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Article ; Online: ReaLigands: A Ligand Library Cultivated from Experiment and Intended for Molecular Computational Catalyst Design.

Chen, Shu-Sen / Meyer, Zack / Jensen, Brendan / Kraus, Alex / Lambert, Allison / Ess, Daniel H

Journal of chemical information and modeling

2023 Volume 63, Issue 23, Page(s) 7412–7422

Abstract: Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are ... ...

Abstract	Computational catalyst design requires identification of a metal and ligand that together result in the desired reaction reactivity and/or selectivity. A major impediment to translating computational designs to experiments is evaluating ligands that are likely to be synthesized. Here, we provide a solution to this impediment with our ReaLigands library that contains >30,000 monodentate, bidentate (didentate), tridentate, and larger ligands cultivated by dismantling experimentally reported crystal structures. Individual ligands from mononuclear crystal structures were identified using a modified depth-first search algorithm and charge was assigned using a machine learning model based on quantum-chemical calculated features. In the library, ligands are sorted based on direct ligand-to-metal atomic connections and on denticity. Representative principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analyses were used to analyze several tridentate ligand categories, which revealed both the diversity of ligands and connections between ligand categories. We also demonstrated the utility of this library by implementing it with our building and optimization tools, which resulted in the very rapid generation of barriers for 750 bidentate ligands for Rh-hydride ethylene migratory insertion.
MeSH term(s)	Ligands ; Small Molecule Libraries
Chemical Substances	Ligands ; Small Molecule Libraries
Language	English
Publishing date	2023-11-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01310
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Article ; Online: Machine Learning Models for Predicting Zirconocene Properties and Barriers.

Kirkland, Justin K / Kumawat, Jugal / Shaban Tameh, Maliheh / Tolman, Tyson / Lambert, Allison C / Lief, Graham R / Yang, Qing / Ess, Daniel H

Journal of chemical information and modeling

2024 Volume 64, Issue 3, Page(s) 775–784

Abstract: Zr metallocenes have significant potential to be highly tunable polyethylene catalysts through modification of the aromatic ligand framework. Here we report the development of multiple machine learning models using a large library (>700 systems) of DFT- ... ...

Abstract	Zr metallocenes have significant potential to be highly tunable polyethylene catalysts through modification of the aromatic ligand framework. Here we report the development of multiple machine learning models using a large library (>700 systems) of DFT-calculated zirconocene properties and barriers for ethylene polymerization. We show that very accurate machine learning models are possible for HOMO-LUMO gaps of precatalysts but the performance significantly depends on the machine learning algorithm and type of featurization, such as fingerprints, Coulomb matrices, smooth overlap of atomic positions, or persistence images. Surprisingly, the description of the bonding hapticity, the number of direct connections between Zr and the ligand aromatic carbons, only has a moderate influence on the performance of most models. Despite robust models for HOMO-LUMO gaps, these types of machine learning models based on structure connectivity type features perform poorly in predicting ethylene migratory insertion barrier heights. Therefore, we developed several relatively robust and accurate machine learning models for barrier heights that are based on quantum-chemical descriptors (QCDs). The quantitative accuracy of these models depends on which potential energy surface structure QCDs were harvested from. This revealed a Hammett-type principle to naturally emerge showing that QCDs from the π-coordination complexes provide much better descriptions of the transition states than other potential-energy structures. Feature importance analysis of the QCDs provides several fundamental principles that influence zirconocene catalyst reactivity.
MeSH term(s)	Ligands ; Organometallic Compounds/chemistry ; Ethylenes/chemistry ; Machine Learning ; Zirconium
Chemical Substances	Zirconocene dichloride (1291-32-3) ; Ligands ; Organometallic Compounds ; ethylene (91GW059KN7) ; Ethylenes ; Zirconium (C6V6S92N3C)
Language	English
Publishing date	2024-01-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01575
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Article ; Online: Respiratory symptoms in smokers with normal spirometry: clinical significance and management considerations.

