Validated machine learning tools to distinguish immune checkpoint inhibitor, radiotherapy, COVID-19 and other infective pneumonitis.

BACKGROUND: Pneumonitis is a well-described, potentially disabling, or fatal adverse effect associated with both immune checkpoint inhibitors (ICI) and thoracic radiotherapy. Accurate differentiation between checkpoint inhibitor pneumonitis (CIP) radiation pneumonitis (RP), and infective pneumonitis (IP) is crucial for swift, appropriate, and tailored management to achieve optimal patient outcomes. However, correct diagnosis is often challenging, owing to overlapping clinical presentations and radiological patterns. METHODS: In this multi-centre study of 455 patients, we used machine learning with radiomic features extracted from chest CT imaging to develop and validate five models to distinguish CIP and RP from COVID-19, non-COVID-19 infective pneumonitis, and each other. Model performance was compared to that of two radiologists. RESULTS: Models to distinguish RP from COVID-19, CIP from COVID-19 and CIP from non-COVID-19 IP out-performed radiologists (test set AUCs of 0.92 vs 0.8 and 0.8; 0.68 vs 0.43 and 0.4; 0.71 vs 0.55 and 0.63 respectively). Models to distinguish RP from non-COVID-19 IP and CIP from RP were not superior to radiologists but demonstrated modest performance, with test set AUCs of 0.81 and 0.8 respectively. The CIP vs RP model performed less well on patients with prior exposure to both ICI and radiotherapy (AUC 0.54), though the radiologists also had difficulty distinguishing this test cohort (AUC values 0.6 and 0.6). CONCLUSION: Our results demonstrate the potential utility of such tools as a second or concurrent reader to support oncologists, radiologists, and chest physicians in cases of diagnostic uncertainty. Further research is required for patients with exposure to both ICI and thoracic radiotherapy.

It's a Trap! Aldolase-Prescribed C4 Deoxyradiofluorination Affords Intracellular Trapping and the Tracing of Fructose Metabolism by PET.

Fructose metabolism has been implicated in various diseases, including metabolic disorders, neurodegenerative disorders, cardiac disorders, and cancer. However, the limited availability of a quantitative imaging radiotracer has hindered its exploration in pathology and diagnostic imaging. Methods: We adopted a molecular design strategy based on the catalytic mechanism of aldolase, a key enzyme in fructolysis. We successfully synthesized a radiodeoxyfluorinated fructose analog, [18F]4-fluoro-4-deoxyfructose ([18F]4-FDF), in high molar activity. Results: Through heavy isotope tracing by mass spectrometry, we demonstrated that C4-deoxyfluorination of fructose led to effective trapping as fluorodeoxysorbitol and fluorodeoxyfructose-1-phosphate in vitro, unlike C1- and C6-fluorinated analogs that resulted in fluorolactate accumulation. This observation was consistent in vivo, where [18F]6-fluoro-6-deoxyfructose displayed substantial bone uptake due to metabolic processing whereas [18F]4-FDF did not. Importantly, [18F]4-FDF exhibited low uptake in healthy brain and heart tissues, known for their high glycolytic activity and background levels of [18F]FDG uptake. [18F]4-FDF PET/CT allowed for sensitive mapping of neuro- and cardioinflammatory responses to systemic lipopolysaccharide administration. Conclusion: Our study highlights the significance of aldolase-guided C4 radiodeoxyfluorination of fructose in enabling effective radiotracer trapping, overcoming limitations of C1 and C6 radioanalogs toward a clinically viable tool for imaging fructolysis in highly glycolytic tissues.

Gross tumour volume radiomics for prognostication of recurrence & death following radical radiotherapy for NSCLC.

Recurrence occurs in up to 36% of patients treated with curative-intent radiotherapy for NSCLC. Identifying patients at higher risk of recurrence for more intensive surveillance may facilitate the earlier introduction of the next line of treatment. We aimed to use radiotherapy planning CT scans to develop radiomic classification models that predict overall survival (OS), recurrence-free survival (RFS) and recurrence two years post-treatment for risk-stratification. A retrospective multi-centre study of >900 patients receiving curative-intent radiotherapy for stage I-III NSCLC was undertaken. Models using radiomic and/or clinical features were developed, compared with 10-fold cross-validation and an external test set, and benchmarked against TNM-stage. Respective validation and test set AUCs (with 95% confidence intervals) for the radiomic-only models were: (1) OS: 0.712 (0.592-0.832) and 0.685 (0.585-0.784), (2) RFS: 0.825 (0.733-0.916) and 0.750 (0.665-0.835), (3) Recurrence: 0.678 (0.554-0.801) and 0.673 (0.577-0.77). For the combined models: (1) OS: 0.702 (0.583-0.822) and 0.683 (0.586-0.78), (2) RFS: 0.805 (0.707-0.903) and 0·755 (0.672-0.838), (3) Recurrence: 0·637 (0.51-0.·765) and 0·738 (0.649-0.826). Kaplan-Meier analyses demonstrate OS and RFS difference of >300 and >400 days respectively between low and high-risk groups. We have developed validated and externally tested radiomic-based prediction models. Such models could be integrated into the routine radiotherapy workflow, thus informing a personalised surveillance strategy at the point of treatment. Our work lays the foundations for future prospective clinical trials for quantitative personalised risk-stratification for surveillance following curative-intent radiotherapy for NSCLC.

