Faculty Opinions recommendation of Genetic segregation of inflammatory lung disease and autoimmune disease severity in SHIP-1-/- mice.

Author(s):  
John Cambier ◽  
Thomas Packard
2011 ◽  
Vol 186 (12) ◽  
pp. 7164-7175 ◽  
Author(s):  
Mhairi J. Maxwell ◽  
Mubing Duan ◽  
Jane E. Armes ◽  
Gary P. Anderson ◽  
David M. Tarlinton ◽  
...  

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. Wong ◽  
Z. Q. Lin ◽  
L. Wang ◽  
A. G. Chung ◽  
B. Shen ◽  
...  

AbstractA critical step in effective care and treatment planning for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause for the coronavirus disease 2019 (COVID-19) pandemic, is the assessment of the severity of disease progression. Chest x-rays (CXRs) are often used to assess SARS-CoV-2 severity, with two important assessment metrics being extent of lung involvement and degree of opacity. In this proof-of-concept study, we assess the feasibility of computer-aided scoring of CXRs of SARS-CoV-2 lung disease severity using a deep learning system. Data consisted of 396 CXRs from SARS-CoV-2 positive patient cases. Geographic extent and opacity extent were scored by two board-certified expert chest radiologists (with 20+ years of experience) and a 2nd-year radiology resident. The deep neural networks used in this study, which we name COVID-Net S, are based on a COVID-Net network architecture. 100 versions of the network were independently learned (50 to perform geographic extent scoring and 50 to perform opacity extent scoring) using random subsets of CXRs from the study, and we evaluated the networks using stratified Monte Carlo cross-validation experiments. The COVID-Net S deep neural networks yielded R$$^2$$ 2 of $$0.664 \pm 0.032$$ 0.664 ± 0.032 and $$0.635 \pm 0.044$$ 0.635 ± 0.044 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively, in stratified Monte Carlo cross-validation experiments. The best performing COVID-Net S networks achieved R$$^2$$ 2 of 0.739 and 0.741 between predicted scores and radiologist scores for geographic extent and opacity extent, respectively. The results are promising and suggest that the use of deep neural networks on CXRs could be an effective tool for computer-aided assessment of SARS-CoV-2 lung disease severity, although additional studies are needed before adoption for routine clinical use.


Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 441
Author(s):  
Fanny Pineau ◽  
Davide Caimmi ◽  
Sylvie Taviaux ◽  
Maurane Reveil ◽  
Laura Brosseau ◽  
...  

Cystic fibrosis (CF) is a chronic genetic disease that mainly affects the respiratory and gastrointestinal systems. No curative treatments are available, but the follow-up in specialized centers has greatly improved the patient life expectancy. Robust biomarkers are required to monitor the disease, guide treatments, stratify patients, and provide outcome measures in clinical trials. In the present study, we outline a strategy to select putative DNA methylation biomarkers of lung disease severity in cystic fibrosis patients. In the discovery step, we selected seven potential biomarkers using a genome-wide DNA methylation dataset that we generated in nasal epithelial samples from the MethylCF cohort. In the replication step, we assessed the same biomarkers using sputum cell samples from the MethylBiomark cohort. Of interest, DNA methylation at the cg11702988 site (ATP11A gene) positively correlated with lung function and BMI, and negatively correlated with lung disease severity, P. aeruginosa chronic infection, and the number of exacerbations. These results were replicated in prospective sputum samples collected at four time points within an 18-month period and longitudinally. To conclude, (i) we identified a DNA methylation biomarker that correlates with CF severity, (ii) we provided a method to easily assess this biomarker, and (iii) we carried out the first longitudinal analysis of DNA methylation in CF patients. This new epigenetic biomarker could be used to stratify CF patients in clinical trials.


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 7.2-7
Author(s):  
A. Santaniello ◽  
C. Bellocchi ◽  
L. Bettolini ◽  
M. Cassavia ◽  
G. Montanelli ◽  
...  

