Adaptive multi-interventional trial platform to improve patient care for fibrotic interstitial lung diseases

BACKGROUND

Fibrotic interstitial lung diseases (fILDs) are a heterogeneous group of lung diseases associated with significant morbidity and mortality. Despite a large increase in the number of clinical trials in the last 10 years, current regulatory-approved management approaches are limited to two therapies that prevent the progression of fibrosis. The drug development pipeline is long and there is an urgent need to accelerate this process. This manuscript introduces the concept and design of an innovative research approach to drug development in fILD: a global Randomised Embedded Multifactorial Adaptive Platform in fILD (REMAP-ILD).

METHODS

Description of the REMAP-ILD concept and design: the specific terminology, design characteristics (multifactorial, adaptive features, statistical approach), target population, interventions, outcomes, mission and values, and organisational structure.

RESULTS

The target population will be adult patients with fILD, and the primary outcome will be a disease progression model incorporating forced vital capacity and mortality over 12 months. Responsive adaptive randomisation, prespecified thresholds for success and futility will be used to assess the effectiveness and safety of interventions. REMAP-ILD embraces the core values of diversity, equity, and inclusion for patients and researchers, and prioritises an open-science approach to data sharing and dissemination of results.

CONCLUSION

By using an innovative and efficient adaptive multi-interventional trial platform design, we aim to accelerate and improve care for patients with fILD. Through worldwide collaboration, novel analytical methodology and pragmatic trial delivery, REMAP-ILD aims to overcome major limitations associated with conventional randomised controlled trial approaches to rapidly improve the care of people living with fILD.

Mapping the blood vasculature in an intact human kidney using hierarchical phase-contrast tomography

The architecture of the kidney vasculature is essential for its function. Although structural profiling of the intact rodent kidney vasculature has been performed, it is challenging to map vascular architecture of larger human organs. We hypothesised that hierarchical phase-contrast tomography (HiP-CT) would enable quantitative analysis of the entire human kidney vasculature. Combining label-free HiP-CT imaging of an intact kidney from a 63-year-old male with topology network analysis, we quantitated vasculature architecture in the human kidney down to the scale of arterioles. Although human and rat kidney vascular topologies are comparable, vascular radius decreases at a significantly faster rate in humans as vessels branch from artery towards the cortex. At branching points of large vessels, radii are theoretically optimised to minimise flow resistance, an observation not found for smaller arterioles. Structural differences in the vasculature were found in different spatial zones of the kidney reflecting their unique functional roles. Overall, this represents the first time the entire arterial vasculature of a human kidney has been mapped providing essential inputs for computational models of kidney vascular flow and synthetic vascular architectures, with implications for understanding how the structure of individual blood vessels collectively scales to facilitate organ function.

Delineating excess comorbidities in idiopathic pulmonary fibrosis: an observational study

BACKGROUND

Our study examined whether prevalent and incident comorbidities are increased in idiopathic pulmonary fibrosis (IPF) patients when compared to matched chronic obstructive pulmonary disease (COPD) patients and control subjects without IPF or COPD.

METHODS

IPF and age, gender and smoking matched COPD patients, diagnosed between 01/01/1997 and 01/01/2019 were identified from the Clinical Practice Research Datalink GOLD database multiple registrations cohort at the first date an ICD-10 or read code mentioned IPF/COPD. A control cohort comprised age, gender and pack-year smoking matched subjects without IPF or COPD. Prevalent (prior to IPF/COPD diagnosis) and incident (after IPF/COPD diagnosis) comorbidities were examined. Group differences were estimated using a t-test. Mortality relationships were examined using multivariable Cox proportional hazards adjusted for patient age, gender and smoking status.

RESULTS

Across 3055 IPF patients, 38% had 3 or more prevalent comorbidities versus 32% of COPD patients and 21% of matched control subjects. Survival time reduced as the number of comorbidities in an individual increased (p < 0.0001). In IPF, prevalent heart failure (Hazard ratio [HR] = 1.62, 95% Confidence Interval [CI]: 1.43-1.84, p < 0.001), chronic kidney disease (HR = 1.27, 95%CI: 1.10-1.47, p = 0.001), cerebrovascular disease (HR = 1.18, 95%CI: 1.02-1.35, p = 0.02), abdominal and peripheral vascular disease (HR = 1.29, 95%CI: 1.09-1.50, p = 0.003) independently associated with reduced survival. Key comorbidities showed increased incidence in IPF (versus COPD) 7-10 years prior to IPF diagnosis.

