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Book ; Online ; E-Book: Lung health and the exposome

Khatri, Sumita B. / Pennington, Emily J.

how environmental factors influence lung health

(Respiratory medicine)

2022

Author's details	Sumita B. Khatri, Emily J. Pennington editors
Series title	Respiratory medicine
Keywords	Lungs/Diseases/Environmental aspects ; Environmentally induced diseases/Molecular aspects ; Lungs/Microbiology
Subject code	616.24071
Language	English
Size	1 Online-Ressource (x, 206 Seiten), Illustrationen
Publisher	Humana Press
Publishing place	New York, NY
Publishing country	United States
Document type	Book ; Online ; E-Book
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
HBZ-ID	HT021265407
ISBN	978-3-030-90185-1 ; 9783030901844 ; 3-030-90185-8 ; 303090184X
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Asthma increases risk of severity of COVID-19.

Pennington, Emily

Cleveland Clinic journal of medicine

2020

Abstract: Current Centers for Disease Control and Prevention guidelines state that patients with moderate to severe asthma may be at greater risk for more severe disease if infected with SARS-CoV-2; however, no published data support this suggestion. During this ... ...

Abstract	Current Centers for Disease Control and Prevention guidelines state that patients with moderate to severe asthma may be at greater risk for more severe disease if infected with SARS-CoV-2; however, no published data support this suggestion. During this pandemic, it is recommended that patients with asthma continue taking all controller inhalers and other asthma medication as prescribed to prevent exacerbations and limit outpatient clinic and emergency room exposure. Symptoms that may differentiate COVID-19 from asthma exacerbations caused by another trigger may include fever, fatigue, anorexia, or myalgias. Patients with suspected or confirmed COVID-19 should avoid nebulizer treatments due to the risk of aerosolization.
Keywords	covid19
Language	English
Publishing date	2020-05-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	639116-3
ISSN	1939-2869 ; 0891-1150
ISSN (online)	1939-2869
ISSN	0891-1150
DOI	10.3949/ccjm.87a.ccc002
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Article: Asthma increases risk of severity of COVID-19

Pennington, Emily

Clevel. clin. j. med

Abstract	Current Centers for Disease Control and Prevention guidelines state that patients with moderate to severe asthma may be at greater risk for more severe disease if infected with SARS-CoV-2; however, no published data support this suggestion. During this pandemic, it is recommended that patients with asthma continue taking all controller inhalers and other asthma medication as prescribed to prevent exacerbations and limit outpatient clinic and emergency room exposure. Symptoms that may differentiate COVID-19 from asthma exacerbations caused by another trigger may include fever, fatigue, anorexia, or myalgias. Patients with suspected or confirmed COVID-19 should avoid nebulizer treatments due to the risk of aerosolization.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #186708
Database	COVID19

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Article: Trials underestimate the impact of preventive treatment for household contacts exposed to multidrug-resistant tuberculosis: a simulation study.

Kasaie, Parastu / Pennington, Jeff / Gupta, Amita / Dowdy, David W / Kendall, Emily A

medRxiv : the preprint server for health sciences

2023

Abstract: Background: Several clinical trials of tuberculosis preventive treatment (TPT) for household contacts of patients with multidrug-resistant tuberculosis (MDR-TB) are nearing completion. The potential benefits of TPT for MDR-TB contacts extend beyond the ... ...

