network's Common Measures Working Group. Genet Med 2017; 20:655-663. [PMID: 28914267 PMCID: PMC5851794 DOI: 10.1038/gim.2017.144] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/20/2017] [Indexed: 12/23/2022] Open
Abstract
Purpose Implementation research provides a structure for evaluating the clinical integration of genomic medicine interventions. This paper describes the Implementing GeNomics In PracTicE (IGNITE) Network’s efforts to promote: 1) a broader understanding of genomic medicine implementation research; and 2) the sharing of knowledge generated in the network. Methods To facilitate this goal the IGNITE Network Common Measures Working Group (CMG) members adopted the Consolidated Framework for Implementation Research (CFIR) to guide their approach to: identifying constructs and measures relevant to evaluating genomic medicine as a whole, standardizing data collection across projects, and combining data in a centralized resource for cross network analyses. Results CMG identified ten high-priority CFIR constructs as important for genomic medicine. Of those, eight didn’t have standardized measurement instruments. Therefore, we developed four survey tools to address this gap. In addition, we identified seven high-priority constructs related to patients, families, and communities that did not map to CFIR constructs. Both sets of constructs were combined to create a draft genomic medicine implementation model. Conclusion We developed processes to identify constructs deemed valuable for genomic medicine implementation and codified them in a model. These resources are freely available to facilitate knowledge generation and sharing across the field.
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Affiliation(s)
- Lori A Orlando
- Department of Medicine and The Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Nina R Sperber
- Center for Health Services Research in Primary Care, Veterans Affairs Medical Center, Durham, North Carolina, USA
| | - Corrine Voils
- Center for Health Services Research in Primary Care, Veterans Affairs Medical Center, Durham, North Carolina, USA
| | - Marshall Nichols
- Department of Medicine and The Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Rachel A Myers
- Department of Medicine and The Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - R Ryanne Wu
- Department of Medicine and The Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Tejinder Rakhra-Burris
- Department of Medicine and The Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Kenneth D Levy
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Mia Levy
- Department of Medicine and the Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Toni I Pollin
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Yue Guan
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Carol R Horowitz
- Department of Population Health Sciences and Policy and The Center for Health Equity and Community Engaged Research, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michelle Ramos
- Department of Population Health Sciences and Policy and The Center for Health Equity and Community Engaged Research, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen E Kimmel
- Department of Medicine, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Ebony B Madden
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Laura J Damschroder
- Implementation Pathways, LLC, Ann Arbor, Michigan, USA.,VA Center for Clinical Management Research, Ann Arbor, Michigan, USA
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24
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Burke TW, Henao R, Soderblom E, Tsalik EL, Thompson JW, McClain MT, Nichols M, Nicholson BP, Veldman T, Lucas JE, Moseley MA, Turner RB, Lambkin-Williams R, Hero AO, Woods CW, Ginsburg GS. Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection. EBioMedicine 2017; 17:172-181. [PMID: 28238698 PMCID: PMC5360578 DOI: 10.1016/j.ebiom.2017.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 12/09/2022] Open
Abstract
Infection of respiratory mucosa with viral pathogens triggers complex immunologic events in the affected host. We sought to characterize this response through proteomic analysis of nasopharyngeal lavage in human subjects experimentally challenged with influenza A/H3N2 or human rhinovirus, and to develop targeted assays measuring peptides involved in this host response allowing classification of acute respiratory virus infection. Unbiased proteomic discovery analysis identified 3285 peptides corresponding to 438 unique proteins, and revealed that infection with H3N2 induces significant alterations in protein expression. These include proteins involved in acute inflammatory response, innate immune response, and the complement cascade. These data provide insights into the nature of the biological response to viral infection of the upper respiratory tract, and the proteins that are dysregulated by viral infection form the basis of signature that accurately classifies the infected state. Verification of this signature using targeted mass spectrometry in independent cohorts of subjects challenged with influenza or rhinovirus demonstrates that it performs with high accuracy (0.8623 AUROC, 75% TPR, 97.46% TNR). With further development as a clinical diagnostic, this signature may have utility in rapid screening for emerging infections, avoidance of inappropriate antibacterial therapy, and more rapid implementation of appropriate therapeutic and public health strategies.
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Affiliation(s)
- Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Erik Soderblom
- Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27708, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA; Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27708, USA
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA; Section for Infectious Diseases, Medicine Service, Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA
| | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA
| | | | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Joseph E Lucas
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - M Arthur Moseley
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27708, USA
| | - Ronald B Turner
- School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Alfred O Hero
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA; Section for Infectious Diseases, Medicine Service, Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA.
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
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25
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Elustondo PA, Nichols M, Negoda A, Thirumaran A, Zakharian E, Robertson GS, Pavlov EV. Mitochondrial permeability transition pore induction is linked to formation of the complex of ATPase C-subunit, polyhydroxybutyrate and inorganic polyphosphate. Cell Death Discov 2016; 2:16070. [PMID: 27924223 PMCID: PMC5137186 DOI: 10.1038/cddiscovery.2016.70] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/10/2016] [Accepted: 08/19/2016] [Indexed: 12/25/2022] Open
Abstract
Mitochondrial permeability transition pore (mPTP) opening allows free movement of ions and small molecules leading to mitochondrial membrane depolarization and ATP depletion that triggers cell death. A multi-protein complex of the mitochondrial ATP synthase has an essential role in mPTP. However, the molecular identity of the central 'pore' part of mPTP complex is not known. A highly purified fraction of mammalian mitochondria containing C-subunit of ATPase (C-subunit), calcium, inorganic polyphosphate (polyP) and polyhydroxybutyrate (PHB) forms ion channels with properties that resemble the native mPTP. We demonstrate here that amount of this channel-forming complex dramatically increases in intact mitochondria during mPTP activation. This increase is inhibited by both Cyclosporine A, an inhibitor of mPTP and Ruthenium Red, an inhibitor of the Mitochondrial Calcium Uniporter. Similar increases in the amount of complex formation occurs in areas of mouse brain damaged by ischemia-reperfusion injury. These findings suggest that calcium-induced mPTP is associated with de novo assembly of a channel comprising C-subunit, polyP and PHB.