INTERPRETATION

The mortality impact of excessive prevalent comorbidities in IPF versus COPD and smoking matched controls suggests that multiorgan mechanisms of injury need elucidation in patients that develop IPF.

Enhancing cancer prediction in challenging screen-detected incident lung nodules using time-series deep learning

Lung cancer screening (LCS) using annual computed tomography (CT) scanning significantly reduces mortality by detecting cancerous lung nodules at an earlier stage. Deep learning algorithms can improve nodule malignancy risk stratification. However, they have typically been used to analyse single time point CT data when detecting malignant nodules on either baseline or incident CT LCS rounds. Deep learning algorithms have the greatest value in two aspects. These approaches have great potential in assessing nodule change across time-series CT scans where subtle changes may be challenging to identify using the human eye alone. Moreover, they could be targeted to detect nodules developing on incident screening rounds, where cancers are generally smaller and more challenging to detect confidently. Here, we show the performance of our Deep learning-based Computer-Aided Diagnosis model integrating Nodule and Lung imaging data with clinical Metadata Longitudinally (DeepCAD-NLM-L) for malignancy prediction. DeepCAD-NLM-L showed improved performance (AUC = 88%) against models utilizing single time-point data alone. DeepCAD-NLM-L also demonstrated comparable and complementary performance to radiologists when interpreting the most challenging nodules typically found in LCS programs. It also demonstrated similar performance to radiologists when assessed on out-of-distribution imaging dataset. The results emphasize the advantages of using time-series and multimodal analyses when interpreting malignancy risk in LCS.

Predicting histopathological features of aggressiveness in lung cancer using CT radiomics: a systematic review

PURPOSE

To examine the accuracy of CT radiomics to predict histopathological features of aggressiveness in lung cancer using a systematic review of test accuracy studies.

METHODS

Data sources searched included Medline, Embase, Web of Science, and Cochrane Library from up to 3 November 2023. Included studies reported test accuracy of CT radiomics models to detect the presence of: spread through air spaces (STAS), predominant adenocarcinoma pattern, adenocarcinoma grade, lymphovascular invasion (LVI), tumour infiltrating lymphocytes (TIL) and tumour necrosis, in patients with lung cancer. The primary outcome was test accuracy. Two reviewers independently assessed articles for inclusion and assessed methodological quality using the QUality Assessment of Diagnostic Accuracy Studies-2 tool. A single reviewer extracted data, which was checked by a second reviewer. Narrative data synthesis was performed.

RESULTS

Eleven studies were included in the final analysis. 10/11 studies were in East Asian populations. 4/11 studies investigated STAS, 6/11 investigated adenocarcinoma invasiveness or growth pattern, and 1/11 investigated LVI. No studies investigating TIL or tumour necrosis met inclusion criteria. Studies were of generally mixed to poor methodological quality. Reported accuracies for radiomic models ranged from 0.67 to 0.94.

CONCLUSION

Due to the high risk of bias and concerns regarding applicability, the evidence is inconclusive as to whether radiomic features can accurately predict prognostically important histopathological features of cancer aggressiveness. Many studies were excluded due to lack of external validation. Rigorously conducted prospective studies with sufficient external validity will be required for radiomic models to play a role in improving lung cancer outcomes.

Prognosis of glioblastoma patients improves significantly over time interrogating historical controls

BACKGROUND

Glioblastoma (GBM) is the most common devastating primary brain cancer in adults. In our clinical practice, median overall survival (mOS) of GBM patients seems increasing over time.

METHODS

To address this observation, we have retrospectively analyzed the prognosis of 722 newly diagnosed GBM patients, aged below 70, in good clinical conditions (i.e. Karnofsky Performance Status -KPS- above 70%) and treated in our department according to the standard of care (SOC) between 2005 and 2018. Patients were divided into two groups according to the year of diagnosis (group 1: from 2005 to 2012; group 2: from 2013 to 2018).

