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Song J, Guha S, Li Y. Bayesian Inference for High Dimensional Cox Models with Gaussian and Diffused-Gamma Priors: A Case Study of Mortality in COVID-19 Patients Admitted to the ICU. STATISTICS IN BIOSCIENCES 2024; 16:221-249. [PMID: 38651050 PMCID: PMC11034914 DOI: 10.1007/s12561-023-09395-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 04/25/2024]
Abstract
Bayesian approaches have been utilized to address the challenge of variable selection and statistical inference in high-dimensional survival analysis. However, the discontinuity of the ℓ 0 -norm prior, including the useful spike-and-slab prior, may lead to computational and implementation challenges, potentially limiting the widespread use of Bayesian methods. The Gaussian and diffused-gamma (GD) prior has emerged as a promising alternative due to its continuous-and-differentiable ℓ 0 -norm approximation and computational efficiency in generalized linear models. In this paper, we extend the GD prior to semi-parametric Cox models by proposing a rank-based Bayesian inference procedure with the Cox partial likelihood. We develop a computationally efficient algorithm based on the iterative conditional mode (ICM) and Markov chain Monte Carlo methods for posterior inference. Our simulations demonstrate the effectiveness of the proposed method, and we apply it to an electronic health record dataset to identify risk factors associated with COVID-19 mortality in ICU patients at a regional medical center.
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Affiliation(s)
- Jiyeon Song
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Subharup Guha
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Yi Li
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
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Queipo M, Barbado J, Torres AM, Mateo J. Approaching Personalized Medicine: The Use of Machine Learning to Determine Predictors of Mortality in a Population with SARS-CoV-2 Infection. Biomedicines 2024; 12:409. [PMID: 38398012 PMCID: PMC10886784 DOI: 10.3390/biomedicines12020409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The COVID-19 pandemic demonstrated the need to develop strategies to control a new viral infection. However, the different characteristics of the health system and population of each country and hospital would require the implementation of self-systems adapted to their characteristics. The objective of this work was to determine predictors that should identify the most severe patients with COVID-19 infection. Given the poor situation of the hospitals in the first wave, the analysis of the data from that period with an accurate and fast technique can be an important contribution. In this regard, machine learning is able to objectively analyze data in hourly sets and is used in many fields. This study included 291 patients admitted to a hospital in Spain during the first three months of the pandemic. After screening seventy-one features with machine learning methods, the variables with the greatest influence on predicting mortality in this population were lymphocyte count, urea, FiO2, potassium, and serum pH. The XGB method achieved the highest accuracy, with a precision of >95%. Our study shows that the machine learning-based system can identify patterns and, thus, create a tool to help hospitals classify patients according to their severity of illness in order to optimize admission.
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Affiliation(s)
- Mónica Queipo
- Autoimmunity and Inflammation Research Group, Río Hortega University Hospital, 47012 Valladolid, Spain
- Cooperative Research Network Focused on Health Results—Advanced Therapies (RICORS TERAV), 28220 Madrid, Spain
| | - Julia Barbado
- Autoimmunity and Inflammation Research Group, Río Hortega University Hospital, 47012 Valladolid, Spain
- Cooperative Research Network Focused on Health Results—Advanced Therapies (RICORS TERAV), 28220 Madrid, Spain
- Internal Medicine, Río Hortega University Hospital, 47012 Valladolid, Spain
| | - Ana María Torres
- Medical Analysis Expert Group, Institute of Technology, University of Castilla-La Mancha, 16071 Cuenca, Spain
- Medical Analysis Expert Group, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
| | - Jorge Mateo
- Medical Analysis Expert Group, Institute of Technology, University of Castilla-La Mancha, 16071 Cuenca, Spain
- Medical Analysis Expert Group, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), 45071 Toledo, Spain
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Genovesi S, Regolisti G, Rebora P, Occhino G, Belli M, Molon G, Citerio G, Beltrame A, Maloberti A, Generali E, Giannattasio C, Epis OM, Rossetti C, Bellelli G, De Nalda AL, Capua I, Valsecchi MG. Negative prognostic impact of electrolyte disorders in patients hospitalized for Covid-19 in a large multicenter study. J Nephrol 2023; 36:621-626. [PMID: 36001295 PMCID: PMC9400003 DOI: 10.1007/s40620-022-01429-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The prognostic impact of electrolyte disorders in hospitalized COVID-19 patients is unclear. METHODS The study included all adult patients hospitalized for COVID-19 in four hospitals in Northern Italy between January 2020 and May 2021 with at least one serum potassium and sodium measurement performed within 3 days since admission. Primary outcome was in-hospital death; secondary outcome was Intensive Care Unit (ICU) admission. A cause-specific Cox proportional-hazards regression model was used for investigating the association between potassium and sodium (as either categorical or continuous variables) and mortality or admission to ICU. RESULTS Analyses included 3,418 adult hospitalized COVID-19 patients. At multivariable analysis, both hyperkalemia (Hazard Ratio, [HR] 1.833, 95% Confidence Interval [CI] 1.371-2.450) and sK above the median (K 5.1 vs 4.1 mmol/L: HR 1.523, 95% CI 1.295-1.798), and hypernatremia (HR 2.313, 95%CI 1.772-3.018) and sNa above the median (Na 149 vs 139 mmol/L: HR 1.442, 95% CI 1.234-1.686), were associated with in-hospital death, whereas hypokalemia and hyponatremia were not. Hyponatremia was associated with increased hazard of ICU admission (HR 1.884, 95%CI 1.389-2.556). CONCLUSIONS Electrolyte disorders detected at hospital admission may allow early identification of COVID-19 patients at increased risk of adverse outcomes.