Background:The staging of interstitial lung disease (ILD) is important to monitor disease progression and for prognostication. A disease severity scale of Systemic Sclerosis (SSc)-related lung disease has long been proposed (i.e. Medsger’s severity scale). This scale was mostly developed by discussion and consensus and stage thresholds were not computed by a data-driven approach. Hidden Markov models (HMM) are methods to estimate population quantities for chronic diseases with a staged interpretation which are diagnosed by markers measured at irregular intervals.Objectives:To build a SSc-ILD specific disease severity scale with prognostic relevance via HMM modeling.Methods:A total of 358 SSc patients at risk for or with ILD were enrolled in a discovery (207 cases, Milan1) and in a validation (151 cases, Milan2, Pavia and Rome) cohort. Patients were included if satisfied the following criteria: 1) Diagnosis of SSc according to the EULAR/ACR 2013 criteria, 2) absence of anticentromere antibodies, 3) dcSSc subset or 4) other subsets with either 4a) ILD-related antibodies (Scl70, PmScl, Ku) or 4b) evidence of ILD on HRCT, 5) disease duration < 5 years at the time of the first pulmonary function test (PFT). Serial PFTs were retrieved and the time up to the last available visit -if the patient alive-, or to death due to pulmonary complications, was recorded. HMM were used to estimate the threshold of a 3-stage model (SL3SI, Scleroderma Lung 3-Stage Index) based on PFT functional values (normal/mild, moderate, severe involvement) in the discovery cohort. Survival estimates of the SL3SI model were compared to Medsger’s severity classes estimates and their predictive capability evaluated via the explained residual variation (R2) of prediction errors (the higher the better). One-hundred random replicates were generated to simulate the prediction effort in patients with different disease duration and lung severity.Results:Patients characteristics are summarized in the Table. Fifteen-years survival estimates for Mesdger’s classes in the discovery set were: normal=0.88, mild=0.86, moderate=0.84 and severe=0.71. The SL3SI was defined by the following thresholds: normal/mild, FVC and DLco >=75%; moderate FVC or DLco 74-55%; severe, FVC or DLco <55%. SL3SI 15-yrs survival estimates were: normal/mild=0.89, moderate=0.82 and severe=0.63. Prediction analysis showed a higher R2values at 15 yrs for the SL3SI compared to Medsger’s classes, providing evidence for a better predictive capability of the former (discovery: 0.31 vs 0.25; validation: 0.28 vs 0.19).Conclusion:The SL3SI, a simplified 3-stage functional model of SSc-ILD, yields better survival estimates and long-term prognostic information than Medsger’s classes. Its reproducibility and ease of use make it a useful tool for the functional and prognostic evaluation of SSc patients at risk for or with ILD.Table:VariablesDiscovery (n=207)Replication (n=151)DcSSc62 (30%)98 (64%)Age at first PFR48.6±1249.1±14.4Disease duration at first PFR1.7±1.61.3±2.4FVC90.5±18.191.1±20.2DLco70.7±19.861.3±20.1ILD on HRCT179 (86%)125 (80%)Scl70157 (76%)153 (78%)SSA63 (30%)32 (21%)n of visits38571473Follow-up time, yrs11±5.610.6±5.7Deaths27 (13%)23 (15%)Disclosure of Interests:Alessandro Santaniello: None declared, Chiara Bellocchi: None declared, Luca Bettolini: None declared, Marcello Cassavia: None declared, Gaia Montanelli: None declared, Adriana Severino: None declared, Monica Caronni: None declared, Corrado Campochiaro Speakers bureau: Novartis, Pfizer, Roche, GSK, SOBI, Enrico De Lorenzis: None declared, Gerlando Natalello: None declared, Paolo Delvino: None declared, Claudio Tirelli: None declared, Lorenzo Cavagna: None declared, Giacomo De Luca Speakers bureau: SOBI, Novartis, Celgene, Pfizer, MSD, Silvia Laura Bosello: None declared, Lorenzo Beretta Grant/research support from: Pfizer


2021 ◽  
pp. 106539
Author(s):  
Yannick Molgat-Seon ◽  
Sabina A. Guler ◽  
Carli M. Peters ◽  
Dragoş M. Vasilescu ◽  
Joseph H. Puyat ◽  
...  

2004 ◽  
Vol 98 (11) ◽  
pp. 1131-1137 ◽  
Author(s):  
Fumiko Kinoshita ◽  
Hidefumi Hamano ◽  
Hiromi Harada ◽  
Toshibumi Kinoshita ◽  
Tadashi Igishi ◽  
...  

2017 ◽  
Vol 13 (6) ◽  
pp. 1172-1181 ◽  
Author(s):  
Li Su ◽  
Lei Shi ◽  
Jian Liu ◽  
Lifei Huang ◽  
Yi Huang ◽  
...  

Asthma is a chronic inflammatory lung disease that leads to 250 000 deaths annually.


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