RESULTS

Characteristics of patients and tumors of both groups were very similar regarding confounding factors (age, KPS, MGMT promoter methylation status and treatments). Follow-up time was fixed at 24 months to ensure comparable survival times between both groups. Group 1 patients had a mOS of 19 months ([17.3-21.3]) while mOS of group 2 patients was not reached. The recent period of diagnosis was significantly associated with a longer mOS in univariate analysis (HR=0.64, 95% CI [0.51 - 0.81]), p < 0.001). Multivariate Cox analysis showed that the period of diagnosis remained significantly prognostic after adjustment on confounding factors (adjusted Hazard Ratio (aHR) 0.49, 95% CI [0.36-0.67], p < 0.001).

CONCLUSION

This increase of mOS over time in newly diagnosed GBM patients could be explained by better management of potentially associated non-neurological diseases, optimization of validated SOC, better management of treatments side effects, supportive care and participation in clinical trials.

Frequency and Nature of Genomic Alterations in ERBB2-Altered Urothelial Bladder Cancer

BACKGROUND

Human epidermal growth factor-2 (HER2) overexpression is an oncogenic driver in many solid tumors, including urothelial bladder cancer (UBC). In addition, activating mutations in the ERBB2 gene have been shown to play an oncogenic role similar to ERBB2 amplification.

OBJECTIVE

To describe and compare the frequency and nature of genomic alterations (GA) of ERBB2-altered (mutations, amplification) and ERBB2 wild-type UBC.

PATIENTS AND METHODS

Using a hybrid capture-based comprehensive profiling assay, 9518 UBC cases were grouped by ERBB2 alteration and evaluated for all classes of genomic alterations (GA), tumor mutational burden (TMB), microsatellite instability (MSI), genome-wide loss of heterozygosity (gLOH), and genomic mutational signature. PD-L1 expression was measured by immunohistochemistry (Dako 22C3). Categorical statistical comparisons were performed using Fisher's exact tests.

RESULTS

A total of 602 (6.3%) UBC cases featured ERBB2 extracellular domain short variant (SV) GA (ECDmut+), 253 (2.7%) cases featured ERBB2 kinase domain SV GA (KDmut+), 866 (9.1%) cases had ERBB2 amplification (amp+), and 7797 (81.9%) cases were ERBB2 wild-type (wt). European genetic ancestry of ECDmut+ was higher than ERBB2wt. Numerous significant associations were observed when comparing GA by group. Notably among these, CDKN2A/MTAP loss were more frequent in ERBB2wt versus ECDmut+ and amp+. ERBB3 GA were more frequent in ECDmut+ and KDmut+ than ERBB2wt. TERT GA were more frequent in ECDmut+, KDmut+, and amp+ versus ERBB2wt. TOP2A amplification was significantly more common in ECDmut+ and amp+ versus ERBB2wt, and TP53 SV GA were significantly higher in ERBB2 amp+ versus ERBB2wt. Mean TMB levels were significantly higher in ECDmut+, KDmut+, and amp+ than in ERBB2wt. Apolipoprotein B mRNA-editing enzyme, catalytic polypeptides (APOBEC) signature was more frequent in ECDmut+, KDmut+, and amp+ versus ERBB2wt. No significant differences were observed in PD-L1 status between groups, while gLOH-high status was more common in amp+ versus ERBB2wt. MSI-high status was more frequent in KDmut+ versus ERBB2wt, and in ERBB2wt than in amp+.

CONCLUSIONS

We noted important differences in co-occurring GA in ERBB2-altered (ECDmut+, KDmut+, amp+) versus ERBB2wt UBC, as well as higher mean TMB and higher APOBEC mutational signature in the ERBB2-altered groups. Our results can help refine future clinical trial designs and elucidate possible response and resistance mechanisms for ERBB2-altered UBC.

PICO questions and DELPHI methodology for improving the management of patients with acute hepatic porphyria

BACKGROUND

Acute hepatic porphyrias (AHPs) are a group of rare diseases that encompasses acute intermittent porphyria, variegate porphyria, hereditary coproporphyria, and 5-aminolaevulinic acid dehydratase deficiency porphyria. Symptoms of AHP are nonspecific which, together with its low prevalence, difficult the diagnosis and follow-up of these patients.

MATERIAL AND METHODS

This project used DELPHI methodology to answer PICO questions related to management of patients with AHPs. The objective was to reach a consensus among multidisciplinary porhyria experts providing answers to those PICO questions for improving diagnosis and follow-up of patients with AHP.