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Affiliation(s)
- P A Elustondo
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University , Halifax, NS, B3H 4R2 Canada
| | - M Nichols
- Departments of Psychiatry and Pharmacology, Brain Repair Centre, Faculty of Medicine Dalhousie University , Halifax, NS, B3H 4R2f Canada
| | - A Negoda
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University , Halifax, NS, B3H 4R2 Canada
| | - A Thirumaran
- Departments of Psychiatry and Pharmacology, Brain Repair Centre, Faculty of Medicine Dalhousie University , Halifax, NS, B3H 4R2f Canada
| | - E Zakharian
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine , 1 Illini Drive, Peoria, IL 61605, USA
| | - G S Robertson
- Departments of Psychiatry and Pharmacology, Brain Repair Centre, Faculty of Medicine Dalhousie University , Halifax, NS, B3H 4R2f Canada
| | - E V Pavlov
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University, Halifax, NS, B3H 4R2 Canada; Department of Basic Sciences, New York University, College of Dentistry, 345 East 24th Street, New York, NY 10010, USA
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26
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McClain MT, Woods CW, Tsalik EL, Ginsburg GS, Nicholson BP, Burke T, Hudson L, Veldman T, Better O, Dobos S, Suchindran S, Nichols M, Valente A, Park L, Henao R. Host Transcriptomic Signatures for Early Diagnosis of Acute Respiratory Viral Infection in a University-Based Index-Cluster Cohort. Open Forum Infect Dis 2016. [DOI: 10.1093/ofid/ofw194.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Micah T. McClain
- Internal Medicine/Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
- Durham Veterans Affairs Medical Center, Durham, North Carolina
| | | | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | | | - Thomas Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Lori Hudson
- Duke Center for Applied Genomics and Precision Medicine, Durham, North Carolina
| | | | - Olga Better
- Durham VA Medical Center, Durham, North Carolina
| | | | - Sunil Suchindran
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Marshall Nichols
- Duke Center for Applied Genomics and Precision Medicine, Durham, North Carolina
| | - Ashlee Valente
- Duke Center for Applied Genomics and Precision Medicine, Durham, North Carolina
| | - Lawrence Park
- Infectious Diseases, Durham VA Medical Center, Durham, North Carolina
| | - Ricardo Henao
- Duke Center for Applied Genomics and Precision Medicine, Durham, North Carolina
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27
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Glen AS, Anderson D, Veltman CJ, Garvey PM, Nichols M. Wildlife detector dogs and camera traps: a comparison of techniques for detecting feral cats. New Zealand Journal of Zoology 2016. [DOI: 10.1080/03014223.2015.1103761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- AS Glen
- Landcare Research, Auckland, New Zealand
| | | | - CJ Veltman
- Department of Conservation, c/o Landcare Research, Palmerston North, New Zealand
| | - PM Garvey
- Centre for Biodiversity and Biosecurity, School of Biological Sciences, University of Auckland, New Zealand
| | - M Nichols
- Centre for Wildlife Management and Conservation, Lincoln University, Canterbury, New Zealand
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28
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Tsalik EL, Henao R, Nichols M, Burke T, Ko ER, McClain MT, Hudson LL, Mazur A, Freeman DH, Veldman T, Langley RJ, Quackenbush EB, Glickman SW, Cairns CB, Jaehne AK, Rivers EP, Otero RM, Zaas AK, Kingsmore SF, Lucas J, Fowler VG, Carin L, Ginsburg GS, Woods CW. Host gene expression classifiers diagnose acute respiratory illness etiology. Sci Transl Med 2016; 8:322ra11. [PMID: 26791949 PMCID: PMC4905578 DOI: 10.1126/scitranslmed.aad6873] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Acute respiratory infections caused by bacterial or viral pathogens are among the most common reasons for seeking medical care. Despite improvements in pathogen-based diagnostics, most patients receive inappropriate antibiotics. Host response biomarkers offer an alternative diagnostic approach to direct antimicrobial use. This observational cohort study determined whether host gene expression patterns discriminate noninfectious from infectious illness and bacterial from viral causes of acute respiratory infection in the acute care setting. Peripheral whole blood gene expression from 273 subjects with community-onset acute respiratory infection (ARI) or noninfectious illness, as well as 44 healthy controls, was measured using microarrays. Sparse logistic regression was used to develop classifiers for bacterial ARI (71 probes), viral ARI (33 probes), or a noninfectious cause of illness (26 probes). Overall accuracy was 87% (238 of 273 concordant with clinical adjudication), which was more accurate than procalcitonin (78%, P < 0.03) and three published classifiers of bacterial versus viral infection (78 to 83%). The classifiers developed here externally validated in five publicly available data sets (AUC, 0.90 to 0.99). A sixth publicly available data set included 25 patients with co-identification of bacterial and viral pathogens. Applying the ARI classifiers defined four distinct groups: a host response to bacterial ARI, viral ARI, coinfection, and neither a bacterial nor a viral response. These findings create an opportunity to develop and use host gene expression classifiers as diagnostic platforms to combat inappropriate antibiotic use and emerging antibiotic resistance.