Lambert, Allison A / Bhatt, Surya P

Current opinion in pulmonary medicine

2018 Volume 25, Issue 2, Page(s) 138–143

Abstract: Purpose of review: Current respiratory society guidelines recommend confirming the diagnosis of chronic obstructive pulmonary disease (COPD) with demonstration of airflow obstruction on spirometry. However, multiple recent studies have demonstrated that ...

Abstract	Purpose of review: Current respiratory society guidelines recommend confirming the diagnosis of chronic obstructive pulmonary disease (COPD) with demonstration of airflow obstruction on spirometry. However, multiple recent studies have demonstrated that smokers without overt airflow obstruction on spirometry, termed symptomatic smokers, have evidence of structural lung disease on imaging, have a substantial symptom burden, and also suffer respiratory exacerbations. In this review, we provide an overview of the epidemiology of symptomatic smokers, and address issues of screening and diagnosis, evaluation, and management considerations. Recent findings: Two large prospective cohorts of adults with and at risk for COPD quantified the respiratory morbidity of symptomatic smokers. These studies demonstrated that approximately half of smokers without spirometrically defined airflow obstruction have increased respiratory symptoms, poor quality of life, low functional capacity, and suffer from respiratory exacerbations. Symptomatic smokers also have evidence of structural lung disease on imaging, and are at risk for faster lung function decline compared with those without respiratory symptoms. Several methods have been proposed to detect smoking-related lung damage among symptomatic smokers with normal forced expired volume in 1 second (FEV1)/forced vital capacity (FVC) ratio. Novel spirometry measures have been reported to diagnose disease before detection using traditional spirometry thresholds. Small airway involvement can be detected earlier using impulse oscillometry and metrics on multiple breath nitrogen washout tests. Imaging biomarkers have been developed that are associated with respiratory morbidity and lung function decline in symptomatic smokers. The translation of novel methods for COPD disease detection into more timely introduction of therapeutics and a consequent reduction in long-term morbidity and mortality has not yet been observed. Summary: A better understanding of the pathobiologic basis of disease in smokers without overt airflow limitation, and earlier recognition of lung disease, while also appropriately evaluating for comorbidities that may account for the symptoms, will enhance the management of symptomatic smokers with preserved lung function.
MeSH term(s)	Early Diagnosis ; Humans ; Lung/diagnostic imaging ; Lung/physiopathology ; Lung Diseases/diagnosis ; Lung Diseases/etiology ; Lung Diseases/physiopathology ; Respiratory Function Tests/methods ; Respiratory Function Tests/trends ; Smoking/adverse effects ; Smoking/epidemiology ; Smoking/physiopathology ; Symptom Assessment
Language	English
Publishing date	2018-10-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1285505-4
ISSN	1531-6971 ; 1070-5287 ; 1078-1641
ISSN (online)	1531-6971
ISSN	1070-5287 ; 1078-1641
DOI	10.1097/MCP.0000000000000550
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Article ; Online: Abnormal Lung Function in HIV-infected Adults: An Under-recognized Risk Factor for Early Mortality.

Lambert, Allison A / Crothers, Kristina

Annals of the American Thoracic Society

2018 Volume 15, Issue 2, Page(s) 160–162

MeSH term(s)	Adult ; HIV ; HIV Infections ; Humans ; Respiratory Physiological Phenomena ; Risk Factors
Language	English
Publishing date	2018-01-09
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2717461-X
ISSN	2325-6621 ; 1943-5665 ; 2325-6621
ISSN (online)	2325-6621 ; 1943-5665
ISSN	2325-6621
DOI	10.1513/AnnalsATS.201711-904ED
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Article: COPD Overlap Syndromes: Asthma and Beyond.

Lambert, Allison A / Dransfield, Mark T

Chronic obstructive pulmonary diseases (Miami, Fla.)

2016 Volume 3, Issue 1, Page(s) 459–465

Abstract: This article serves as a CME-available, enduring material summary of the following ... ...

Abstract	This article serves as a CME-available, enduring material summary of the following COPD9
Language	English
Publishing date	2016-01-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2771715-X
ISSN	2372-952X
ISSN	2372-952X
DOI	10.15326/jcopdf.3.1.2015.0176
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Article ; Online: Lung Diseases Unique to Women.