RESULTS

Ten PICO questions were defined and grouped in four domains: 1. Biochemical diagnosis of patients with AHP. 2. Molecular tests for patients with AHP. 3. Follow-up of patients with AHP. 4. Screening for long-term complications of patients with AHP.

CONCLUSIONS

PICO questions and DELPHI methodology have provided a consensus on relevant and controversial issues for improving the management of patients with AHP.

Expectation maximisation pseudo labels

In this paper, we study pseudo-labelling. Pseudo-labelling employs raw inferences on unlabelled data as pseudo-labels for self-training. We elucidate the empirical successes of pseudo-labelling by establishing a link between this technique and the Expectation Maximisation algorithm. Through this, we realise that the original pseudo-labelling serves as an empirical estimation of its more comprehensive underlying formulation. Following this insight, we present a full generalisation of pseudo-labels under Bayes' theorem, termed Bayesian Pseudo Labels. Subsequently, we introduce a variational approach to generate these Bayesian Pseudo Labels, involving the learning of a threshold to automatically select high-quality pseudo labels. In the remainder of the paper, we showcase the applications of pseudo-labelling and its generalised form, Bayesian Pseudo-Labelling, in the semi-supervised segmentation of medical images. Specifically, we focus on: (1) 3D binary segmentation of lung vessels from CT volumes; (2) 2D multi-class segmentation of brain tumours from MRI volumes; (3) 3D binary segmentation of whole brain tumours from MRI volumes; and (4) 3D binary segmentation of prostate from MRI volumes. We further demonstrate that pseudo-labels can enhance the robustness of the learned representations. The code is released in the following GitHub repository: https://github.com/moucheng2017/EMSSL.

Interstitial lung disease: a review of classification, etiology, epidemiology, clinical diagnosis, pharmacological and non-pharmacological treatment

Interstitial lung diseases (ILDs) refer to a heterogeneous and complex group of conditions characterized by inflammation, fibrosis, or both, in the interstitium of the lungs. This results in impaired gas exchange, leading to a worsening of respiratory symptoms and a decline in lung function. While the etiology of some ILDs is unclear, most cases can be traced back to factors such as genetic predispositions, environmental exposures (including allergens, toxins, and air pollution), underlying autoimmune diseases, or the use of certain medications. There has been an increase in research and evidence aimed at identifying etiology, understanding epidemiology, improving clinical diagnosis, and developing both pharmacological and non-pharmacological treatments. This review provides a comprehensive overview of the current state of knowledge in the field of interstitial lung diseases.

Ethnic differences in treatment outcome for children and young people accessing mental health support

Children and Young People (CYP) from minoritized ethnic backgrounds experience structural inequalities in Children and Young People's Mental Health Settings (CYPMHS). This mixed methods study explores whether CYP's ethnicity is associated with their treatment outcomes (operationalised as 'measurable change') from CYPMHS. A multilevel multi-nominal regression analysis, controlling for age, gender, referral source, presenting difficulty, case closure reason, suggests that CYP from Asian backgrounds (OR = 0.82, CI [0.70, 0.96]) and Mixed-race (odds ratio (OR) = 0.80; 95% CI [0.69, 0.92]) are less likely to report measurable improvement in mental health difficulties compared to White British CYP. Three themes from a thematic analysis of semi-structured interviews with 15 CYP from minoritized ethnic backgrounds focused on views and experiences of ending mental health support are also presented. CYP view personalised support and the right therapist as conducive to good endings and valued a range of outcomes pertaining to empowerment. Experiences of stigma and inequalities may begin to explain the less positive outcomes experienced by Asian and Mixed-race CYP found in the regression analysis. The implications of these findings and future areas of research are suggested.

Mortality surrogates in combined pulmonary fibrosis and emphysema

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) with coexistent emphysema, termed combined pulmonary fibrosis and emphysema (CPFE) may associate with reduced forced vital capacity (FVC) declines compared to non-CPFE IPF patients. We examined associations between mortality and functional measures of disease progression in two IPF cohorts.

