Citations

PURPOSE Manual extraction of treatment outcomes from unstructured oncology clinical notes is a significant challenge for real-world evidence (RWE) generation. This study aimed to develop and evaluate a robust natural language processing (NLP) system to automatically extract cancer treatments and their associated RECIST-based response categories (complete response, partial response, stable disease, and progressive disease) from non–small cell lung cancer (NSCLC) clinical notes. METHODS This retrospective NLP development and validation study used a corpus of 250 NSCLC oncology notes from University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, annotated by physician experts. An end-to-end NLP pipeline was designed, integrating a rule-based module for entity extraction (treatments and responses) and a machine learning module using biomedical clinical bidirectional encoder representations from transformers for relation classification. The system's performance was evaluated on a held-out test set, with partial external validation for relation extraction on a Mayo Clinic data set. RESULTS The NLP system achieved high overall accuracy. On the UPMC test set (64 notes), the relation classification model attained an area under the receiver operating characteristic curve of 0.94 and an F1 score of 0.92 for linking treatments with documented responses. The rule-based entity extraction demonstrated a macro-averaged F1 score of 0.87 (precision 0.98, recall 0.81). Although precision was high for chemotherapy and most response types (1.00), recall for cancer surgery was 0.45. External validation at Mayo Clinic showed moderate relation extraction F1 scores (range: 0.51-0.64). CONCLUSION The proposed NLP system can reliably extract structured treatment and response information from unstructured NSCLC oncology notes with high accuracy. This automated approach can assist in abstracting critical cancer treatment outcomes from clinical narrative text, thereby streamlining real-world data analysis and supporting the generation of RWE in oncology.

The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Small Cell Lung Cancer provide recommendations for diagnostic workup, staging, and treatment. These NCCN Guidelines Insights highlight recent updates, with a particular focus on changes to systemic therapies and radiation treatment in the NCCN Guidelines for Small Cell Lung Cancer.

Abstract Introduction: Maintenance of donor lung pressure is recommended to maintain inflation pressures of 12-15 mm Hg. This is particularly important given graft transportation in aircraft, due to the inevitable pressure changes. Case: We describe a case of a donor lung preservation system which maintained proper airway pressure during sudden cabin pressure loss requiring emergent landing. Discussion: The donor lungs were implanted without complication. Post-transplant course was notable for primary graft dysfunction (PGD) grade 1 at 24 hours, grade 2 at 48 hours, and grade 1 at 72 hours. At 3 months post-transplant, the patient has had no respiratory complications and has been noted to be doing well.

Airway hyperreactivity and hASM cell proliferation (hyperplasia) are hallmark characteristics of asthma. The results of the present study showed that short-term exposure of nonasthmatic hASM to TNFα (a proinflammatory cytokine) can also induce hASM cell proliferation via activation of an ER stress pathway. Identification of the ER stress signaling pathway as important in mediating hASM hyperplasia may provide an important therapeutic target for treating asthma or acute inflammation.

Background: Studies in the past have demonstrated an association between sarcoidosis and pulmonary embolism (PE), but little is known about its impact, especially in young adults. We aim to determine the burden and impact of PE in young adults hospitalized with sarcoidosis. Methods: This study investigates the prevalence and consequences of PE in young adults aged 18–44 years hospitalized with sarcoidosis using data from the National Inpatient Sample (2016–2020) with relevant International Classification of Diseases (ICD)-10 codes. This study aims to address the primary outcomes of the burden and trends of PE and its associated impact on in-hospital mortality. Additionally, it explores secondary outcomes such as healthcare resource utilization and discharge patterns. Results: Among 50,385 young adults (median age 37 years) hospitalized with sarcoidosis, 1120 had PE, showing a linear increase from 2% in 2016 to 2.9% ( P < 0.001) in 2020. The sarcoidosis–PE+ group, predominantly in young blacks, exhibited a higher prevalence of comorbidities such as obesity, smoking, drug use, peripheral vascular disease, hypothyroidism and prior history of venous thrombus embolism. In contrast, the sarcoidosis–PE− group had a higher prevalence of diabetes (with/without chronic complication), hyperlipidemia and chronic pulmonary disease. Multivariable regression analysis adjusted for all potential sociodemographic and comorbid variables showed higher odds of all-cause mortality (odds ratio [OR]: 2.92, 95% confidence interval [CI]: 1.18–7.24, P < 0.02) in the sarcoidosis–PE+ group as compared to the sarcoidosis–PE− group. The sarcoidosis–PE+ group also had higher hospital costs and length of stay. Conclusion: The higher odds of in-hospital mortality with an increased length of stay and hospital cost observed in the sarcoidosis–PE+ group highlight the often underreported complications of sarcoidosis, particularly in a younger demographic. The relevance of this study stems from its potential to uncover trends that could lead to improved diagnostic and therapeutic strategies.