Criner, Rachel N / Al-Abcha, Abdullah / Lambert, Allison A / Han, MeiLan K

Clinics in chest medicine

2021 Volume 42, Issue 3, Page(s) 507–516

Abstract: The differences in the respiratory system between women and men begin in utero. Biologic sex plays a critical role in fetal development, airway anatomy, inhalational exposures, and inhaled particle deposition of the respiratory system, thus leading to ... ...

Abstract	The differences in the respiratory system between women and men begin in utero. Biologic sex plays a critical role in fetal development, airway anatomy, inhalational exposures, and inhaled particle deposition of the respiratory system, thus leading to differences in risk for disease, as well as clinical manifestations, morbidity, and mortality. In this article, we focus on those respiratory diseases unique to females: lymphangioleiomyomatosis and thoracic endometriosis syndrome.
MeSH term(s)	Female ; Humans ; Lung Diseases/etiology ; Lung Diseases/therapy ; Lymphangioleiomyomatosis/diagnosis ; Lymphangioleiomyomatosis/epidemiology ; Lymphangioleiomyomatosis/therapy ; Male ; Sirolimus
Chemical Substances	Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2021-05-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	447455-7
ISSN	1557-8216 ; 0272-5231
ISSN (online)	1557-8216
ISSN	0272-5231
DOI	10.1016/j.ccm.2021.04.014
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Article: High-fidelity detection, subtyping, and localization of five skin neoplasms using supervised and semi-supervised learning.

Requa, James / Godard, Tuatini / Mandal, Rajni / Balzer, Bonnie / Whittemore, Darren / George, Eva / Barcelona, Frenalyn / Lambert, Chalette / Lee, Jonathan / Lambert, Allison / Larson, April / Osmond, Gregory

Journal of pathology informatics

2022 Volume 14, Page(s) 100159

Abstract: Background: Skin cancers are the most common malignancies diagnosed worldwide. While the early detection and treatment of pre-cancerous and cancerous skin lesions can dramatically improve outcomes, factors such as a global shortage of pathologists, ... ...

Abstract	Background: Skin cancers are the most common malignancies diagnosed worldwide. While the early detection and treatment of pre-cancerous and cancerous skin lesions can dramatically improve outcomes, factors such as a global shortage of pathologists, increased workloads, and high rates of diagnostic discordance underscore the need for techniques that improve pathology workflows. Although AI models are now being used to classify lesions from whole slide images (WSIs), diagnostic performance rarely surpasses that of expert pathologists. Objectives: The objective of the present study was to create an AI model to detect and classify skin lesions with a higher degree of sensitivity than previously demonstrated, with potential to match and eventually surpass expert pathologists to improve clinical workflows. Methods: We combined supervised learning (SL) with semi-supervised learning (SSL) to produce an end-to-end multi-level skin detection system that not only detects 5 main types of skin lesions with high sensitivity and specificity, but also subtypes, localizes, and provides margin status to evaluate the proximity of the lesion to non-epidermal margins. The Supervised Training Subset consisted of 2188 random WSIs collected by the PathologyWatch (PW) laboratory between 2013 and 2018, while the Weakly Supervised Subset consisted of 5161 WSIs from daily case specimens. The Validation Set consisted of 250 curated daily case WSIs obtained from the PW tissue archives and included 50 "mimickers". The Testing Set (3821 WSIs) was composed of non-curated daily case specimens collected from July 20, 2021 to August 20, 2021 from PW laboratories. Results: The performance characteristics of our AI model (i.e., Mihm) were assessed retrospectively by running the Testing Set through the Mihm Evaluation Pipeline. Our results show that the sensitivity of Mihm in classifying melanocytic lesions, basal cell carcinoma, and atypical squamous lesions, verruca vulgaris, and seborrheic keratosis was 98.91% (95% CI: 98.27%, 99.55%), 97.24% (95% CI: 96.15%, 98.33%), 95.26% (95% CI: 93.79%, 96.73%), 93.50% (95% CI: 89.14%, 97.86%), and 86.91% (95% CI: 82.13%, 91.69%), respectively. Additionally, our multi-level (i.e., patch-level, ROI-level, and WSI-level) detection algorithm includes a qualitative feature that subtypes lesions, an AI overlay in the front-end digital display that localizes diagnostic ROIs, and reports on margin status by detecting overlap between lesions and non-epidermal tissue margins. Conclusions: Our AI model, developed in collaboration with dermatopathologists, detects 5 skin lesion types with higher sensitivity than previously published AI models, and provides end users with information such as subtyping, localization, and margin status in a front-end digital display. Our end-to-end system has the potential to improve pathology workflows by increasing diagnostic accuracy, expediting the course of patient care, and ultimately improving patient outcomes.
Language	English
Publishing date	2022-11-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2579241-6
ISSN	2153-3539 ; 2229-5089
ISSN (online)	2153-3539
ISSN	2229-5089
DOI	10.1016/j.jpi.2022.100159
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Article ; Online: High-dose N-acetylcysteine in chronic obstructive pulmonary disease, prone positioning in acute respiratory distress syndrome, and continuous positive airway pressure and exhaled nitric oxide in obstructive sleep apnea.