METHODS

Visual emphysema presence (>0% emphysema) scored on computed tomography identified CPFE patients (CPFE/non-CPFE: derivation cohort n=317/n=183, replication cohort n=358/n=152), who were subgrouped using 10% or 15% visual emphysema thresholds, and an unsupervised machine-learning model considering emphysema and interstitial lung disease extents. Baseline characteristics, 1-year relative FVC and diffusing capacity of the lung for carbon monoxide (D LCO) decline (linear mixed-effects models), and their associations with mortality (multivariable Cox regression models) were compared across non-CPFE and CPFE subgroups.

RESULTS

In both IPF cohorts, CPFE patients with ≥10% emphysema had a greater smoking history and lower baseline D LCO compared to CPFE patients with <10% emphysema. Using multivariable Cox regression analyses in patients with ≥10% emphysema, 1-year D LCO decline showed stronger mortality associations than 1-year FVC decline. Results were maintained in patients suitable for therapeutic IPF trials and in subjects subgrouped by ≥15% emphysema and using unsupervised machine learning. Importantly, the unsupervised machine-learning approach identified CPFE patients in whom FVC decline did not associate strongly with mortality. In non-CPFE IPF patients, 1-year FVC declines ≥5% and ≥10% showed strong mortality associations.

CONCLUSION

When assessing disease progression in IPF, D LCO decline should be considered in patients with ≥10% emphysema and a ≥5% 1-year relative FVC decline threshold considered in non-CPFE IPF patients.

Small Airway Disease in Pre-Chronic Obstructive Pulmonary Disease with Emphysema: A Cross-Sectional Study

Rationale: Small airway disease is an important pathophysiological feature of chronic obstructive pulmonary disease (COPD). Recently, "pre-COPD" has been put forward as a potential precursor stage of COPD that is defined by abnormal spirometry findings or significant emphysema on computed tomography (CT) in the absence of airflow obstruction. Objective: To determine the degree and nature of (small) airway disease in pre-COPD using microCT in a cohort of explant lobes/lungs. Methods: We collected whole lungs/lung lobes from patients with emphysematous pre-COPD (n = 10); Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage I (n = 6), II (n = 6), and III/IV (n = 7) COPD; and controls (n = 10), which were analyzed using CT and microCT. The degree of emphysema and the number and morphology of small airways were compared between groups, and further correlations were investigated with physiologic measures. Airway and parenchymal pathology was also validated with histopathology. Measurements and Main Results: The numbers of transitional bronchioles and terminal bronchioles per milliliter of lung were significantly lower in pre-COPD and GOLD stages I, II, and III/IV COPD compared with controls. In addition, the number of alveolar attachments of the transitional bronchioles and terminal bronchioles was also lower in pre-COPD and all COPD groups compared with controls. We did not find any differences between the pre-COPD and COPD groups in CT or microCT measures. The percentage of emphysema on CT showed the strongest correlation with the number of small airways in the COPD groups. Histopathology showed an increase in the mean chord length and a decrease in alveolar surface density in pre-COPD and all GOLD COPD stages compared with controls. Conclusions: Lungs of patients with emphysematous pre-COPD already show fewer small airways and airway remodeling even in the absence of physiologic airway obstruction.

Serum C-reactive protein is associated with earlier mortality across different interstitial lung diseases

BACKGROUND AND OBJECTIVE

The acute-phase protein C-reactive protein (CRP) is known to be associated with poor outcomes in cancer and cardiovascular disease, but there is limited evidence of its prognostic implications in interstitial lung diseases (ILDs). We therefore set out to test whether baseline serum CRP levels are associated with mortality in four different ILDs.

METHODS

In this retrospective study, clinically measured CRP levels, as well as baseline demographics and lung function measures, were collected for ILD patients first presenting to the Royal Brompton Hospital between January 2010 and December 2019. Cox regression analysis was used to determine the relationship with 5-year mortality.

RESULTS

Patients included in the study were: idiopathic pulmonary fibrosis (IPF) n = 422, fibrotic hypersensitivity pneumonitis (fHP) n = 233, rheumatoid arthritis associated ILD (RA-ILD) n = 111 and Systemic Sclerosis associated ILD (SSc-ILD) n = 86. Patients with a recent history of infection were excluded. Higher CRP levels were associated with shorter 5-year survival in all four disease groups on both univariable analyses, and after adjusting for age, gender, smoking history, immunosuppressive therapy and baseline disease severity (IPF: HR (95% CI): 1.3 (1.1-1.5), p = 0.003, fHP: 1.5 (1.2-1.9), p = 0.001, RA-ILD: 1.4 (1.1-1.84), p = 0.01 and SSc-ILD: 2.7 (1.6-4.5), p < 0.001).