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Affiliation(s)
- Simonetta Genovesi
- School of Medicine and Surgery, Nephrology Clinic, Milano-Bicocca University, Milan, Italy.
- Istituto Auxologico Italiano, IRCCS, Milan, Italy.
| | - Giuseppe Regolisti
- Clinica e Immunologia Medica, Azienda Ospedaliero-Universitaria, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Paola Rebora
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre, School of Medicine and Surgery Milano-Bicocca University, Milan, Italy
| | - Giuseppe Occhino
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre, School of Medicine and Surgery Milano-Bicocca University, Milan, Italy
| | - Michele Belli
- School of Medicine and Surgery, Nephrology Clinic, Milano-Bicocca University, Milan, Italy
| | - Giulio Molon
- Cardiology Department, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Giuseppe Citerio
- School of Medicine and Surgery, Milano-Bicocca University, Milan, Italy
- NeuroIntensive Care Unit, ASST-Monza, Monza, Italy
| | - Anna Beltrame
- Department of Infectious/Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Alessandro Maloberti
- School of Medicine and Surgery, Milano-Bicocca University, Milan, Italy
- Cardiology 4, Cardio Center, ASST GOM Niguarda Hospital, Milan, Italy
| | - Elena Generali
- Department of Biomedical Sciences, Humanitas University, Emanuele, Italy
- Internal Medicine and Hepatology Unit, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Cristina Giannattasio
- School of Medicine and Surgery, Milano-Bicocca University, Milan, Italy
- Cardiology 4, Cardio Center, ASST GOM Niguarda Hospital, Milan, Italy
| | - Oscar Massimiliano Epis
- Division of Rheumatology, Multispecialist Medical Department, Niguarda Hospital, Milan, Italy
| | - Claudio Rossetti
- Department of Training and Research, Niguarda Hospital, Milan, Italy
| | - Giuseppe Bellelli
- School of Medicine and Surgery, Milano-Bicocca University, Milan, Italy
- Acute Geriatric Unit, ASST San Gerardo Hospital, Monza, Italy
| | - Ana Lleo De Nalda
- Department of Biomedical Sciences, Humanitas University, Emanuele, Italy
- Internal Medicine and Hepatology Unit, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Ilaria Capua
- One Health Center of Excellence, University of Florida, Gainesville, FL, 32611, USA
| | - Maria Grazia Valsecchi
- Bicocca Bioinformatics Biostatistics and Bioimaging Centre, School of Medicine and Surgery Milano-Bicocca University, Milan, Italy
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Leal J, O'Grady HM, Armstrong L, Dixit D, Khawaja Z, Snedeker K, Ellison J, Erebor J, Jamieson P, Weiss A, Salcedo D, Roberts K, Wiens K, Croxen MA, Berenger BM, Pabbaraju K, Lin YC, Evans D, Conly JM. Patient and ward related risk factors in a multi-ward nosocomial outbreak of COVID-19: Outbreak investigation and matched case-control study. Antimicrob Resist Infect Control 2023; 12:21. [PMID: 36949510 PMCID: PMC10031162 DOI: 10.1186/s13756-023-01215-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND Risk factors for nosocomial COVID-19 outbreaks continue to evolve. The aim of this study was to investigate a multi-ward nosocomial outbreak of COVID-19 between 1st September and 15th November 2020, occurring in a setting without vaccination for any healthcare workers or patients. METHODS Outbreak report and retrospective, matched case-control study using incidence density sampling in three cardiac wards in an 1100-bed tertiary teaching hospital in Calgary, Alberta, Canada. Patients were confirmed/probable COVID-19 cases and contemporaneous control patients without COVID-19. COVID-19 outbreak definitions were based on Public Health guidelines. Clinical and environmental specimens were tested by RT-PCR and as applicable quantitative viral cultures and whole genome sequencing were conducted. Controls were inpatients on the cardiac wards during the study period confirmed to be without COVID-19, matched to outbreak cases by time of symptom onset dates, age within ± 15 years and were admitted in hospital for at least 2 days. Demographics, Braden Score, baseline medications, laboratory measures, co-morbidities, and hospitalization characteristics were collected on cases and controls. Univariate and multivariate conditional logistical regression was used to identify independent risk factors for nosocomial COVID-19. RESULTS The outbreak involved 42 healthcare workers and 39 patients. The strongest independent risk factor for nosocomial COVID-19 (IRR 3.21, 95% CI 1.47-7.02) was exposure in a multi-bedded room. Of 45 strains successfully sequenced, 44 (97.8%) were B.1.128 and differed from the most common circulating community lineages. SARS-CoV-2 positive cultures were detected in 56.7% (34/60) of clinical and environmental specimens. The multidisciplinary outbreak team observed eleven contributing events to transmission during the outbreak. CONCLUSIONS Transmission routes of SARS-CoV-2 in hospital outbreaks are complex; however multi-bedded rooms play a significant role in the transmission of SARS-CoV-2.