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Affiliation(s)
- Ephraim L. Tsalik
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Emergency Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC 27710
| | - Ricardo Henao
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Department of Electrical & Computer Engineering, Duke University, Durham, NC 27708
| | - Marshall Nichols
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
| | - Thomas Burke
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
| | - Emily R. Ko
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Duke Regional Hospital, Department of Medicine, Duke University, Durham, NC 27710
| | - Micah T. McClain
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC 27710
- Section for Infectious Diseases, Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705
| | - Lori L. Hudson
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
| | - Anna Mazur
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
| | - Debra H. Freeman
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC 27710
| | - Tim Veldman
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
| | - Raymond J. Langley
- Immunology Division, Lovelace Respiratory Research Institute, Albuquerque, NM 87108
| | - Eugenia B. Quackenbush
- Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Seth W. Glickman
- Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Charles B. Cairns
- Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599
- Department of Emergency Medicine, University of Arizona Health Sciences Center, Tucson, AZ 85724
| | - Anja K. Jaehne
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, MI 48202
| | - Emanuel P. Rivers
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, MI 48202
| | - Ronny M. Otero
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, MI 48202
| | - Aimee K. Zaas
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC 27710
| | - Stephen F. Kingsmore
- Rady Pediatric Genomic and Systems Medicine Institute, Rady Children’s Hospital, San Diego, CA 92123
| | - Joseph Lucas
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
| | - Vance G. Fowler
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC 27710
| | - Lawrence Carin
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Department of Electrical & Computer Engineering, Duke University, Durham, NC 27708
| | - Geoffrey S. Ginsburg
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
| | - Christopher W. Woods
- Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC 27710
- Section for Infectious Diseases, Medicine Service, Durham Veteran’s Affairs Medical Center, Durham, NC 27705
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29
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McClain MT, Nicholson BP, Park LP, Liu TY, Hero AO, Tsalik EL, Zaas AK, Veldman T, Hudson LL, Lambkin-Williams R, Gilbert A, Burke T, Nichols M, Ginsburg GS, Woods CW. A Genomic Signature of Influenza Infection Shows Potential for Presymptomatic Detection, Guiding Early Therapy, and Monitoring Clinical Responses. Open Forum Infect Dis 2016; 3:ofw007. [PMID: 26933666 PMCID: PMC4771939 DOI: 10.1093/ofid/ofw007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/14/2016] [Indexed: 11/25/2022] Open
Abstract
Early, presymptomatic intervention with oseltamivir (corresponding to the onset of a published host-based genomic signature of influenza infection) resulted in decreased overall influenza symptoms (aggregate symptom scores of 23.5 vs 46.3), more rapid resolution of clinical disease (20 hours earlier), reduced viral shedding (total median tissue culture infectious dose [TCID50] 7.4 vs 9.7), and significantly reduced expression of several inflammatory cytokines (interferon-γ, tumor necrosis factor-α, interleukin-6, and others). The host genomic response to influenza infection is robust and may provide the means for early detection, more timely therapeutic interventions, a meaningful reduction in clinical disease, and an effective molecular means to track response to therapy.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University; Durham Veterans Affairs Medical Center; Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | | | - Lawrence P Park
- Durham Veterans Affairs Medical Center; Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Tzu-Yu Liu
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley; National Center for Genome Resources, Santa Fe, New Mexico
| | - Alfred O Hero
- Center for Computational Biology and Bioinformatics , University of Michigan , Ann Arbor
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University; Durham Veterans Affairs Medical Center; Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Aimee K Zaas
- Center for Applied Genomics and Precision Medicine, Duke University; Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine , Duke University
| | - Lori L Hudson
- Center for Applied Genomics and Precision Medicine , Duke University
| | | | | | - Thomas Burke
- Center for Applied Genomics and Precision Medicine , Duke University
| | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine , Duke University
| | | | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University; Durham Veterans Affairs Medical Center; Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
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Nichols M, Zhang J, Polster BM, Elustondo PA, Thirumaran A, Pavlov EV, Robertson GS. Synergistic neuroprotection by epicatechin and quercetin: Activation of convergent mitochondrial signaling pathways. Neuroscience 2015; 308:75-94. [PMID: 26363153 DOI: 10.1016/j.neuroscience.2015.09.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/25/2015] [Accepted: 09/03/2015] [Indexed: 01/08/2023]
Abstract
In view of evidence that increased consumption of epicatechin (E) and quercetin (Q) may reduce the risk of stroke, we have measured the effects of combining E and Q on mitochondrial function and neuronal survival following oxygen-glucose deprivation (OGD). Relative to mouse cortical neuron cultures pretreated (24h) with either E or Q (0.1-10μM), E+Q synergistically attenuated OGD-induced neuronal cell death. E, Q and E+Q (0.3μM) increased spare respiratory capacity but only E+Q (0.3μM) preserved this crucial parameter of neuronal mitochondrial function after OGD. These improvements were accompanied by corresponding increases in cyclic AMP response element binding protein (CREB) phosphorylation and the expression of CREB-target genes that promote neuronal survival (Bcl-2) and mitochondrial biogenesis (PGC-1α). Consistent with these findings, E+Q (0.1 and 1.0μM) elevated mitochondrial gene expression (MT-ND2 and MT-ATP6) to a greater extent than E or Q after OGD. Q (0.3-3.0μM), but not E (3.0μM), elevated cytosolic calcium (Ca(2+)) spikes and the mitochondrial membrane potential. Conversely, E and E+Q (0.1 and 0.3μM), but not Q (0.1 and 0.3μM), activated protein kinase B (Akt). Nitric oxide synthase (NOS) inhibition with L-N(G)-nitroarginine methyl ester (1.0μM) blocked neuroprotection by E (0.3μM) or Q (1.0μM). Oral administration of E+Q (75mg/kg; once daily for 5days) reduced hypoxic-ischemic brain injury. These findings suggest E and Q activate Akt- and Ca(2+)-mediated signaling pathways that converge on NOS and CREB resulting in synergistic improvements in neuronal mitochondrial performance which confer profound protection against ischemic injury.
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Affiliation(s)
- M Nichols
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Brain Repair Centre, Faculty of Medicine, Dalhousie University, Life Sciences Research Institute, 1348 Summer Street, P.O. Box 15000, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - J Zhang
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Brain Repair Centre, Faculty of Medicine, Dalhousie University, Life Sciences Research Institute, 1348 Summer Street, P.O. Box 15000, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - B M Polster
- Department of Anesthesiology, Center for Shock Trauma and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - P A Elustondo
- Department of Physiology and Biophysics, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - A Thirumaran
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Brain Repair Centre, Faculty of Medicine, Dalhousie University, Life Sciences Research Institute, 1348 Summer Street, P.O. Box 15000, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - E V Pavlov
- Department of Basic Sciences, College of Dentistry, New York University, 345 East 24th Street, New York, NY 10010, USA.
| | - G S Robertson
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Psychiatry, 5909 Veterans' Memorial Lane, 8th Floor Abbie J. Lane Memorial Building, QEII Health Sciences Centre, Halifax, Nova Scotia B3H 2E2, Canada.
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Hoare E, Millar L, Fuller-Tyskiewicz M, Skouteris H, Nichols M, Jacka F, Swinburn B, Chikwendu C, Allender S. Associations between obesogenic risk and depressive symptomatology in Australian adolescents: a cross-sectional study. Eur J Public Health 2014. [DOI: 10.1093/eurpub/cku161.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Baldwin M, Nichols M, Edelman A, Jensen J. Early versus standard interval postpartum IUD placement. Contraception 2014. [DOI: 10.1016/j.contraception.2014.05.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Benjamin AM, Nichols M, Burke TW, Ginsburg GS, Lucas JE. Comparing reference-based RNA-Seq mapping methods for non-human primate data. BMC Genomics 2014; 15:570. [PMID: 25001289 PMCID: PMC4112205 DOI: 10.1186/1471-2164-15-570] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 06/25/2014] [Indexed: 12/03/2022] Open
Abstract
Background The application of next-generation sequencing technology to gene expression quantification analysis, namely, RNA-Sequencing, has transformed the way in which gene expression studies are conducted and analyzed. These advances are of particular interest to researchers studying organisms with missing or incomplete genomes, as the need for knowledge of sequence information is overcome. De novo assembly methods have gained widespread acceptance in the RNA-Seq community for organisms with no true reference genome or transcriptome. While such methods have tremendous utility, computational cost is still a significant challenge for organisms with large and complex genomes. Results In this manuscript, we present a comparison of four reference-based mapping methods for non-human primate data. We utilize TopHat2 and GSNAP for mapping to the human genome, and Bowtie2 and Stampy for mapping to the human genome and transcriptome for a total of six mapping approaches. For each of these methods, we explore mapping rates and locations, number of detected genes, correlations between computed expression values, and the utility of the resulting data for differential expression analysis. Conclusions We show that reference-based mapping methods indeed have utility in RNA-Seq analysis of mammalian data with no true reference, and the details of mapping methods should be carefully considered when doing so. Critical algorithm features include short seed sequences, the allowance of mismatches, and the allowance of gapped alignments in addition to splice junction gaps. Such features facilitate sensitive alignment of non-human primate RNA-Seq data to a human reference. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-570) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ashlee M Benjamin
- Center for Applied Genomics, Department of Medicine, Duke University, Durham, North Carolina, USA.