CONCLUSION

Higher CRP levels are independently associated with reduced 5-year survival in IPF, fHP, RA-ILD and SSc-ILD.

A formula for predicting emphysema extent in combined idiopathic pulmonary fibrosis and emphysema

BACKGROUND

No single pulmonary function test captures the functional effect of emphysema in idiopathic pulmonary fibrosis (IPF). Without experienced radiologists, other methods are needed to determine emphysema extent. Here, we report the development and validation of a formula to predict emphysema extent in patients with IPF and emphysema.

METHODS

The development cohort included 76 patients with combined IPF and emphysema at the Royal Brompton Hospital, London, United Kingdom. The formula was derived using stepwise regression to generate the weighted combination of pulmonary function data that fitted best with emphysema extent on high-resolution computed tomography. Test cohorts included patients from two clinical trials (n = 455 [n = 174 with emphysema]; NCT00047645, NCT00075998) and a real-world cohort from the Royal Brompton Hospital (n = 191 [n = 110 with emphysema]). The formula is only applicable for patients with IPF and concomitant emphysema and accordingly was not used to detect the presence or absence of emphysema.

RESULTS

The formula was: predicted emphysema extent = 12.67 + (0.92 x percent predicted forced vital capacity) - (0.65 x percent predicted forced expiratory volume in 1 second) - (0.52 x percent predicted carbon monoxide diffusing capacity). A significant relationship between the formula and observed emphysema extent was found in both cohorts (R2 = 0.25, P < 0.0001; R2 = 0.47, P < 0.0001, respectively). In both, the formula better predicted observed emphysema extent versus individual pulmonary function tests. A 15% emphysema extent threshold, calculated using the formula, identified a significant difference in absolute changes from baseline in forced vital capacity at Week 48 in patients with baseline-predicted emphysema extent < 15% versus ≥ 15% (P = 0.0105).

CONCLUSION

The formula, designed for use in patients with IPF and emphysema, demonstrated enhanced ability to predict emphysema extent versus individual pulmonary function tests.

TRIAL REGISTRATION

NCT00047645; NCT00075998.

Imaging of pulmonary fibrosis in children: A review, with proposed diagnostic criteria

Computed tomography (CT) imaging findings of pulmonary fibrosis are well established for adults and have been shown to correlate with prognosis and outcome. Recognition of fibrotic CT findings in children is more limited. With approved treatments for adult pulmonary fibrosis, it has become critical to define CT criteria for fibrosis in children, to identify patients in need of treatment and those eligible for clinical trials. Understanding how pediatric fibrosis compares with idiopathic pulmonary fibrosis and other causes of fibrosis in adults is increasingly important as these patients transition to adult care teams. Here, we review what is known regarding the features of pulmonary fibrosis in children compared with adults. Pulmonary fibrosis in children may be associated with genetic surfactant dysfunction disorders, autoimmune systemic disorders, and complications after radiation, chemotherapy, transplantation, and other exposures. Rather than a basal-predominant usual interstitial pneumonia pattern with honeycombing, pediatric fibrosis is primarily characterized by reticulation, traction bronchiectasis, architectural distortion, or cystic lucencies/abnormalities. Ground-glass opacities are more frequent in children with fibrotic interstitial lung disease than adults, and disease distribution appears more diffuse, without clearly defined axial or craniocaudal predominance. Following discussion and consensus amongst a panel of expert radiologists, pathologists and physicians, distinctive disease features were integrated to develop criteria for the first global Phase III trial in children with pulmonary fibrosis.