Lambert, Allison A / Parker, Ann M / Moon, Karoline K

American journal of respiratory and critical care medicine

2014 Volume 189, Issue 2, Page(s) 223–224

MeSH term(s)	Acetylcysteine/therapeutic use ; Continuous Positive Airway Pressure ; Free Radical Scavengers/therapeutic use ; Humans ; Nitric Oxide/metabolism ; Prone Position ; Pulmonary Disease, Chronic Obstructive/drug therapy ; Respiratory Distress Syndrome/therapy ; Sleep Apnea, Obstructive/physiopathology ; Sleep Apnea, Obstructive/therapy
Chemical Substances	Free Radical Scavengers ; Nitric Oxide (31C4KY9ESH) ; Acetylcysteine (WYQ7N0BPYC)
Language	English
Publishing date	2014-01-15
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1180953-x
ISSN	1535-4970 ; 0003-0805 ; 1073-449X
ISSN (online)	1535-4970
ISSN	0003-0805 ; 1073-449X
DOI	10.1164/rccm.201308-1555RR
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Article ; Online: A pragmatic randomized trial of home-based testing for COVID-19 in rural Native American and Latino communities: Protocol for the "Protecting our Communities" study.

Thompson, Matthew J / Drain, Paul K / Gregor, Charlie E / Hassell, Laurie A / Ko, Linda K / Lyon, Victoria / Ahmed, Selena / Bishop, Sonia / Dupuis, Virgil / Garza, Lorenzo / Lambert, Allison A / Rowe, Carly / Warne, Teresa / Webber, Eliza / Westbroek, Wendy / Adams, Alexandra K

Contemporary clinical trials

2022 Volume 119, Page(s) 106820

Abstract: Background: Home-based testing for COVID-19 has potential to reduce existing health care disparities among underserved populations in the United States. However, implementation of home-based tests in these communities may face significant barriers. This ...

