Michael Y. Lin
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View article: Odyssey: reconstructing evolution through emergent consensus in the global proteome
Odyssey: reconstructing evolution through emergent consensus in the global proteome Open
We present Odyssey, a family of multimodal protein language models for sequence and structure generation, protein editing and design. We scale Odyssey to more than 102 billion parameters, trained over 1.1 × 10 23 FLOPs. The Odyssey archite…
View article: Considerations for healthcare wastewater surveillance of targeted antimicrobial-resistant organisms
Considerations for healthcare wastewater surveillance of targeted antimicrobial-resistant organisms Open
Wastewater surveillance (WWS) at healthcare facilities paired with CDC- recommended patient screening methods may enable earlier detection of targeted antimicrobial resistant (AR) pathogens. However, this is a nascent field with knowledge …
View article: Application of a Model Using Prior Healthcare Information to Predict Multidrug-Resistant Organism (MDRO) Carriage
Application of a Model Using Prior Healthcare Information to Predict Multidrug-Resistant Organism (MDRO) Carriage Open
Background: Early identification of patients colonized with MDROs can help healthcare facilities improve infection control and treatment. We evaluated whether a model previously validated to predict carbapenem-resistant Enterobacterales (C…
View article: A Trial of Automated Outbreak Detection to Reduce Hospital Pathogen Spread
A Trial of Automated Outbreak Detection to Reduce Hospital Pathogen Spread Open
Automated detection of hospital outbreaks using statistical surveillance did not reduce overall outbreak size in the context of an ongoing pandemic. (Funded by the Centers for Disease Control and Prevention; ClinicalTrials.gov number, NCT0…
View article: Reducing Hospitalizations and Multidrug-Resistant Organisms via Regional Decolonization in Hospitals and Nursing Homes
Reducing Hospitalizations and Multidrug-Resistant Organisms via Regional Decolonization in Hospitals and Nursing Homes Open
Importance Infections due to multidrug-resistant organisms (MDROs) are associated with increased morbidity, mortality, length of hospitalization, and health care costs. Regional interventions may be advantageous in mitigating MDROs and ass…
View article: Potential PD-1 inhibitor immune dysregulation as a risk factor for Listeria monocytogenes bacteremia and meningitis
Potential PD-1 inhibitor immune dysregulation as a risk factor for Listeria monocytogenes bacteremia and meningitis Open
As immune checkpoint inhibitor (ICI) therapy becomes increasingly popular for the treatment of cancer, there is a growing body of literature on opportunistic infections associated with ICI therapy. Pembrolizumab binds specifically to the P…
View article: Potential PD-1 inhibitor immune dysregulation as a risk factor for Listeria monocytogenes bacteremia and meningitis
Potential PD-1 inhibitor immune dysregulation as a risk factor for Listeria monocytogenes bacteremia and meningitis Open
As immune checkpoint inhibitor (ICI) therapy becomes increasingly popular for the treatment of cancer, there is a growing body of literature on opportunistic infections associated with ICI therapy. Pembrolizumab binds specifically to the P…
View article: Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit
Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit Open
Despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States. Current prevention strategies are limited by their failure to account for patients …
View article: Impact of measurement and feedback on chlorhexidine gluconate bathing among intensive care unit patients: A multicenter study
Impact of measurement and feedback on chlorhexidine gluconate bathing among intensive care unit patients: A multicenter study Open
Objective: To assess whether measurement and feedback of chlorhexidine gluconate (CHG) skin concentrations can improve CHG bathing practice across multiple intensive care units (ICUs). Design: A before-and-after quality improvement study m…
View article: ICE volume 44 issue 9 Cover and Front matter
ICE volume 44 issue 9 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: Author response: Quantifying healthcare-acquired coronavirus disease 2019 (COVID-19) in hospitalized patients: A closer look
Author response: Quantifying healthcare-acquired coronavirus disease 2019 (COVID-19) in hospitalized patients: A closer look Open
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View article: <i>Candida auris</i> in skilled nursing facilities
<i>Candida auris</i> in skilled nursing facilities Open
Candida auris is a fungal organism resistant to several classes of antifungals. Since its identification in 2009, it has gained worldwide attention in healthcare for its virulence and resistance to commonly used antifungal therapeutics. Al…
View article: 403. Strain Epidemiology of Clostridioides difficile across Three Geographically Distinct Medical Centers in Chicago
403. Strain Epidemiology of Clostridioides difficile across Three Geographically Distinct Medical Centers in Chicago Open
Background Clostridioides difficile infections (CDI) are caused by a large and diverse group of strains with differences in prevalence and associated morbidity. Over the past 20 years the C. difficile (CD) molecular epidemiology has change…
View article: 88. Increasing Bioburden of <i>Candida auris</i> Body Site Colonization is Associated with Environmental Contamination
88. Increasing Bioburden of <i>Candida auris</i> Body Site Colonization is Associated with Environmental Contamination Open
Background Environmental contamination is suspected to play a key role in transmission of Candida auris in healthcare facilities. We recently showed that environmental surfaces near C. auris-colonized patients are commonly recontaminated w…
View article: 1211. Assessing the Applicability of Enhanced Barrier Precautions among Adult Hospitalized Patients
1211. Assessing the Applicability of Enhanced Barrier Precautions among Adult Hospitalized Patients Open
Background In nursing homes, the CDC has endorsed an interim approach for containment of multidrug-resistant organisms called Enhanced Barrier Precautions (EBP). With an EBP approach, residents with either indwelling medical devices or chr…
View article: Genomic Investigation to Identify Sources of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Personnel in an Acute Care Hospital
Genomic Investigation to Identify Sources of Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Healthcare Personnel in an Acute Care Hospital Open
Background Identifying the source of healthcare personnel (HCP) coronavirus disease 2019 (COVID-19) is important to guide occupational safety efforts. We used a combined whole genome sequencing (WGS) and epidemiologic approach to investiga…
View article: Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis
Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis Open
US Center for Disease Control and Prevention and University of Michigan.