CenTime: Event-conditional modelling of censoring in survival analysis

Survival analysis is a valuable tool for estimating the time until specific events, such as death or cancer recurrence, based on baseline observations. This is particularly useful in healthcare to prognostically predict clinically important events based on patient data. However, existing approaches often have limitations; some focus only on ranking patients by survivability, neglecting to estimate the actual event time, while others treat the problem as a classification task, ignoring the inherent time-ordered structure of the events. Additionally, the effective utilisation of censored samples-data points where the event time is unknown- is essential for enhancing the model's predictive accuracy. In this paper, we introduce CenTime, a novel approach to survival analysis that directly estimates the time to event. Our method features an innovative event-conditional censoring mechanism that performs robustly even when uncensored data is scarce. We demonstrate that our approach forms a consistent estimator for the event model parameters, even in the absence of uncensored data. Furthermore, CenTime is easily integrated with deep learning models with no restrictions on batch size or the number of uncensored samples. We compare our approach to standard survival analysis methods, including the Cox proportional-hazard model and DeepHit. Our results indicate that CenTime offers state-of-the-art performance in predicting time-to-death while maintaining comparable ranking performance. Our implementation is publicly available at https://github.com/ahmedhshahin/CenTime.

Multi-task localization of the hemidiaphragms and lung segmentation in portable chest X-ray images of COVID-19 patients

Background

The COVID-19 can cause long-term symptoms in the patients after they overcome the disease. Given that this disease mainly damages the respiratory system, these symptoms are often related with breathing problems that can be caused by an affected diaphragm. The diaphragmatic function can be assessed with imaging modalities like computerized tomography or chest X-ray. However, this process must be performed by expert clinicians with manual visual inspection. Moreover, during the pandemic, the clinicians were asked to prioritize the use of portable devices, preventing the risk of cross-contamination. Nevertheless, the captures of these devices are of a lower quality.

Objectives

The automatic quantification of the diaphragmatic function can determine the damage of COVID-19 on each patient and assess their evolution during the recovery period, a task that could also be complemented with the lung segmentation.

Methods

We propose a novel multi-task fully automatic methodology to simultaneously localize the position of the hemidiaphragms and to segment the lung boundaries with a convolutional architecture using portable chest X-ray images of COVID-19 patients. For that aim, the hemidiaphragms' landmarks are located adapting the paradigm of heatmap regression.

Results

The methodology is exhaustively validated with four analyses, achieving an 82.31% ± 2.78% of accuracy when localizing the hemidiaphragms' landmarks and a Dice score of 0.9688 ± 0.0012 in lung segmentation.

Conclusions

The results demonstrate that the model is able to perform both tasks simultaneously, being a helpful tool for clinicians despite the lower quality of the portable chest X-ray images.

HPV-positive clinically advanced squamous cell carcinoma of the urinary bladder (aBSCC): A comprehensive genomic profiling (CGP) study

BACKGROUND

Advanced bladder squamous cell carcinoma (aBSCC) is an uncommon form of urinary bladder malignancy when compared with the much higher urothelial carcinoma incidence. We studied the genomic alteration (GA) landscape in a series of aBSCC based on the association with human papilloma virus (HPV) to determine if differences in GA would be observed between the positive and negative groups.

METHODS

Using a hybrid capture-based FDA-approved CGP assay, a series of 171 aBSCC were sequenced to evaluate all classes of GA. Tumor mutational burden (TMB) was determined on up to 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined on up to 114 loci. Programmed cell death ligand -1 (PD-L1) expression was determined by IHC (Dako 22C3) with negative expression when PD-L1 was 0, lower expression of positivity set at 1 to 49%, and higher expression set at ≥50% expression.

RESULTS

Overall, 11 (6.4%) of the aBSCC were found to harbor HPV sequences (10 HPV16 and 1 HPV 11). HPV+ status was identified slightly more often in women (NS) and in younger patients (P = 0.04); 2 female patients with aBSCC had a prior history of SCC including 1 anal SCC and 1 vaginal SCC. HPV+ aBSCC had fewer GA/tumor (P < 0.0001), more inactivating mutations in RB1 (P = 0.032), and fewer inactivating GA in CDKN2A (P < 0.0001), CDKN2B (P = 0.05), TERT promoter (P = 0.0004) and TP53 (P < 0.0001). GA in genes associated with urothelial carcinoma including FGFR2 and FGFR3 were similar in both HPV+ and HPV- aBSCC groups. MTAP loss (homozygous deletion) which has emerged as a biomarker for PRMT5 inhibitor-based clinical trials was not identified in any of the 11 HPV+ aBSCC cases, which was significantly lower than the 28% positive frequency of MTAP loss in the HPV- aBSCC group (P < 0.0001). MTOR and PIK3CA pathway GA were not significantly different in the 2 groups. Putative biomarkers associated with immunotherapy (IO) response, including MSI and TMB status, were also similar in the 2 groups. PD-L1 expression data was available for a subset of both HPV+ and HPV- cases and showed high frequencies of positive staining which was not different in the 2 groups.