Multiplex immunofluorescence and immunohistochemistry (mIF/IHC) are increasingly employed antibody-based technologies that use tissue sparingly and facilitate the detection of co-localized or neighboring biomarkers. Specifically, these platforms enable spatial analyses of the tumor microenvironment as well as extended applications, for example, describing normal tissue anatomy, autoimmunity, infectious diseases, etc. mIF/IHC has greatly enhanced biomarker discovery efforts, and a growing number of studies suggest superiority to traditional IHC. Standardization of staining approaches, reporting of image analysis strategies and resultant data is critical for facilitating cross-study comparisons, validation, deployment, and generalization of findings. To address this challenge, The Society for Immunotherapy of Cancer (SITC) previously published two articles providing best practice guidelines for mIF/IHC staining, image analysis, and data sharing. Here, SITC convened stakeholders to develop the third article in the series, a consensus checklist for scientific reporting of mIF/IHC data to support and complement the best practice guidelines. The checklist includes critical components of mIF/IHC applications to be defined within publications such as detailed descriptions of analytical validation; image acquisition, selection, and registration methods; and cell clustering and spatial analysis strategies, amongst others. Such information will help with data reproducibility and comparison across studies towards future drug and assay development.

Introduction Despite the identification of multiple susceptibility loci by genome-wide association studies (GWAS), considerable chronic obstructive pulmonary disease (COPD) heritability remains unexplained. Aim To identify interaction networks of airway epithelial cell DNA methylation in COPD and further explore potential correlations with airway bacterial composition, as potentially collective regulators of biological pathways influencing COPD severity. Methods Using DNA isolated from bronchial airway brushings of 67 ever-smokers (>20 pack-years) from the SubPopulations and InteRmediate Outcomes Measures in COPD Study (SPIROMICS), we assessed proportion of DNA methylation (β) by epigenome-wide association study (EWAS) and examined associations of differentially methylated CpG probes (DMPs) with risk for moderate-to-severe COPD (N=34) versus absent or mild COPD (N=33). We tested co-methylation modules generated by Weighted Correlation Network Analyses (WGCNA) for associations with moderate-to-severe COPD and with bacterial genus-level relative abundances (16S rRNA sequencing). Results EWAS-identified nominally significant DMPs enriched for lung function GWAS loci. Eigengenes in six WGCNA modules were associated with moderate-to-severe COPD (false discovery rate <0.05). Four of those modules were enriched for forced expiratory volume in 1 s/forced vital capacity GWAS loci, and five overlapped with DMPs from EWAS. Overlapping CpG loci in three COPD-associated modules were adjacent to mucin genes; one had 10 genes highly ranked by connectivity with MUC5B, including important pathway genes: B3GNT6 , DGKI and ITGA8 . CpGs in an independent COPD-associated module showed the most correlations with Rothia , with directionality suggestive of negative associations with moderate-severe COPD. Conclusions Bronchial epithelial DNA methylation modules enriched for lung function GWAS loci associate with COPD severity in SPIROMICS. Potential module relationships to bronchial bacterial composition require further validation.