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Nichols M, Takacs N, Ragsdale J, Levenson D, Marquez C, Roache K, Tarr CL. Listeria monocytogenesInfection in a Sugar Glider (Petaurus breviceps) - New Mexico, 2011. Zoonoses Public Health 2014; 62:254-7. [DOI: 10.1111/zph.12134] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Indexed: 01/15/2023]
Affiliation(s)
- M. Nichols
- New Mexico Department of Health; Epidemiology and Response Division; Santa Fe NM USA
| | - N. Takacs
- New Mexico Department of Agriculture; Veterinary Diagnostic Services; Albuquerque NM USA
| | - J. Ragsdale
- New Mexico Department of Agriculture; Veterinary Diagnostic Services; Albuquerque NM USA
| | - D. Levenson
- Southwest Veterinary Medical Center; Corrales NM USA
| | - C. Marquez
- New Mexico Department of Health; Scientific Laboratory Division; Albuquerque NM USA
| | - K. Roache
- Enteric Diseases Laboratory Branch; Centers for Disease Control and Prevention; Atlanta GA USA
| | - C. L. Tarr
- Enteric Diseases Laboratory Branch; Centers for Disease Control and Prevention; Atlanta GA USA
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Hoare E, Millar L, Fuller-Tyszkiewicz M, Skouteris H, Nichols M, Jacka F, Swinburn B, Chikwendu C, Allender S. Associations between obesogenic risk and depressive symptomatology in Australian adolescents: a cross-sectional study. J Epidemiol Community Health 2014; 68:767-72. [PMID: 24711573 DOI: 10.1136/jech-2013-203562] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Depression and obesity are significant health concerns currently facing adolescents worldwide. This paper investigates the associations between obesity and related risk behaviours and depressive symptomatology in an Australian adolescent population. METHODS Data from the Australian Capital Territory It's Your Move project, an Australian community-based intervention project were used. In 2012, 800 students (440 females, 360 males) aged 11-14 years (M=13.11 years, SD=0.62 years), from 6 secondary schools were weighed and measured and completed a questionnaire which included physical activity, sedentary behaviour and dietary intake. Weight status was defined by WHO criteria. A cut-off score ≥10 on the Short Mood and Feelings Questionnaire indicated symptomatic depression. Logistic regression was used to test associations. RESULTS After controlling for potential confounders, results showed significantly higher odds of depressive symptomatology in males (OR=1.22, p<0.05) and females (OR=1.12, p<0.05) who exceeded guidelines for daily screen-time leisure sedentary activities. Higher odds of depressive symptoms were seen in females who consumed greater amounts of sweet drink (OR=1.18, p<0.05), compared to lower female consumers of sweet drinks, and males who were overweight/obese also had greater odds of depressive symptoms (OR=1.83, p<0.05) compared to male normal weight adolescents. CONCLUSIONS This study demonstrates the associations between obesogenic risks and depression in adolescents. Further research should explore the direction of these associations and identify common determinants of obesity and depression. Mental health outcomes need to be included in the rationale and evaluation for diet and activity interventions.
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Affiliation(s)
- E Hoare
- Faculty of Health, School of Health and Social Development, Deakin University, Geelong, Victoria, Australia
| | - L Millar
- Faculty of Health, School of Health and Social Development, Deakin University, Geelong, Victoria, Australia Faculty of Health, WHO Collaborating Centre for Obesity Prevention, Population Health Strategic Research Centre, Deakin University, Geelong, Victoria, Australia Faculty of Health, School of Psychology, Deakin University, Geelong, Victoria, Australia Faculty of Health, School of Medicine, Deakin University, Geelong, Victoria, Australia Population Nutrition and Global Health, University of Auckland, Auckland, New Zealand Health Directorate, Australia Capital Territory Government, Canberra, Australian Capital Territory, Australia
| | - M Fuller-Tyszkiewicz
- Faculty of Health, WHO Collaborating Centre for Obesity Prevention, Population Health Strategic Research Centre, Deakin University, Geelong, Victoria, Australia Faculty of Health, School of Psychology, Deakin University, Geelong, Victoria, Australia
| | - H Skouteris
- Faculty of Health, School of Psychology, Deakin University, Geelong, Victoria, Australia
| | - M Nichols
- Faculty of Health, WHO Collaborating Centre for Obesity Prevention, Population Health Strategic Research Centre, Deakin University, Geelong, Victoria, Australia
| | - F Jacka
- Faculty of Health, School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - B Swinburn
- Faculty of Health, WHO Collaborating Centre for Obesity Prevention, Population Health Strategic Research Centre, Deakin University, Geelong, Victoria, Australia Population Nutrition and Global Health, University of Auckland, Auckland, New Zealand
| | - C Chikwendu
- Health Directorate, Australia Capital Territory Government, Canberra, Australian Capital Territory, Australia
| | - S Allender
- Faculty of Health, WHO Collaborating Centre for Obesity Prevention, Population Health Strategic Research Centre, Deakin University, Geelong, Victoria, Australia
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Patil E, Orme-Evans K, Beckley E, Bergander L, Nichols M, Bednarek P. Outcomes of first-trimester surgical abortion with immediate iud insertion compared between advance practice clinician and physician providers. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Renner R, Nichols M, Edelman A, Jensen J, Bednarek P. REFINING THE PARACERVICAL BLOCK TECHNIQUE FOR PAIN CONTROL IN FIRST TRIMESTER SURGICAL ABORTION. Contraception 2013. [DOI: 10.1016/j.contraception.2013.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Jensen BW, Nichols M, Allender S, de Silva-Sanigorski A, Millar L, Kremer P, Lacy K, Swinburn B. Inconsistent associations between sweet drink intake and 2-year change in BMI among Victorian children and adolescents. Pediatr Obes 2013; 8:271-83. [PMID: 23785025 DOI: 10.1111/j.2047-6310.2013.00174.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/29/2013] [Accepted: 04/08/2013] [Indexed: 11/28/2022]
Abstract
OBJECTIVE The aim of this study was to examine whether baseline (T1) or 2-year change in sweet drink intake in children and adolescents was associated with age- and gender-standardized body mass index (BMIz) at time two (T2), 2 years later. METHODS Data on 1465 children and adolescents from the comparison groups of two quasi-experimental intervention studies from Victoria, Australia were analysed. At two time points between 2003 and 2008 (mean interval: 2.2 years) height and weight were measured and sweet drink consumption (soft drink and fruit juice/cordial) was assessed. RESULTS No association was observed between T1 sweet drink intake and BMIz at T2 among children or adolescents. Children from higher socioeconomic status families who reported an increased intake of sweet drinks at T2 compared with T1 had higher mean BMIz at T2 (β: 0.13, P = 0.05). There was no evidence of a dose-response relationship between sweet drink intake and BMIz. In supplementary analyses, we observed that more frequent usual consumption of fruit juice/cordial was associated with a higher BMIz at T2 among children. CONCLUSION This study showed limited evidence of an association between sweet drink intake and BMIz. However, the association is complex and may be confounded by both dietary and activity behaviours.