Abstract	Background: Home-based testing for COVID-19 has potential to reduce existing health care disparities among underserved populations in the United States. However, implementation of home-based tests in these communities may face significant barriers. This study evaluates the acceptability, feasibility, and success of home-based testing and the potential added benefit of active support from trusted community health workers for Native Americans and Hispanic/Latino adults living in rural Montana and Washington states. Methods/design: The academic-community research team designed the trial to be responsive to community needs for understanding barriers and supports to home-based COVID-19 testing. The "Protecting Our Community" study is a two-arm pragmatic randomized controlled trial in which a total of 400 participants are randomized to active or passive arms. Participants of both study arms receive a commercially available home collection COVID-19 test kit, which is completed by mailing a self-collected nasal swab to a central laboratory. The primary study outcome is return of the kit to the central lab within 14 days. The cultural, social, behavioral, and economic barriers to home-based COVID-19 testing are also assessed by qualitative research methods. A survey and semi-structured interviews are conducted after the trial to evaluate perceptions and experience of home-based testing. Discussion: Implementing home-based testing in underserved populations, including among Native American and Hispanic/Latino communities, may require additional support to be successful. The Protecting Our Community trial examines the effect of trusted community health workers on use of home-based testing, which may be adaptable for community-driven models of home-based testing in other underserved populations.
MeSH term(s)	COVID-19 ; COVID-19 Testing ; Hispanic or Latino ; Humans ; Pragmatic Clinical Trials as Topic ; Randomized Controlled Trials as Topic ; SARS-CoV-2 ; United States ; American Indian or Alaska Native
Language	English
Publishing date	2022-06-09
Publishing country	United States
Document type	Clinical Trial Protocol ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2182176-8
ISSN	1559-2030 ; 1551-7144
ISSN (online)	1559-2030
ISSN	1551-7144
DOI	10.1016/j.cct.2022.106820
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Article ; Online: Plasma cathelicidin and longitudinal lung function in current and former smokers.

Burkes, Robert M / Astemborski, Jacquie / Lambert, Allison A / Brown, Todd T / Wise, Robert A / Kirk, Gregory D / Drummond, M Bradley

PloS one

2019 Volume 14, Issue 2, Page(s) e0212628

Abstract: Introduction: Cathelicidin (also known as LL-37 in humans) is an antimicrobial peptide secreted by epithelial and immune cells and regulated by vitamin D. The immunological roles of cathelicidin make it a putative biomarker to identify individuals at ... ...

Abstract	Introduction: Cathelicidin (also known as LL-37 in humans) is an antimicrobial peptide secreted by epithelial and immune cells and regulated by vitamin D. The immunological roles of cathelicidin make it a putative biomarker to identify individuals at risk for reduced lung function. The objective of this study is to determine potential independent associations between low plasma cathelicidin and longitudinal lung function in current or former smokers without COPD. Methods: In a nested analysis of 308 participants from an observational cohort study, plasma cathelicidin and serum 25-hydroxy-vitamin D measurements were obtained at baseline, years three and five. The independent association between lowest quartile cathelicidin (<35 ng/ml) and forced-expiratory-volume-in-1-second (FEV1) at baseline, six and 18 months from each cathelicidin measurement was assessed with generalized estimating equations after adjusting for age, sex, race, smoking status and intensity. The long-term stability of cathelicidin and relationship with vitamin D was evaluated. Results: The cohort was 91% African-American, mean age 48.6 years, 32% female, and 81% current smokers. Participants with low cathelicidin were more likely to be female and have lower FEV1. Low cathelicidin was not independently associated with baseline FEV1. There was an independent association between low cathelicidin and reduced FEV1 at six months [-72 ml (95% CI, -140 to -8ml); p = 0.027] and 18 months [-103 ml (95% CI, -180 to -27 ml); p = 0.007]. Cathelicidin was stable over time and not correlated with vitamin D level. Conclusion: In current and former smokers with preserved lung function, low cathelicidin is associated with sustained lung function reductions at six and 18 months, suggesting that cathelicidin may be an informative biomarker to predict persistent lung function disparities among at-risk individuals.
MeSH term(s)	Adult ; Antimicrobial Cationic Peptides/blood ; Biomarkers/blood ; Female ; Forced Expiratory Volume/physiology ; Humans ; Longitudinal Studies ; Lung/physiopathology ; Male ; Middle Aged ; Non-Smokers/statistics & numerical data ; Predictive Value of Tests ; Prognosis ; Prospective Studies ; Pulmonary Disease, Chronic Obstructive/diagnosis ; Pulmonary Disease, Chronic Obstructive/physiopathology ; Risk Factors ; Smokers/statistics & numerical data ; Smoking/blood ; Smoking/immunology ; Smoking/physiopathology ; Vitamin D/blood
Chemical Substances	Antimicrobial Cationic Peptides ; Biomarkers ; Vitamin D (1406-16-2) ; ropocamptide (3DD771JO2H)
Language	English
Publishing date	2019-02-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0212628
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