View article: Duration of Replication-Competent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Shedding Among Patients With Severe or Critical Coronavirus Disease 2019 (COVID-19)
Duration of Replication-Competent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Shedding Among Patients With Severe or Critical Coronavirus Disease 2019 (COVID-19) Open
Background Patterns of shedding replication-competent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in severe or critical COVID-19 are not well characterized. We investigated the duration of replication-competent SARS-CoV-2 …
View article: Indwelling medical devices and skin microorganisms on ICU patients bathed with chlorhexidine gluconate
Indwelling medical devices and skin microorganisms on ICU patients bathed with chlorhexidine gluconate Open
Background: Bathing ICU patients with chlorhexidine gluconate (CHG) decreases bloodstream infections and multidrug-resistant organism transmission. The efficacy of CHG bathing on skin microorganism reduction may be influenced by patient-le…
View article: Hospital-acquired coronavirus disease 2019 (COVID-19) among patients of two acute-care hospitals: Implications for surveillance
Hospital-acquired coronavirus disease 2019 (COVID-19) among patients of two acute-care hospitals: Implications for surveillance Open
Objectives: We quantified hospital-acquired coronavirus disease 2019 (COVID-19) during the early phases of the pandemic, and we evaluated solely temporal determinations of hospital acquisition. Design: Retrospective observational study dur…
View article: 399. Epidemiology of Laboratory-identified Late-onset SARS-CoV-2 Positivity in Two Large, Urban, Acute-Care Hospitals: Implications for Surveillance of Hospital-Acquired COVID-19
399. Epidemiology of Laboratory-identified Late-onset SARS-CoV-2 Positivity in Two Large, Urban, Acute-Care Hospitals: Implications for Surveillance of Hospital-Acquired COVID-19 Open
Background Laboratory identification (Lab-ID) of late-onset SARS-CoV-2 positive tests during a hospital stay is a potential public health surveillance approach for hospital-acquired COVID-19. However, prolonged RNA fragment shedding and in…
View article: ICE volume 42 issue 11 Cover and Front matter
ICE volume 42 issue 11 Cover and Front matter Open
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
View article: Admission and Discharge Sampling Underestimates Multidrug-Resistant Organism (MDRO) Acquisition in an Intensive Care Unit
Admission and Discharge Sampling Underestimates Multidrug-Resistant Organism (MDRO) Acquisition in an Intensive Care Unit Open
Background: Identification of hospitalized patients with enteric multidrug-resistant organism (MDRO) carriage, combined with implementation of targeted infection control interventions, may help reduce MDRO transmission. However, the optima…
View article: Healthcare personnel experiences implementing carbapenem-resistant Enterobacterales infection control measures at a ventilator-capable skilled nursing facility—A qualitative analysis
Healthcare personnel experiences implementing carbapenem-resistant Enterobacterales infection control measures at a ventilator-capable skilled nursing facility—A qualitative analysis Open
Objective: Ventilator-capable skilled nursing facilities (vSNFs) are critical to the epidemiology and control of antibiotic-resistant organisms. During an infection prevention intervention to control carbapenem-resistant Enterobacterales (…
View article: Integrated genomic, epidemiologic investigation of Candida auris skin colonization in a skilled nursing facility
Integrated genomic, epidemiologic investigation of Candida auris skin colonization in a skilled nursing facility Open
View article: Regional Spread of <i>bla</i> NDM-1-Containing <i>Klebsiella pneumoniae</i> ST147 in Post-Acute Care Facilities
Regional Spread of <i>bla</i> NDM-1-Containing <i>Klebsiella pneumoniae</i> ST147 in Post-Acute Care Facilities Open
Background Carbapenem-resistant Enterobacterales (CRE) harboring blaKPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016–2019, a series of regional point-prevalence surveys identified increasing pre…
View article: Inferring, comparing and exploring ecological networks from time-series data through R packages constructnet, disgraph and dynet
Inferring, comparing and exploring ecological networks from time-series data through R packages constructnet, disgraph and dynet Open
Network inference is a major field of interest for the ecological community, especially in light of the high cost and difficulty of manual observation, and easy availability of remote, long term monitoring data. In addition, comparing acro…
View article: Inferring, comparing and exploring ecological networks from time-series\n data through R packages constructnet, disgraph and dynet
Inferring, comparing and exploring ecological networks from time-series\n data through R packages constructnet, disgraph and dynet Open
Network inference is a major field of interest for the ecological community,\nespecially in light of the high cost and difficulty of manual observation, and\neasy availability of remote, long term monitoring data. In addition, comparing\na…
View article: Regional spread of bla<sub>NDM-1</sub>-containing <i>Klebsiella pneumoniae</i> Sequence Type 147 in post-acute care facilities
Regional spread of bla<sub>NDM-1</sub>-containing <i>Klebsiella pneumoniae</i> Sequence Type 147 in post-acute care facilities Open
Background Carbapenem-resistant Enterobacterales (CRE) harboring bla KPC have been endemic in Chicago-area healthcare networks for more than a decade. During 2016-2019, a series of regional point prevalence surveys identified increasing pr…
View article: Risk Factors Associated With SARS-CoV-2 Seropositivity Among US Health Care Personnel
Risk Factors Associated With SARS-CoV-2 Seropositivity Among US Health Care Personnel Open
In this cross-sectional study of US HCP in 3 states, community exposures were associated with seropositivity to SARS-CoV-2, but workplace factors, including workplace role, environment, or contact with patients with known COVID-19, were no…