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Affiliation(s)
- B W Jensen
- Research Unit for Dietary Studies, Institute of Preventive Medicine, Bispebjerg; Frederiksberg Hospitals, Copenhagen University Hospital, Frederiksberg, Denmark.
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Millar L, Nichols M, Allender S, Swinburn B. Using the SysANGELO approach to develop action plans for systems change. Obes Res Clin Pract 2012. [DOI: 10.1016/j.orcp.2012.08.085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Allender S, Swinburn B, Foulkes C, Waters E, Gill T, Coveney J, Nichols M, Armstrong R, Sanigorski ADS, Pettman T, Millar L. A new platform for increasing capacity in community based intervention: CO-OPS Mark II. Obes Res Clin Pract 2012. [DOI: 10.1016/j.orcp.2012.08.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Allender S, Terry J, Nichols M, Millar L, Hayward J, Nicholls L, Chikwendu C, Swinburn B. Developing systems maps for interventions in the prevention of obesity in adolescents. Obes Res Clin Pract 2012. [DOI: 10.1016/j.orcp.2012.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Wate J, Snowdon W, Millar L, Nichols M, Mavoa H, Kama A, Goundar R, Swinburn B. Adolescents’ dietary patterns in Fiji and relationship with standardized BMI. Obes Res Clin Pract 2012. [DOI: 10.1016/j.orcp.2012.08.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Brooks B, Williams N, Bravver E, Desai U, Wright A, Sanjak M, Bockenek W, Nichols M, Russo P, Smith N, Blythe A, Lindblom S, Pacicco T, Smrcina J, Ward A, Langford V, Fischer M, O'Neill M, Henderson A, Holsten S, Frumkin L, Walgren K, Corey Q, Oplinger H, Price M, Fortier C. Development and Deployment of Performance Measures Based on American Academy of Neurology (AAN) Amyotrophic Lateral Sclerosis (ALS) Guidelines To Assess Provider Implementation, Patient Acceptance and Patient Adherence of Evidence-Based Recommendations at the Carolinas Neuromuscular/ALS-MDA Center: Accountability Assessment According to the Joint Commission (TJC) Disease Specific Certification (DSC) Protocol - The First Year (P01.106). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.p01.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Zahos K, Mehendale S, Ward AJ, Smith EJ, Nichols M. The 15° face-changing acetabular component for treatment of osteoarthritis secondary to developmental dysplasia of the hip. J Bone Joint Surg Br 2012; 94:163-166. [PMID: 22323679 DOI: 10.1302/0301-620x.94b2.27348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report the use of a 15° face-changing cementless acetabular component in patients undergoing total hip replacement for osteoarthritis secondary to developmental dysplasia of the hip. The rationale behind its design and the surgical technique used for its implantation are described. It is distinctly different from a standard cementless hemispherical component as it is designed to position the bearing surface at the optimal angle of inclination, that is, < 45°, while maximising the cover of the component by host bone.
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Affiliation(s)
- K Zahos
- Southmead Hospital, Avon Orthopaedic Centre, North Bristol NHS Trust, Westbury-on-Trym, Bristol BS10 5NB, UK
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Andvik S, Soto C, Jackson A, Pye R, Nichols M, Fulde G, Granger E. CPR-ECMO for In-Hospital Cardiac Arrest: What are the Predictive Factors for Survival and are We Missing Anyone? Heart Lung Circ 2012. [DOI: 10.1016/j.hlc.2012.05.582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Nichols M, Reynolds R, Swinburn B, Allender S. A pilot survey of community-based obesity prevention projects in Australia. Obes Res Clin Pract 2011. [DOI: 10.1016/j.orcp.2011.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Botha R, Jensen J, Nichols M, Bednarek P, Renner R, Edelman A. A randomized controlled trial of sevoflurane during anesthesia for second-trimester abortion: does it alter bleeding? Contraception 2011. [DOI: 10.1016/j.contraception.2011.05.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Fallows R, McCoy K, Hertza J, Klosson E, Estes B, Stroescu I, Salinas C, Stringer A, Aronson S, MacAllister W, Spurgin A, Morriss M, Glasier P, Stavinoha P, Houshyarnejad A, Jacobus J, Norman M, Peery S, Mattingly M, Pennuto T, Anderson-Hanley C, Miele A, Dunnam M, Edwards M, O'Bryant S, Johnson L, Barber R, Inscore A, Kegel J, Kozlovsky A, Tarantino B, Goldberg A, Herrera-Pino J, Jubiz-Bassi N, Rashid K, Noniyeva Y, Vo K, Stephens V, Gomez R, Sanders C, Kovacs M, Walton B, Schmitter-Edgecombe M, Schmitter-Edgecombe M, Parsey C, Cook D, Woods S, Weinborn M, Velnoweth A, Rooney A, Bucks R, Adalio C, White S, Blair J, Barber B, Marcy S, Barber B, Marcy S, Boseck J, McCormick C, Davis A, Berry K, Koehn E, Tiberi N, Gelder B, Brooks B, Sherman E, Garcia M, Robillard R, Gunner J, Miele A, Lynch J, McCaffrey R, Hamilton J, Froming K, Nemeth D, Steger A, Lebby P, Harrison J, Mounoutoua A, Preiss J, Brimager A, Gates E, Chang J, Cisneros