Abstract	Background: Several clinical trials of tuberculosis preventive treatment (TPT) for household contacts of patients with multidrug-resistant tuberculosis (MDR-TB) are nearing completion. The potential benefits of TPT for MDR-TB contacts extend beyond the outcomes that clinical trials can measure. Methods: We developed an agent-based, household-structured TB and MDR-TB transmission model, calibrated to an illustrative setting in India, the country accounting for 26% of global MDR-TB burden. We simulated household contact investigation for contacts of patients with MDR-TB, comparing an MDR-TPT regimen against alternatives of isoniazid preventive treatment, household contact investigation without TPT, or no household contact intervention. We simulated outcomes of a clinical trial and estimated the patient-level and population-level effects over a longer time horizon. Findings: During two years of follow-up per recipient, a simulated 6-month MDR-TPT regimen with 70% efficacy against both DS- and MDR-TB infection could prevent 72% [Interquartile range (IQR): 45 - 100%] of incident MDR-TB among TPT recipients (number needed to treat (NNT) 73 [44 - 176] to prevent one MDR-TB case), compared to household contact investigation without TPT. This NNT decreased to 54 [30 - 183] when median follow-up was increased from two to 16 years, to 27 [11 - Inf] when downstream transmission effects were also considered, and to 12 [8 - 22] when these effects were compared to a scenario of no household contact intervention. Interpretation: If forthcoming trial results demonstrate efficacy, the long-term population impact of MDR-TPT implementation could be much greater than suggested by trial outcomes alone. Funding: NIH K01AI138853 and K08AI127908; Johns Hopkins Catalyst Award.
Language	English
Publishing date	2023-02-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.06.23285528
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Article ; Online: A comparison of confocal and epifluorescence microscopy for quantification of RNAScope and immunohistochemistry fluorescent images.

Honzel, Emily / Joshi, Abhinav / Hernandez-Morato, Ignacio / Pennington-FitzGerald, William / Pitman, Michael J

Journal of neuroscience methods

2023 Volume 403, Page(s) 110050

Abstract: Background: Quantification of RNA expression and protein production in fluorescent stainings provides critical information concerning neurodevelopment. A trustable independent quantification technique requires acquisition of reliable images prior to ... ...

Abstract	Background: Quantification of RNA expression and protein production in fluorescent stainings provides critical information concerning neurodevelopment. A trustable independent quantification technique requires acquisition of reliable images prior to image processing. There is uncertainty in existing literature regarding the use of confocal microscopy compared to standard epifluorescence microscopy, especially in the context of RNA in situ hybridization protocols. New method: The hindbrains of developing rat embryos from embryologic day 14 (E14) to E20 were sectioned and stained for expression of Hoxb1, Hoxb2, and Phox2b using both RNAScope and immunohistochemistry. Islet1 was used for identification of hindbrain motoneuron cell bodies. Slides were imaged using both confocal and epifluorescence microscopy. Results: Expression patterns of both mRNA and protein were similar in both imaging modalities. Analyses of Hoxb1 and Hoxb2 mRNA expression were particularly concordant between-scopes, with similar p-values and posthoc differences between timepoints. Confocal imaging of Hoxb2 protein yielded a significant peak at E18, but this level of significance was not reached using epifluorescence microscopy. Although similar trends were observed, only Phox2b RNAScope results were statistically significant when analyzed with confocal microscopy. In contrast, Phox2b immunostaining analyses showed significant differences using both microscopes. Comparison with existing methods: Researchers may save time and financial resources if epifluorescence microscopy provides comparable or equal results as confocal. Conclusions: Epifluorescence microscopy appears sufficient for quantification of RNAScope experiments with relatively low puncta per cell, while confocal microscopy gives clearer definition to immunohistochemical protein relationships and may be preferable especially in targets with low protein production.
MeSH term(s)	Rats ; Animals ; Immunohistochemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism ; RNA ; RNA, Messenger ; Microscopy, Confocal/methods
Chemical Substances	Transcription Factors ; RNA (63231-63-0) ; RNA, Messenger
Language	English
Publishing date	2023-12-23
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	282721-9
ISSN	1872-678X ; 0165-0270
ISSN (online)	1872-678X
ISSN	0165-0270
DOI	10.1016/j.jneumeth.2023.110050
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Article ; Online: The Impact of Preventive Treatment for Multidrug- and Rifampin-Resistant Tuberculosis Exceeds Trial-Based Estimates.

