Dataset Information

Plethy: management of whole body plethysmography data in R.

ABSTRACT: Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known as plethysmographs that can measure thoracic movement. One such approach (the Buxco platform) performs unrestrained whole body plethysmography on mice which infers thoracic movements from pressure differences from the act of inhalation and exhalation. While proprietary software is available to perform basic statistical analysis as part of machine's bundled software, it is desirable to be able to incorporate these analyses into high-throughput pipelines and integrate them with other data types, as well as leverage the wealth of analytic and visualization approaches provided by the R statistical computing environment.This manuscript describes the plethy package which is an R/Bioconductor framework for pre-processing and analysis of plethysmography data with emphasis on larger scale longitudinal experiments. The plethy package was designed to facilitate quality control and exploratory data analysis. We provide a demonstration of the features of plethy using a dataset assessing the respiratory effects over time of SARS and Influenza infection in mice.The plethy package provides functionality for users to import, perform quality assessment and exploratory data analysis in a manner that allows interoperability with existing modelling tools. Our package is implemented in R and is freely available as part of the Bioconductor project http://www.bioconductor.org/packages/release/bioc/html/plethy.html .

SUBMITTER: Bottomly D

PROVIDER: S-EPMC4434826 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

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plethy: management of whole body plethysmography data in R.

Bottomly Daniel D Wilmot Beth B McWeeney Shannon K SK

BMC bioinformatics 20150429

<h4>Background</h4>Characterization of respiratory phenotypes can enhance complex trait and genomic studies involving allergic/autoimmune and infectious diseases. Many aspects of respiration can be measured using devices known as plethysmographs that can measure thoracic movement. One such approach (the Buxco platform) performs unrestrained whole body plethysmography on mice which infers thoracic movements from pressure differences from the act of inhalation and exhalation. While proprietary sof ...[more]

PMID: 25924931

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Project description:Brachycephalic obstructive airway syndrome (BOAS) is an important health and welfare problem in several popular dog breeds. Whole-body barometric plethysmography (WBBP) is a non-invasive method that allows safe and repeated quantitative measurements of respiratory cycles on unsedated dogs. Here respiratory flow traces in French bulldogs from the pet population were characterised using WBBP, and a computational application was developed to recognise affected animals. Eighty-nine French bulldogs and twenty non-brachycephalic controls underwent WBBP testing. A respiratory functional grading system was used on each dog based on respiratory signs (i.e. respiratory noise, effort, etc.) before and after exercise. For development of an objective BOAS classifier, functional Grades 0 and I were considered to have insignificant clinical signs (termed here BOAS-) and Grades II and III to have significant signs (termed here BOAS+). A comparison between owner-perception of BOAS and functional grading revealed that 60 % of owners failed to recognise BOAS in dogs that graded BOAS+ in this study.WBBP flow traces were found to be significantly different between non-brachycephalic controls and Grade 0 French bulldogs; BOAS- and BOAS+ French bulldogs. A classifier was developed using quadratic discriminant analysis of the respiratory parameters to distinguish BOAS- and BOAS + French bulldogs, and a BOAS Index was calculated for each dog. A cut-off value of the BOAS Index was selected based on a receiver operating characteristic (ROC) curve. Sensitivity, specificity, positive predictive value, and negative predictive value of the classifier on the training group (n=69) were 0.97, 0.93, 0.95, and 0.97, respectively. The classifier was validated using a test group of French bulldogs (n=20) with an accuracy of 0.95. WBBP offers objective screening for the diagnosis of BOAS in French Bulldogs. The technique may be applied to other brachycephalic breeds affected by BOAS, and possibly to other respiratory disease in dogs.

Project description:ObjectivesFeline lower airway disease (FLAD) is a common respiratory condition in cats. Traditionally, response to therapy is monitored only by evaluation of clinical signs and radiographic examination of the lungs. Barometric whole-body plethysmography (BWBP) is considered a non-invasive, well-tolerated form of measuring airway reactivity in cats. The aim of the study was to assess pulmonary function testing by BWBP for non-invasive evaluation of response to therapy in cats with FLAD and to investigate whether BWBP parameters correlate with clinical severity.Material and methodsThe prospective study included 25 client-owned cats, diagnosed with FLAD on the basis of their medical history, clinical signs, radiographic findings, and bronchoalveolar lavage fluid (BALF) examination. At three time points (day 0, 14, and 60), a standardised owner questionnaire, a clinical examination and BWBP measurements were carried out. Results of the questionnaire and the clinical examination were evaluated using a clinical 12-point score. Individual therapy was administered to all patients after diagnosis, based on the severity of disease and compliance of the cat.ResultsThe total clinical score significantly improved over the entire study period (p<0.001). Significant improvement was detected for the frequency of coughing (p = 0.009), respiratory distress (p = 0.001), lung auscultation findings (p = 0.002), and general condition and appetite (p = 0.045). The BWBP parameter Penh, an indicator of bronchoconstriction, improved significantly under initial therapy between day 0 and 14 (p = 0.009). A significant correlation between Penh and the severity of auscultation findings was seen on day 0 (r = 0.40; p = 0.013).ConclusionThe study supports the role of Penh as a non-invasive parameter for monitoring initial treatment response in cats with FLAD. Further studies are needed to address whether other BWBP parameters might be suitable for non-invasive therapy monitoring of FLAD. Clinical evaluation is always essential in cats with FLAD to evaluate treatment response.

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Plethy: management of whole body plethysmography data in R.

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plethy: management of whole body plethysmography data in R.

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