H, Long J, Petrauskas V, Casey J, Picard E, Long J, Petrauskas V, Casey J, Picard E, Miele A, Gunner J, Lynch J, McCaffrey R, Rodriguez M, Fonseca F, Golden C, Davis J, Wall J, DeRight J, Jorgensen R, Lewandowski L, Ortigue S, Etherton J, Axelrod B, Green C, Snead H, Semrud-Clikeman M, Kirk J, Connery A, Kirkwood M, Hanson ML, Fazio R, Denney R, Myers W, McGuire A, Tree H, Waldron-Perrine B, Goldenring Fine J, Spencer R, Pangilinan P, Bieliauskas L, Na S, Waldron-Perrine B, Tree H, Spencer R, Pangilinan P, Bieliauskas L, Peck C, Bledsoe J, Schroeder R, Boatwright B, Heinrichs R, Baade L, Rohling M, Hill B, Ploetz D, Womble M, Shenesey J, Schroeder R, Semrud-Clikeman M, Baade L, VonDran E, Webster B, Brockman C, Burgess A, Heinrichs R, Schroeder R, Baade L, VonDran E, Webster B, Goldenring Fine J, Brockman C, Heinrichs R, Schroeder R, Baade L, VonDran E, Webster B, Brockman C, Heinrichs R, Schroeder R, Baade L, Bledsoe J, VonDran E, Webster B, Brockman C, Heinrichs R, Schroeder R, Baade L, VonDran E, Webster B, Brockman C, Heinrichs R, Thaler N, Strauss G, White T, Gold J, Tree H, Waldron-Perrine B, Spencer R, McGuire A, Na S, Pangilinan P, Bieliauskas L, Allen D, Vincent A, Roebuck-Spencer T, Cooper D, Bowles A, Gilliland K, Watts A, Ahmed F, Miller L, Yon A, Gordon B, Bello D, Bennett T, Yon A, Gordon B, Bennett T, Wood N, Etcoff L, Thede L, Oraker J, Gibson F, Stanford L, Gray S, Vroman L, Semrud-Clikeman M, Taylor T, Seydel K, Bure-Reyes A, Stewart J, Tourgeman I, Demsky Y, Golden C, Burns W, Gray S, Burns K, Calderon C, Tourgeman I, Golden C, Neblina C, San Miguel Montes L, Allen D, Strutt A, Scott B, Strutt A, Scott B, Armstrong P, Booth C, Blackstone K, Moore D, Gouaux B, Ellis R, Atkinson J, Grant I, Brennan L, Schultheis M, Hurtig H, Weintraub D, Duda J, Moberg P, Chute D, Siderowf A, Brescian N, Gass C, Brewster R, King T, Morris R, Krawiecki N, Dinishak D, Richardson G, Estes B, Knight M, Hertza J, Fallows R, McCoy K, Garcia S, Strain G, Devlin M, Cohen R, Paul R, Crosby R, Mitchell J, Gunstad J, Hancock L, Bruce J, Roberg B, Lynch S, Hertza J, Klosson E, Varnadore E, Schiff W, Estes B, Hertza J, Varnadore E, Estes B, Kaufman R, Rinehardt E, Schoenberg M, Mattingly M, Rosado Y, Velamuri S, LeBlanc M, Pimental P, Lynch-Chee S, Broshek D, Lyons P, McKeever J, Morse C, Ang J, Leist T, Tracy J, Schultheis M, Morgan E, Woods S, Rooney A, Perry W, Grant I, Letendre S, Morse C, McKeever J, Schultheis M, Musso M, Jones G, Hill B, Proto D, Barker A, Gouvier W, Nersesova K, Drexler M, Cherkasova E, Sakamoto M, Marcotte T, Hilsabeck R, Perry W, Carlson M, Barakat F, Hassanein T, Shevchik K, McCaw W, Schrock B, Smith M, Moser D, Mills J, Epping E, Paulsen J, Somogie M, Bruce J, Bryan F, Buscher L, Tyrer J, Stabler A, Thelen J, Lovelace C, Spurgin A, Graves D, Greenberg B, Harder L, Szczebak M, Glisky M, Thelen J, Lynch S, Hancock L, Bruce J, Ukueberuwa D, Arnett P, Vahter L, Ennok M, Pall K, Gross-Paju K, Vargas G, Medaglia J, Chiaravalloti N, Zakrzewski C, Hillary F, Andrews A, Golden C, Belloni K, Nicewander J, Miller D, Johnson S, David Z, Weideman E, Lawson D, Currier E, Morton J, Robinson J, Musso M, Hill B, Barker A, Pella R, Jones G, Proto D, Gouvier W, Vertinski M, Allen D, Thaler N, Heisler D, Park B, Barney S, Kucukboyaci N, Girard H, Kemmotsu N, Cheng C, Kuperman J, McDonald C, Carroll C, Odland A, Miller L, Mittenberg W, Coalson D, Wahlstrom D, Raiford S, Holdnack J, Ennok M, Vahter L, Gardner E, Dasher N, Fowler B, Vik P, Grajewski M, Lamar M, Penney D, Davis R, Korthauer L, Libon D, Kumar A, Holdnack J, Iverson G, Chelune G, Hunter C, Zimmerman E, Klein R, Prathiba N, Hopewell A, Cooper D, Kennedy J, Long M, Moses J, Lutz J, Tiberi N, Dean R, Miller J, Axelrod B, Van Dyke S, Rapport L, Schutte C, Hanks R, Pella R, Fallows R, McCoy K, O'Rourke J, Hilsabeck R, Petrauskas V, Bowden S, Romero R, Hulkonen R, Boivin M, Bangirana P, John C, Shapiro E, Slonaker A, Pass L, Smigielski J, Biernacka J, Geske J, Hall-Flavin D, Loukianova L, Schneekloth T, Abulseoud O, Mrazek D, Karpyak V, Terranova J, Safko E, Heisler D, Thaler N, Allen D, Van Dyke S, Axelrod B, Zink D, Puente A, Ames H, LePage J, Carroll C, Knee K, Mittenberg W, Cummings T, Webbe F, Shepherd E, Marcinak J, Diaz-Santos M, Seichepine D, Sullivan K, Neargarder S, Cronin-Golomb A, Franchow E, Suchy Y, Kraybill M, Holland A, Newton S, Hinson D, Smith A, Coe M, Carmona J, Harrison D, Hyer L, Atkinson M, Dalibwala J, Yeager C, Hyer L, Scott C, Atkinson M, Yeager C, Jacobson K, Olson K, Pella R, Fallows R, McCoy K, O'Rourke J, Hilsabeck R, Rosado Y, Kaufman R, Velamuri S, Rinehardt E, Mattingly M, Sartori A, Clay O, Ovalle F, Rothman R, Crowe M, Schmid A, Horne L, Horn G, Johnson-Markve B, Gorman P, Stewart J, Bure-Reyes A, Golden C, Tam J, McAlister C, Schmitter-Edgecombe M, Wagner M, Brenner L, Walker A, Armstrong L, Inman E, Grimmett J, Gray S, Cornelius A, Hertza J, Klosson E, Varnadore E, Schiff W, Estes B, Johnson L, Willingham M, Restrepo L, Bolanos J, Patel F, Golden C, Rice J, Dougherty M, Golden