Kasaie, Parastu / Pennington, Jeff / Gupta, Amita / Dowdy, David W / Kendall, Emily A

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2023 Volume 78, Issue 1, Page(s) 133–143

Abstract: Background: Several clinical trials of tuberculosis preventive treatment (TPT) for household contacts of patients with multidrug- or rifampin-resistant tuberculosis (MDR/RR-TB) are nearing completion. The potential benefits of delivering TPT to MDR/RR- ... ...

Abstract	Background: Several clinical trials of tuberculosis preventive treatment (TPT) for household contacts of patients with multidrug- or rifampin-resistant tuberculosis (MDR/RR-TB) are nearing completion. The potential benefits of delivering TPT to MDR/RR-TB contacts extend beyond the outcomes that clinical trials can measure. Methods: We developed an agent-based, household-structured TB and MDR/RR-TB transmission model, calibrated to an illustrative setting in India. We simulated contact investigation in households of patients with MDR/RR-TB, comparing an MDR/RR-TPT regimen (assuming 6-month duration, 70% efficacy) and associated active case finding against alternatives of contact investigation without TPT or no household intervention. We simulated the TB and MDR/RR-TB incidence averted relative to placebo over 2 years, as measurable by a typical trial, as well as the incidence averted over a longer time horizon, in the broader population, and relative to no contact investigation. Results: Observing TPT and placebo recipients for 2 years as in a typical trial, MDR/RR-TPT was measured to prevent 72% (interquartile range, 45%-100%) of incident MDR/RR-TB among recipients; the median number needed to treat (NNT) to prevent 1 MDR/RR-TB case was 73, compared to placebo. This NNT decreased to 54 with 13-18 years of observation, to 27 when downstream transmission effects were also considered, and to 12 when the effects of active TB screening were included by comparing to a no-household-contact-intervention scenario. Conclusions: If forthcoming trial results demonstrate efficacy, the long-term population impact of TPT for MDR/RR-TB-including the large effect of increased active TB detection among MDR/RR-TB contacts-could be much greater than suggested by trial outcomes alone.
MeSH term(s)	Humans ; Rifampin/therapeutic use ; Tuberculosis, Multidrug-Resistant/drug therapy ; Tuberculosis, Multidrug-Resistant/epidemiology ; Tuberculosis, Multidrug-Resistant/prevention & control ; Contact Tracing ; Family Characteristics ; India/epidemiology ; Antitubercular Agents/therapeutic use
Chemical Substances	Rifampin (VJT6J7R4TR) ; Antitubercular Agents
Language	English
Publishing date	2023-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciad557
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Article: High-Resolution Melting-Based Marker Development for Wheat Leaf Rust Resistance Gene

Kaur, Shivreet / Pennington, Taylor / Conley, Emily J / Green, Andrew / Kolmer, James / Anderson, James / Gupta, Rajeev / Gill, Upinder

Phytopathology

2023 Volume 113, Issue 3, Page(s) 508–515

Abstract: Deploying adult plant resistance (APR) against rust diseases is an important breeding objective of most wheat-breeding programs. The ... ...

Abstract	Deploying adult plant resistance (APR) against rust diseases is an important breeding objective of most wheat-breeding programs. The gene
MeSH term(s)	Reproducibility of Results ; Plant Diseases/genetics ; Plant Diseases/microbiology ; Plant Breeding ; Puccinia ; Basidiomycota/genetics ; Plants ; Disease Resistance/genetics
Language	English
Publishing date	2023-03-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-08-22-0313-R
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Article ; Online: Development and Application of Automated Vocal Fold Tracking Software in a Rat Surgical Model.

Pennington-FitzGerald, William / Joshi, Abhinav / Honzel, Emily / Hernandez-Morato, Ignacio / Pitman, Michael J / Moayedi, Yalda

The Laryngoscope

2023 Volume 134, Issue 1, Page(s) 340–346

Abstract: Objective: The rat is a widely used model for studying vocal fold (VF) function after recurrent laryngeal nerve injury, but common techniques for evaluating rat VF motion remain subjective and imprecise. To address this, we developed a software package, ...