A comparison of machine learning methods for predicting recurrence and death after curative-intent radiotherapy for non-small cell lung cancer: Development and validation of multivariable clinical prediction models.

BACKGROUND: Surveillance is universally recommended for non-small cell lung cancer (NSCLC) patients treated with curative-intent radiotherapy. High-quality evidence to inform optimal surveillance strategies is lacking. Machine learning demonstrates promise in accurate outcome prediction for a variety of health conditions. The purpose of this study was to utilise readily available patient, tumour, and treatment data to develop, validate and externally test machine learning models for predicting recurrence, recurrence-free survival (RFS) and overall survival (OS) at 2 years from treatment. METHODS: A retrospective, multicentre study of patients receiving curative-intent radiotherapy for NSCLC was undertaken. A total of 657 patients from 5 hospitals were eligible for inclusion. Data pre-processing derived 34 features for predictive modelling. Combinations of 8 feature reduction methods and 10 machine learning classification algorithms were compared, producing risk-stratification models for predicting recurrence, RFS and OS. Models were compared with 10-fold cross validation and an external test set and benchmarked against TNM-stage and performance status. Youden Index was derived from validation set ROC curves to distinguish high and low risk groups and Kaplan-Meier analyses performed. FINDINGS: Median follow-up time was 852 days. Parameters were well matched across training-validation and external test sets: Mean age was 73 and 71 respectively, and recurrence, RFS and OS rates at 2 years were 43% vs 34%, 54% vs 47% and 54% vs 47% respectively. The respective validation and test set AUCs were as follows: 1) RFS: 0·682 (0·575-0·788) and 0·681 (0·597-0·766), 2) Recurrence: 0·687 (0·582-0·793) and 0·722 (0·635-0·81), and 3) OS: 0·759 (0·663-0·855) and 0·717 (0·634-0·8). Our models were superior to TNM stage and performance status in predicting recurrence and OS. INTERPRETATION: This robust and ready to use machine learning method, validated and externally tested, sets the stage for future clinical trials entailing quantitative personalised risk-stratification and surveillance following curative-intent radiotherapy for NSCLC. FUNDING: A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.

USP28 deletion and small-molecule inhibition destabilizes c-MYC and elicits regression of squamous cell lung carcinoma.

Lung squamous cell carcinoma (LSCC) is a considerable global health burden, with an incidence of over 600,000 cases per year. Treatment options are limited, and patient's 5-year survival rate is less than 5%. The ubiquitin-specific protease 28 (USP28) has been implicated in tumourigenesis through its stabilization of the oncoproteins c-MYC, c-JUN, and Δp63. Here, we show that genetic inactivation of Usp28-induced regression of established murine LSCC lung tumours. We developed a small molecule that inhibits USP28 activity in the low nanomole range. While displaying cross-reactivity against the closest homologue USP25, this inhibitor showed a high degree of selectivity over other deubiquitinases. USP28 inhibitor treatment resulted in a dramatic decrease in c-MYC, c-JUN, and Δp63 proteins levels and consequently induced substantial regression of autochthonous murine LSCC tumours and human LSCC xenografts, thereby phenocopying the effect observed by genetic deletion. Thus, USP28 may represent a promising therapeutic target for the treatment of squamous cell lung carcinoma.

Synthesis of natural/13C-enriched d-tagatose from natural/13C-enriched d-fructose.

A concise, easily scalable synthesis of a rare ketohexose, d-tagatose, was developed, that is compatible with the preparation of d-[UL-13C6]tagatose. Epimerization of the widely available and inexpensive ketohexose d-fructose at the C-4 position via an oxidation/reduction (Dess-Martin periodinane/NaBH4) was a key step in the synthesis. Overall, fully protected natural d-tagatose (3.21 g) was prepared from d-fructose (9 g) on a 50 mmol scale in 23% overall yield, after five steps and two chromatographic purifications. d-[UL-13C6]Tagatose (92 mg) was prepared from d-[UL-13C6]fructose (465 mg, 2.5 mmol) in 16% overall yield after six steps and four chromatographic purifications.

Hydrate Growth on Methane Gas Bubbles in the Presence of Salt.