C, Sharma V, Martin P, Golden C, Bradley E, Dinishak D, Lockwood C, Poole J, Brickell T, Lange R, French L, Chao L, Klein S, Dunnam M, Miele A, Warner G, Donnelly K, Donnelly J, Kittleson J, Bradshaw C, Alt M, England D, Denney R, Meyers J, Evans J, Lynch-Chee S, Kennedy C, Moore J, Fedor A, Spitznagel M, Gunstad J, Ferland M, Guerrero NK, Davidson P, Collins B, Marshall S, Herrera-Pino J, Samper G, Ibarra S, Parrott D, Steffen F, Backhaus S, Karver C, Wade S, Taylor H, Brown T, Kirkwood M, Stancin T, Krishnan K, Culver C, Arenivas A, Bosworth C, Shokri-Kojori E, Diaz-Arrastia R, Marquez de la PC, Lange R, Ivins B, Marshall K, Schwab K, Parkinson G, Iverson G, Bhagwat A, French L, Lichtenstein J, Adams-Deutsch Z, Fleischer J, Goldberg K, Lichtenstein J, Adams-Deutsch Z, Fleischer J, Goldberg K, Lichtenstein J, Fleischer J, Goldberg K, Lockwood C, Ehrler M, Hull A, Bradley E, Sullivan C, Poole J, Lockwood C, Sullivan C, Hull A, Bradley E, Ehrler M, Poole J, Marcinak J, Schuster D, Al-Khalil K, Webbe F, Myers A, Ireland S, Simco E, Carroll C, Mittenberg W, Palmer E, Poole J, Bradley E, Dinishak D, Piecora K, Marcinak J, Al-Khalil K, Mroczek N, Schuster D, Snyder A, Rabinowitz A, Arnett P, Schatz P, Cameron N, Stolberg P, Hart J, Jones W, Mayfield J, Allen D, Sullivan K, Edmed S, Vanderploeg R, Silva M, Vaughan C, McGuire E, Gerst E, Fricke S, VanMeter J, Newman J, Gioia G, Vaughan C, VanMeter J, McGuire E, Gioia G, Newman J, Gerst E, Fricke S, Wahlberg A, Zelonis S, Chatterjee A, Smith S, Whipple E, Mace L, Manning K, Ang J, Schultheis M, Wilk J, Herrell R, Hoge C, Zakzanis K, Yu S, Jeffay E, Zimmer A, Webbe F, Piecora K, Schuster D, Zimmer A, Piecora K, Schuster D, Webbe F, Adler M, Holster J, Golden C, Andrews A, Schleicher-Dilks S, Golden C, Arffa S, Thornton J, Arffa S, Thornton J, Arffa S, Thornton J, Arffa S, Thornton J, Canas A, Sevadjian C, Fournier A, Miller D, Maricle D, Donders J, Larsen T, Gidley Larson J, Sheehan J, Suchy Y, Higgins K, Rolin S, Dunham K, Akeson S, Horton A, Reynolds C, Horton A, Reynolds C, Jordan L, Gonzalez S, Heaton S, McAlister C, Tam J, Schmitter-Edgecombe M, Olivier T, West S, Golden C, Prinzi L, Martin P, Robbins J, Bruzinski B, Golden C, Riccio C, Blakely A, Yoon M, Reynolds C, Robbins J, Prinzi L, Martin P, Golden C, Schleicher-Dilks S, Andrews A, Adler M, Pearlson J, Golden C, Sevadjian C, Canas A, Fournier A, Miller D, Maricle D, Sheehan J, Gidley LJ, Suchy Y, Sherman E, Carlson H, Gaxiola-Valdez I, Wei X, Beaulieu C, Hader W, Brooks B, Kirton A, Barlow K, Hrabok M, Mohamed I, Wiebe S, Smith K, Ailion A, Ivanisevic M, King T, Smith K, King T, Thorgusen S, Bowman D, Suchy Y, Walsh K, Mitchell F, Jill G, Iris P, Ross K, Madan-Swain A, Gioia G, Isquith P, Webber D, DeFilippis N, Collins M, Hill F, Weber R, Johnson A, Wiley C, Zimmerman E, Burns T, DeFilippis N, Ritchie D, Odland A, Stevens A, Mittenberg W, Hartlage L, Williams B, Weidemann E, Demakis G, Avila J, Razani J, Burkhart S, Adams W, Edwards M, O'Bryant S, Hall J, Johnson L, Grammas P, Gong G, Hargrave K, Mattevada S, Barber R, Hall J, Vo H, Johnson L, Barber R, O'Bryant S, Hill B, Davis J, O'Connor K, Musso M, Rehm-Hamilton T, Ploetz D, Rohling M, Rodriguez M, Potter E, Loewenstein D, Duara R, Golden C, Velamuri S, Rinehardt E, Schoenberg M, Mattingly M, Kaufman R, Rosado Y, Boseck J, Tiberi N, McCormick C, Davis A, Hernandez Finch M, Gelder B, Cannon M, McGregor S, Reitman D, Rey J, Scarisbrick D, Holdnack J, Iverson G, Thaler N, Bello D, Whoolery H, Etcoff L, Vekaria P, Whittington L, Nemeth D, Gremillion A, Olivier T, Amirthavasagam S, Jeffay E, Zakzanis K, Barney S, Umuhoza D, Strauss G, Knatz-Bello D, Allen D, Bolanos J, Bell J, Restrepo L, Frisch D, Golden C, Hartlage L, Williams B, Iverson G, McIntosh D, Kjernisted K, Young A, Kiely T, Tai C, Gomez R, Schatzberg A, Keller J, Rhodes E, Ajilore O, Zhang A, Kumar A, Lamar M, Ringdahl E, Sutton G, Turner A, Snyder J, Allen D, Verbiest R, Thaler N, Strauss G, Allen D, Walkenhorst E, Crowe S, August-Fedio A, Sexton J, Cummings S, Brown K, Fedio P, Grigorovich A, Fish J, Gomez M, Leach L, Lloyd H, Nichols M, Goldberg M, Novakovic-Agopian T, Chen A, Abrams G, Rossi A, Binder D, Muir J, Carlin G, Murphy M, McKim R, Fitsimmons R, D'Esposito M, Shevchik K, McCaw W, Schrock B, Vernon A, Frank R, Ona PZ, Freitag E, Weber E, Woods S, Kellogg E, Grant I, Basso M, Dyer B, Daniel M, Michael P, Fontanetta R, Martin P, Golden C, Gass C, Stripling A, Odland A, Holster J, Corsun-Ascher C, Olivier T, Golden C, Legaretta M, Vik P, Van Ness E, Fowler B, Noll K, Denney D, Wiechman A, Stephanie T, Greenberg B, Lacritz L, Padua M, Sandhu K, Moses J, Sordahl J, Anderson J, Wheaton V, Anderson J, Berggren K, Cheung D, Luber H, Loftis J, Huckans M, Bennett T, Dawson C, Soper H, Bennett T, Soper H, Carter K, Hester A, Ringe W, Spence J, Posamentier M, Hart J, Haley R, Fallows R, Pella R, McCoy K, O'Rourke J, Hilsabeck R, Fallows R, Pella R, McCoy K, O'Rourke J, Hilsabeck R, Gass C, Curiel R, Gass C, Stripling A, Odland A, Goldberg M, Lloyd