CONCLUSIONS

HPV+ aBSCC tends to occur more often in younger patients. As reported in other HPV-associated squamous cell carcinomas, HPV+ aBSCC demonstrates significantly reduced frequencies of inactivating mutations in cell cycle regulatory genes with similar GA in MTOR and PIK3CA pathways. The implication of HPV in the pathogenesis of bladder cancer remains unknown but warrants further exploration and clinical validation.

Evaluating a Remote Monitoring Program for Respiratory Diseases: Prospective Observational Study

BACKGROUND

Patients with chronic respiratory diseases and those in the postdischarge period following hospitalization because of COVID-19 are particularly vulnerable, and little is known about the changes in their symptoms and physiological parameters. Continuous remote monitoring of physiological parameters and symptom changes offers the potential for timely intervention, improved patient outcomes, and reduced health care costs.

OBJECTIVE

This study investigated whether a real-time multimodal program using commercially available wearable technology, home-based Bluetooth-enabled spirometers, finger pulse oximeters, and smartphone apps is feasible and acceptable for patients with chronic respiratory diseases, as well as the value of low-burden, long-term passive data collection.

METHODS

In a 3-arm prospective observational cohort feasibility study, we recruited 60 patients from the Royal Free Hospital and University College Hospital. These patients had been diagnosed with interstitial lung disease, chronic obstructive pulmonary disease, or post-COVID-19 condition (n=20 per group) and were followed for 180 days. This study used a comprehensive remote monitoring system designed to provide real-time and relevant data for both patients and clinicians. Data were collected using REDCap (Research Electronic Data Capture; Vanderbilt University) periodic surveys, Remote Assessment of Disease and Relapses-base active app questionnaires, wearables, finger pulse oximeters, smartphone apps, and Bluetooth home-based spirometry. The feasibility of remote monitoring was measured through adherence to the protocol, engagement during the follow-up period, retention rate, acceptability, and data integrity.

RESULTS

Lowest-burden passive data collection methods, via wearables, demonstrated superior adherence, engagement, and retention compared with active data collection methods, with an average wearable use of 18.66 (SD 4.69) hours daily (77.8% of the day), 123.91 (SD 33.73) hours weekly (72.6% of the week), and 463.82 (SD 156.70) hours monthly (64.4% of the month). Highest-burden spirometry tasks and high-burden active app tasks had the lowest adherence, engagement, and retention, followed by low-burden questionnaires. Spirometry and active questionnaires had the lowest retention at 0.5 survival probability, indicating that they were the most burdensome. Adherence to and quality of home spirometry were analyzed; of the 7200 sessions requested, 4248 (59%) were performed. Of these, 90.3% (3836/4248) were of acceptable quality according to American Thoracic Society grading. Inclusion of protocol holidays improved retention measures. The technologies used were generally well received.

CONCLUSIONS

Our findings provide evidence supporting the feasibility and acceptability of remote monitoring for capturing both subjective and objective data from various sources for respiratory diseases. The high engagement level observed with passively collected data suggests the potential of wearables for long-term, user-friendly remote monitoring in respiratory disease management. The unique piloting of certain features such as protocol holidays, alert notifications for missing data, and flexible support from the study team provides a reference for future studies in this field.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-10.2196/28873.

Water activity in subaerial microbial biofilms on stone monuments

Stone monuments can be difficult environments for life, particularly with respect to liquid water access. Nevertheless, microbial communities are found on them with apparent ubiquity. A variety of strategies for access to liquid water have been proposed. Regardless of their water-retention mechanisms details, though, we argue that water activity (a key indicator for cell viability) is constrained by environmental conditions, largely independently of community structure, and is predicted by the local temperature and relative humidity. However, direct measurement of water activity in SABs, particularly those growing on stone surfaces, is difficult. A method for estimating water activity within SABs is presented that uses a minimally invasive combination of conservative sampling, weather data, confocal imaging, and mathematical modeling. Applying the methodology to measurements from the marble roofs of the Federal Hall National Memorial and of the Thomas Jefferson Memorial, estimations are made for water activity in their subaerial stone communities over the course of an approximately one year period.