Importance Primary mitral regurgitation (MR) is a prevalent valvular lesion. Current American College of Cardiology/American Heart Association guidelines include class I recommendations for intervention for severe primary MR at the onset of symptoms, significant left ventricular (LV) enlargement (end-systolic dimension ≥40 mm), or dysfunction (ejection fraction ≤60%), with a class IIA recommendation for mitral valve repair when performed at an experienced surgical center. Recent data suggest a survival penalty when waiting for class I surgical guideline indications, and novel markers of decompensation are under investigation. Observations Comprehensive assessment of MR severity using echocardiography is critical, and when warranted, cardiac magnetic resonance (CMR) is complementary. Assessment of LV size and function, as well as serial changes in both, is crucial for determining timing of surgery. New-onset atrial fibrillation, left atrial enlargement, pulmonary hypertension, and exercise-induced changes in LV function should also be considered in borderline scenarios. The roles of LV volumes, global longitudinal strain, CMR-derived measures of myocardial dysfunction, and cardiac biomarkers are worthy of further investigation regarding consideration for early surgical intervention. Conclusions and Relevance A more refined approach incorporating assessment of extravalvular cardiac injury, novel imaging markers, and biomarkers is needed to optimize surgical timing in primary MR. Further research is warranted to validate these emerging parameters and refine guidelines to improve patient outcomes.

Background: Interstitial lung disease (ILD) involves numerous chronic pulmonary conditions that damage the lung parenchyma and alveolar interstitium. ILD has overlapping clinical and radiological features with other commonly seen cardiac and respiratory conditions. If not identified and treated in a timely manner, it may lead to irreversible fibrosis and a poor prognosis in the patient. The current diagnostic methods are either invasive or reliant on imaging or specialist interpretation, which can lead to diagnostic delay, increased radiation exposure, and healthcare costs. Lung crackles, often under-recognized as a non-specific feature of ILD, may serve as an important diagnostic clue in identifying not only the early stages of ILD but also its subtypes. This review explores the potential of analyzing the lung sounds in ILD through AI-based auscultation. Objective: To provide a comprehensive analysis of the pathophysiological stages of lung injury in ILD, the specific acoustic features, and the location associated with each ILD subtype and to evaluate the current state-of-the-art non-AI and AI methodologies that are used to diagnose ILD. This review aims to analyze the limitations associated with the current modalities and to envision AI-integrated auscultation as a powerful, cost-effective, non-invasive, radiation-free screening tool for early detection of ILD and its subtypes. Content Overview: The review begins with a detailed analysis of the lung sound pathophysiology, exploring the two-stage mechanism of alveolar epithelial injury and fibrosis formation. Existing hypotheses explaining the mechanism behind crackle production and the role of structural anatomy and surface tension in the generation of pathological lung sounds are examined. A tabulated summary of common ILD subtypes is provided, including their inciting events, pathogenesis, anatomical auscultation locations, and prognostic implications. Current diagnostic modalities for ILD, both non-AI and AI-based, are summarized along with their limitations, emphasizing the need for improved diagnostic tools. Discussion: Existing studies suggest that AI-based auscultation can match or exceed the current modalities in its sensitivity and specificity for detecting ILD-related crackles. Clinicians can identify the specific sound pattern and then correlate it with the ILD subtype and understand the prognosis in real time, thereby providing timely intervention to the patient. Additionally, AI-based auscultation can be used in resource-limited settings and can potentially reduce dependence on pulmonology expertise and radiation-based imaging for monitoring the condition. Conclusions: This literature review highlights the clinical potential of AI-based auscultation for early and accurate diagnoses of ILD. Understanding the associated pathological sounds, biomarkers, and genetic mutations linked to different subtypes opens avenues for future development of non-invasive diagnostic panels for ILD in clinical practice.

We report that moderate hyperoxia during a critical window of mucociliary differentiation disrupts terminal maturation in neonatal airway epithelial cells cultured in a three-dimensional model. Hyperoxia induces mitochondrial bioenergetic dysfunction and metabolic reprogramming, with proteomic analysis identifying complex I disruption as a key driver of impaired differentiation. Overall, these findings reveal a previously underrecognized link between mitochondrial bioenergetics and airway epithelial development, positioning metabolic dysfunction as an early trigger of hyperoxia-induced neonatal airway injury.