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Affiliation(s)
- Jenine Leal
- Infection Prevention and Control, Alberta Health Services, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- O'Brien Institute for Public Health, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Heidi M O'Grady
- Infection Prevention and Control, Alberta Health Services, Calgary, AB, Canada
| | - Logan Armstrong
- Infection Prevention and Control, Alberta Health Services, Edmonton, AB, Canada
| | - Devika Dixit
- Department of Pediatrics, Division of Infectious Diseases, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Zoha Khawaja
- W21C, Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kate Snedeker
- Provincial Population and Public Health, Alberta Health Services, Calgary, AB, Canada
| | - Jennifer Ellison
- Infection Prevention and Control, Alberta Health Services, Lethbridge, AB, Canada
| | - Joyce Erebor
- Infection Prevention and Control, Alberta Health Services, Calgary, AB, Canada
| | - Peter Jamieson
- Department of Family Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
| | - Amanda Weiss
- Cardiac Sciences, Foothills Medical Centre, Alberta Health Services, Calgary, AB, Canada
| | - Daniel Salcedo
- Cardiac Sciences, Foothills Medical Centre, Alberta Health Services, Calgary, AB, Canada
| | - Kimberley Roberts
- Cardiac Sciences, Foothills Medical Centre, Alberta Health Services, Calgary, AB, Canada
| | - Karen Wiens
- Cardiac Sciences, Foothills Medical Centre, Alberta Health Services, Calgary, AB, Canada
| | - Matthew A Croxen
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
- Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Byron M Berenger
- Department of Pathology and Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada
| | - Kanti Pabbaraju
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada
| | - Yi-Chan Lin
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - David Evans
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - John M Conly
- Infection Prevention and Control, Alberta Health Services, Calgary, AB, Canada.
- Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
- O'Brien Institute for Public Health, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.
- Department of Pathology and Laboratory Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
- Synder Institute for Chronic Diseases, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
- W21C, Department of Medicine, University of Calgary, Calgary, AB, Canada.
- Foothills Medical Centre, AGW5 - Special Services Bldg, 1403 29Th Street Nw, Calgary, AB, T2N 2T9, Canada.
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Sempionatto JR, Lasalde-Ramírez JA, Mahato K, Wang J, Gao W. Wearable chemical sensors for biomarker discovery in the omics era. Nat Rev Chem 2022; 6:899-915. [PMID: 37117704 DOI: 10.1038/s41570-022-00439-w] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2022] [Indexed: 11/16/2022]
Abstract
Biomarkers are crucial biological indicators in medical diagnostics and therapy. However, the process of biomarker discovery and validation is hindered by a lack of standardized protocols for analytical studies, storage and sample collection. Wearable chemical sensors provide a real-time, non-invasive alternative to typical laboratory blood analysis, and are an effective tool for exploring novel biomarkers in alternative body fluids, such as sweat, saliva, tears and interstitial fluid. These devices may enable remote at-home personalized health monitoring and substantially reduce the healthcare costs. This Review introduces criteria, strategies and technologies involved in biomarker discovery using wearable chemical sensors. Electrochemical and optical detection techniques are discussed, along with the materials and system-level considerations for wearable chemical sensors. Lastly, this Review describes how the large sets of temporal data collected by wearable sensors, coupled with modern data analysis approaches, would open the door for discovering new biomarkers towards precision medicine.