Methane bubble dispersions in a water column can be observed in both vertical subsea piping as well as subsea gas seepages. Hydrate growth has been shown to occur at the gas-water interface under flowing conditions, yet the majority of the current literature is limited to quiescent systems. Gas hydrate risks in subsea piping have been shown to increase in late life production wells with increased water content and with gas-in-water bubble dispersions. The dissolution of subsea methane seepages into seawater, or methane release into the atmosphere, can be affected by hydrate film growth on rising bubbles. A high-pressure water tunnel (HPWT), was used to generate a turbulent, continuous water flow system representative of a vertical jumper line to study the relationship between bulk methane hydrate growth and bubble size during a production-well restart. The HPWT comprises a flow loop of 19.1 mm inner diameter and 4.9 m length, with a vertical section containing an optical window to enable visualization of the bubble and hydrate flow dynamics via a high-speed, high-resolution video camera. Additional online monitoring includes the differential pressure drop, viscosity, temperature, flow rates, and gas consumption. Experimental conditions were maintained at 275 K and 6.2 MPa during hydrate formation and 298 K and 1.4 MPa during hydrate dissociation. Hydrate growth using freshwater and saltwater (3.5 wt % NaCl) was measured at four flow velocities (0.8, 1.2, 1.6, and 1.9 m s-1). The addition of salt is shown in this work to alter the surface properties of bubbles, which introduces changes to bubble dynamics of dispersion and coalescence. Hydrate volume fractions and growth rates in the presence of salt were on average ∼32% lower compared to that in freshwater. This was observed and validated to be due to bubble size and dynamic factors and not due to the 1.5 K thermodynamic inhibition effect of salt. Throughout hydrate growth, methane bubbles in pure freshwater maintained larger diameters (2.4-4.2 mm), whereas the presence of salt promoted fine gas bubble dispersions (0.1-0.7 mm), increasing gas-water interfacial area. While gas bubble coalescence was observed in all freshwater experiments, the addition of salt limited coalescence between gas bubbles and reduced bubble size. Consequently, earlier formation of solid hydrate shells in saltwater produced early mass-transfer barriers reducing hydrate growth rates. While primarily directed toward flow assurance, the observed relationship between hydrates, bubble size, and saltwater also applies to broader research fields in subsea gas seepages and naturally occurring hydrates.

FPR1 is the plague receptor on host immune cells.

The causative agent of plague, Yersinia pestis, uses a type III secretion system to selectively destroy immune cells in humans, thus enabling Y. pestis to reproduce in the bloodstream and be transmitted to new hosts through fleabites. The host factors that are responsible for the selective destruction of immune cells by plague bacteria are unknown. Here we show that LcrV, the needle cap protein of the Y. pestis type III secretion system, binds to the N-formylpeptide receptor (FPR1) on human immune cells to promote the translocation of bacterial effectors. Plague infection in mice is characterized by high mortality; however, Fpr1-deficient mice have increased survival and antibody responses that are protective against plague. We identified FPR1R190W as a candidate resistance allele in humans that protects neutrophils from destruction by the Y. pestis type III secretion system. Thus, FPR1 is a plague receptor on immune cells in both humans and mice, and its absence or mutation provides protection against Y. pestis. Furthermore, plague selection of FPR1 alleles appears to have shaped human immune responses towards other infectious diseases and malignant neoplasms.

Molecular basis of USP7 inhibition by selective small-molecule inhibitors.

Ubiquitination controls the stability of most cellular proteins, and its deregulation contributes to human diseases including cancer. Deubiquitinases remove ubiquitin from proteins, and their inhibition can induce the degradation of selected proteins, potentially including otherwise 'undruggable' targets. For example, the inhibition of ubiquitin-specific protease 7 (USP7) results in the degradation of the oncogenic E3 ligase MDM2, and leads to re-activation of the tumour suppressor p53 in various cancers. Here we report that two compounds, FT671 and FT827, inhibit USP7 with high affinity and specificity in vitro and within human cells. Co-crystal structures reveal that both compounds target a dynamic pocket near the catalytic centre of the auto-inhibited apo form of USP7, which differs from other USP deubiquitinases. Consistent with USP7 target engagement in cells, FT671 destabilizes USP7 substrates including MDM2, increases levels of p53, and results in the transcription of p53 target genes, induction of the tumour suppressor p21, and inhibition of tumour growth in mice.

Glutathionylation of Yersinia pestis LcrV and Its Effects on Plague Pathogenesis.