H, Gremillion A, Nemeth D, Whittington L, Hu E, Vik P, Dasher N, Fowler B, Jeffay E, Zakzanis K, Jordan S, DeFilippis N, Collins M, Goetsch V, Small S, Mansoor Y, Homer-Smith E, Lockwood C, Moses J, Martin P, Odland A, Fontanetta R, Sharma V, Golden C, Odland A, Martin P, Perle J, Gass C, Simco E, Mittenberg W, Patt V, Minassian A, Perry W, Polott S, Webbe F, Mulligan K, Shaneyfelt K, Wall J, Thompson J, Tai C, Kiely T, Compono V, Trettin L, Gomez R, Schatzberg A, Keller J, Tsou J, Pearlson J, Sharma V, Tourgeman I, Golden C, Waldron-Perrine B, Tree H, Spencer R, McGuire A, Na S, Pangilinan P, Bieliauskas L, You S, Moses J, An K, Jeffay E, Zakzanis K, Biddle C, Fazio R, Willett K, Rolin S, O'Grady M, Denney R, Bresnan K, Erlanger D, Seegmiller R, Kaushik T, Brooks B, Krol A, Carlson H, Sherman E, Davis J, McHugh T, Axelrod B, Hanks R. Grand Rounds. Arch Clin Neuropsychol 2011. [DOI: 10.1093/arclin/acr056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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de Silva-Sanigorski A, Elea D, Bell C, Kremer P, Carpenter L, Nichols M, Smith M, Sharp S, Boak R, Swinburn B. Obesity prevention in the family day care setting: impact of the Romp & Chomp intervention on opportunities for children's physical activity and healthy eating. Child Care Health Dev 2011; 37:385-93. [PMID: 21276039 DOI: 10.1111/j.1365-2214.2010.01205.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The Romp & Chomp intervention reduced the prevalence of overweight/obesity in pre-school children in Geelong, Victoria, Australia through an intervention promoting healthy eating and active play in early childhood settings. This study aims to determine if the intervention successfully created more health promoting family day care (FDC) environments. METHODS The evaluation had a cross-sectional, quasi-experimental design with the intervention FDC service in Geelong and a comparison sample from 17 FDC services across Victoria. A 45-item questionnaire capturing nutrition- and physical activity-related aspects of the policy, socio-cultural and physical environments of the FDC service was completed by FDC care providers (in 2008) in the intervention (n= 28) and comparison (n= 223) samples. RESULTS Select results showed intervention children spent less time in screen-based activities (P= 0.03), organized active play (P < 0.001) and free inside play (P= 0.03) than comparison children. There were more rules related to healthy eating (P < 0.001), more care provider practices that supported children's positive meal experiences (P < 0.001), fewer unhealthy food items allowed (P= 0.05), higher odds of staff being trained in nutrition (P= 0.04) and physical activity (P < 0.001), lower odds of having set minimum times for outside (P < 0.001) and organized (P= 0.01) active play, and of rewarding children with food (P < 0.001). CONCLUSIONS Romp & Chomp improved the FDC service to one that discourages sedentary behaviours and promotes opportunities for children to eat nutritious foods. Ongoing investment to increase children's physical activity within the setting and improving the capacity and health literacy of care providers is required to extend and sustain the improvements.
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Affiliation(s)
- A de Silva-Sanigorski
- WHO Collaborating Centre for Obesity Prevention, Deakin University and McCaughey Centre and Melbourne School of Population Health, The University of Melbourne, Melbourne, Vic. Australia.
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Van Meter E, Lawson AB, Colabianchi N, Nichols M, Hibbert J, Porter D, Liese AD. Spatial accessibility and availability measures and statistical properties in the food environment. Spat Spatiotemporal Epidemiol 2011; 2:35-47. [PMID: 21499528 PMCID: PMC3076953 DOI: 10.1016/j.sste.2010.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Spatial accessibility is of increasing interest in the health sciences. This paper addresses the statistical use of spatial accessibility and availability indices. These measures are evaluated via an extensive simulation based on cluster models for local food outlet density. We derived Monte Carlo critical values for several statistical tests based on the indices. In particular we are interested in the ability to make inferential comparisons between different study areas where indices of accessibility and availability are to be calculated. We derive tests of mean difference as well as tests for differences in Moran's I for spatial correlation for each of the accessibility and availability indices. We also apply these new statistical tests to a data example based on two counties in South Carolina for various accessibility and availability measures calculated for food outlets, stores, and restaurants.
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Affiliation(s)
- E Van Meter
- Division of Biostatistics and Epidemiology, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA.
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