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Electrolyte Imbalance and COVID-19 Severity in Hospitalized Patients. Nephrourol Mon 2022. [DOI: 10.5812/numonthly-128085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Various risk factors have been proposed for severe coronavirus disease 2019 (COVID-19); nonetheless, the prognostic role of serum electrolytes has not been widely studied. Objectives: The present study aimed to identify the potential prognostic role of electrolyte imbalance in hospitalized COVID-19 patients. Methods: This retrospective study was conducted in Imam Reza Hospital, Mashhad, Iran. The medical records of all COVID-19 patients admitted to the emergency department from May to August 2020 were evaluated. Demographic data and clinical findings upon admission were collected. Disease severity, lung involvement severity on imaging, inflammatory serum biomarkers, admission to the intensive care unit, and serum levels of sodium, potassium, magnesium, calcium (corrected by serum albumin level), and phosphorus were documented. Results: Most patients (60%) were male, and the mean age of the total population was 58.87 ± 1.82 years. Severe COVID-19 was detected in most cases (94.9%) who were significantly older (P = 0.037), had hypertension (P = 0.032), ischemic heart disease (P = 0.033), and higher serum urea (P = 0.001) and serum potassium (P < 0.001). Patients with poor prognosis based on computed tomography (CT) scores had significantly higher serum urea (P = 0.002) and magnesium (P = 0.035) than patients with good prognosis, while serum calcium was significantly higher in the latter group (P = 0.007). Furthermore, there was a significant relationship between COVID-19 severity and serum potassium (P < 0.001). Conclusions: Abnormal serum electrolytes are correlated with COVID-19 severity. Moreover, serum potassium level is a predictor of severe disease.
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Hadavi M, Taghinezhad F, Shafiei E, Babakr SH, Bastaminejad S, Kaffashian M, Ahmadi I, Mozafari A. Hypo- and Hyperphosphatemia at Admission as Independent Factors of Mortality of COVID-19 Patients: Findings from a Retrospective Cohort Study. Int J Endocrinol Metab 2022; 20:e126386. [PMID: 36407032 PMCID: PMC9661755 DOI: 10.5812/ijem-126386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/16/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Electrolyte imbalances are common in COVID-19 infection and are associated with poor outcomes in hospitalized patients. OBJECTIVES This study examined whether serum phosphate imbalances at admission are associated with mortality in hospitalized COVID-19 patients. METHODS In this registry-based single-center retrospective cohort study, 1349 inpatients with COVID-19 were included from March 2020 to March 2021 in an academic hospital in Ilam (southwest Iran). The Cox proportional hazard (PH) regression model was applied to the data set of COVID-19. RESULTS The in-hospital median survival time for patients with low, normal, and high serum phosphate levels was 14, 25, and 8 days, respectively. In a multivariate model, adjusted for the other variables, patients with hypophosphatemia (adjusted hazard ratio [HR], 2.53; 95% CI, 1.15 - 5.58; P = 0.02) and hyperphosphatemia (adjusted HR, 1.77; 95% CI, 1.00 - 3.14; P = 0.05) had an increased mortality hazard compared with those who had normal levels of serum phosphate. CONCLUSIONS Our results demonstrate associations of hypophosphatemia and hyperphosphatemia with increased in-hospital mortality in COVID-19 patients. Intensive medical care and more attention must be paid to COVID-19 patients with serum phosphate imbalances at admission.
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Affiliation(s)
- Marzieh Hadavi
- Department of Internal Medicine, School of Medicine, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Sciences, Ilam, Iran
| | - Fakhredin Taghinezhad
- Clinical Research Development Unit, Shahid Mostafa Khomeini Hospital, Ilam University of Medical Sciences, Ilam, Iran
| | - Elham Shafiei
- Non-communicable Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | | | - Saiyad Bastaminejad
- Non-communicable Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohammadreza Kaffashian
- Department of Physiology, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Iraj Ahmadi
- Non-communicable Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Aliashraf Mozafari
- Non-communicable Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
- Corresponding Author: Non-communicable Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran.
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