Abstract	Objective: The rat is a widely used model for studying vocal fold (VF) function after recurrent laryngeal nerve injury, but common techniques for evaluating rat VF motion remain subjective and imprecise. To address this, we developed a software package, called RatVocalTracker1.0 (RVT1.0), to quantify VF motion and tested it on rats with iatrogenic unilateral vocal fold paralysis (VFP). Methods: A deep neural network was trained to identify the positions of the VFs and arytenoid cartilages (ACs) in transoral laryngoscope videos of the rat glottis. Software was developed to estimate glottic midline, VF displacement, VF velocity, and AC angle. The software was applied to laryngoscope videos of adult rats before and after right recurrent and superior laryngeal nerve transection (N = 15; 6M, 9F). All software calculated metrics were compared before and after injury and validated against manually calculated metrics. Results: RVT1.0 accurately tracked and quantified VF displacement, VF velocity, and AC angle. Significant differences were found before and after surgery for all RVT1.0 calculated metrics. There was strong agreement between programmatically and manually calculated measures. Automated analysis was also more efficient than nearly all manual methods. Conclusion: This approach provides fast, accurate assessment of VF motion in rats with minimal labor and allows for quantitative comparison of lateral differences in movement. Through this novel analysis method, we can differentiate healthy movement from unilateral VFP. RVT1.0 is open-source and will be a valuable tool for researchers using the rat model for laryngology research. Level of evidence: NA Laryngoscope, 134:340-346, 2024.
MeSH term(s)	Rats ; Animals ; Vocal Cords/surgery ; Vocal Cord Paralysis/surgery ; Glottis ; Software
Chemical Substances	resolvin T1
Language	English
Publishing date	2023-08-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	80180-x
ISSN	1531-4995 ; 0023-852X
ISSN (online)	1531-4995
ISSN	0023-852X
DOI	10.1002/lary.30930
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Article ; Online: Temporal Expression of Hox Genes and Phox2b in the Rat Nucleus Ambiguus During Development: Implications on Laryngeal Innervation.

Honzel, Emily / Hernandez-Morato, Ignacio / Joshi, Abhinav / Pennington-Fitzgerald, William / Moayedi, Yalda / Pitman, Michael J

The Laryngoscope

2023 Volume 133, Issue 12, Page(s) 3462–3471

Abstract: Objectives: Recurrent laryngeal nerve (RLN) injury results in synkinetic reinnervation and vocal fold paralysis. Investigation of cues expressed in the developing brainstem that influence correct selective targeting of intrinsic laryngeal muscles may ... ...

Abstract	Objectives: Recurrent laryngeal nerve (RLN) injury results in synkinetic reinnervation and vocal fold paralysis. Investigation of cues expressed in the developing brainstem that influence correct selective targeting of intrinsic laryngeal muscles may elucidate post-injury abnormalities contributing to non-functional reinnervation. Primary targets of interest were Hoxb1 and Hoxb2, members of the Hox family that create overlapping gradients in the developing brain, and their target Phox2b, a transcription factor necessary for cranial nerve branchio- and visceromotoneuron survival. Methods: Rat embryos at developmental days E14, E16, E18, and E20 (4 animals/age) were sectioned for RNA in situ hybridization to detect Hoxb1, Hoxb2, and Phox2b mRNA within the brainstem. Slides were costained with Islet1 antibody for identification of the nucleus ambiguus. Results were confirmed using immunohistochemistry. Sections were imaged on a confocal microscope. RNA and protein expressions were quantified using QuPath. Statistical analyses were performed using R. Results: Hoxb1, Hoxb2, and Phox2b expressions varied according to embryologic age. Hoxb1 and Hoxb2 expression peaked at E16, with significant decreases at E18 and E20 (one-way ANOVA p = 0.001 for both). Phox2b expression was highest at E14 and trended downward with increased embryologic age (one-way ANOVA p = 0.005). Conclusion: Peak expression of Hoxb1 and Hoxb2 is observed at time points when the RLN arrives at the larynx and begins to branch toward individual muscles, positioning these gene products to be involved in cueing laryngeal motoneuron identity and target identification. Higher expression of Phox2b earlier in development suggests a role in laryngeal motoneuron formation. Level of evidence: NA Laryngoscope, 133:3462-3471, 2023.
MeSH term(s)	Rats ; Animals ; Genes, Homeobox ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Medulla Oblongata ; Laryngeal Muscles/innervation ; Recurrent Laryngeal Nerve Injuries ; RNA ; Recurrent Laryngeal Nerve
Chemical Substances	Transcription Factors ; RNA (63231-63-0)
Language	English
Publishing date	2023-06-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80180-x
ISSN	1531-4995 ; 0023-852X
ISSN (online)	1531-4995
ISSN	0023-852X
DOI	10.1002/lary.30826
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Article ; Online: High-Resolution Melting-Based Marker Development for Wheat Leaf Rust Resistance Gene Lr34

Kaur, Shivreet / Pennington, Taylor / Conley, Emily J. / Green, Andrew / Kolmer, James / Anderson, James / Gupta, Rajiv / Gill, Upinder

Phytopathology®. 2023 Mar., v. 113, no. 3 p.508-515

2023

Abstract: Deploying adult plant resistance (APR) against rust diseases is an important breeding objective of most wheat-breeding programs. The gene Lr34 is an effective and widely deployed broad-spectrum APR gene in wheat against leaf rust fungus Puccinia ... ...

Abstract	Deploying adult plant resistance (APR) against rust diseases is an important breeding objective of most wheat-breeding programs. The gene Lr34 is an effective and widely deployed broad-spectrum APR gene in wheat against leaf rust fungus Puccinia triticina. Various molecular markers have been developed for Lr34, but they either require post-PCR handling processes or are not economical. Herein, we developed a high-resolution melting (HRM)-based diagnostic assay for Lr34 based on a 3-bp ‘TTC’ deletion in exon 11 of the resistant allele. The susceptible cultivar Thatcher (Tc) and the near-isogenic Thatcher line (RL6058) with Lr34 yielded distinct melting profiles and were differentiated with high reproducibility. For further validation, all three copies of Lr34 were cloned in plasmid vectors, and HRM analysis using individual and combination (equimolar mixture of three copies) homoeologs yielded distinct melting profiles. An additional layer of genotyping was provided by a LunaProbe assay. The allele-specific probes successfully distinguished the homoeologs but not Tc and RL6058. Furthermore, the practical deployment of the HRM assay was tested by running the marker on a set of breeding lines. When compared with a kompetitive allele-specific PCR (KASP) Lr34 assay, the HRM assay had similar genotyping results and was able to accurately differentiate the resistant and susceptible breeding lines. However, our HRM assay was unable to detect the heterozygote. To our knowledge, this is the first report of an HRM assay for genotyping a wheat rust resistance gene.
Keywords	Puccinia recondita ; alleles ; cultivars ; exons ; fungi ; genotyping ; heterozygosity ; leaf rust ; mature plants ; plasmids ; resistance genes ; wheat ; adult plant resistance ; high-resolution melting ; Lr34 ; molecular marker
Language	English
Dates of publication	2023-03
Size	p. 508-515.
Publishing place	The American Phytopathological Society
Document type	Article ; Online
ZDB-ID	208889-7
ISSN	1943-7684 ; 0031-949X
ISSN (online)	1943-7684
ISSN	0031-949X
DOI	10.1094/PHYTO-08-22-0313-R
Database	NAL-Catalogue (AGRICOLA)

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