Glutathionylation, the formation of reversible mixed disulfides between glutathione and protein cysteine residues, is a posttranslational modification previously observed for intracellular proteins of bacteria. Here we show that Yersinia pestis LcrV, a secreted protein capping the type III secretion machine, is glutathionylated at Cys273 and that this modification promotes association with host ribosomal protein S3 (RPS3), moderates Y. pestis type III effector transport and killing of macrophages, and enhances bubonic plague pathogenesis in mice and rats. Secreted LcrV was purified and analyzed by mass spectrometry to reveal glutathionylation, a modification that is abolished by the codon substitution Cys273Ala in lcrV Moreover, the lcrVC273A mutation enhanced the survival of animals in models of bubonic plague. Investigating the molecular mechanism responsible for these virulence attributes, we identified macrophage RPS3 as a ligand of LcrV, an association that is perturbed by the Cys273Ala substitution. Furthermore, macrophages infected by the lcrVC273A variant displayed accelerated apoptotic death and diminished proinflammatory cytokine release. Deletion of gshB, which encodes glutathione synthetase of Y. pestis, resulted in undetectable levels of intracellular glutathione, and we used a Y. pestis ΔgshB mutant to characterize the biochemical pathway of LcrV glutathionylation, establishing that LcrV is modified after its transport to the type III needle via disulfide bond formation with extracellular oxidized glutathione.IMPORTANCEYersinia pestis, the causative agent of plague, has killed large segments of the human population; however, the molecular bases for the extraordinary virulence attributes of this pathogen are not well understood. We show here that LcrV, the cap protein of bacterial type III secretion needles, is modified by host glutathione and that this modification contributes to the high virulence of Y. pestis in mouse and rat models for bubonic plague. These data suggest that Y. pestis exploits glutathione in host tissues to activate a virulence strategy, thereby accelerating plague pathogenesis.

Transcatheter aortic valve implantation and simultaneous closure of associated paravalvular leak.

Paravalvular aortic regurgitation (PAR) following transcatheter aortic valve implantation (TAVI) is a complication which is associated with increased late mortality. When PAR is severe and refractory to standard corrective measures, case reports have now described the successful use of vascular plugs to treat PAR as a follow-up procedure. We describe a case of vascular plug implantation to reduce PAR immediately after implantation of the transcatheter aortic valve prosthesis.

Quantitative Lipoproteomics in Clostridium difficile Reveals a Role for Lipoproteins in Sporulation.

Bacterial lipoproteins are surface exposed, anchored to the membrane by S-diacylglyceryl modification of the N-terminal cysteine thiol. They play important roles in many essential cellular processes and in bacterial pathogenesis. For example, Clostridium difficile is a Gram-positive anaerobe that causes severe gastrointestinal disease; however, its lipoproteome remains poorly characterized. Here we describe the application of metabolic tagging with alkyne-tagged lipid analogs, in combination with quantitative proteomics, to profile protein lipidation across diverse C. difficile strains and on inactivation of specific components of the lipoprotein biogenesis pathway. These studies provide the first comprehensive map of the C. difficile lipoproteome, demonstrate the existence of two active lipoprotein signal peptidases, and provide insights into lipoprotein function, implicating the lipoproteome in transmission of this pathogen.

The impact of HIV infection and antiretroviral therapy on the predicted risk of Down syndrome.

OBJECTIVE: The aim of this study was to assess predicted Down syndrome risk, based on three serum analytes (triple test), with HIV infection status and antiretroviral therapy regimen. METHODS: Screening results in 72 HIV-positive women were compared with results from age-matched and race-matched HIV-negative controls. Mean concentrations of each analyte were compared by serostatus and antiretroviral therapy. Observed Down syndrome incidence in the offspring of HIV-positive women was calculated from national HIV surveillance data. RESULTS: Overall, women with HIV had a significantly higher probability of receiving a 'high-risk' result than uninfected controls (p = 0.002). Compared with matched uninfected controls, women with HIV infection had significantly higher human chorionic gonadotrophin, lower unconjugated estriol, and higher overall predicted risk of their infant having Down syndrome (1/6250 vs. 1/50 000 p = < 0.001). National surveillance data show no evidence of higher than expected incidence of Down syndrome in the offspring of HIV-positive women. CONCLUSIONS: HIV infection impacts the serum analytes used to assay for Down syndrome risk resulting in a high rate of 'high risk' results. However, there is no population-based association between maternal HIV infection and Down syndrome. Care should be taken when interpreting high-risk serum screening results in HIV-positive women to avoid unnecessary invasive diagnostic procedures.

Feasibility and acceptability of routine human immunodeficiency virus testing in general practice: your views.

Early diagnosis of human immunodeficiency virus (HIV) leads to a decreased morbidity and mortality. General practice offers an important window for earlier diagnosis. The British HIV Association produced guidelines in 2008 advocating an increase in HIV testing, with specific references to primary care. This study explores the awareness of, and opinions towards, these guidelines within general practice. An email questionnaire was sent to 191 general practitioners nationwide, in both areas of high and low HIV prevalence. A total of 80 doctors replied, giving a response rate of 42%. In all, 44% of the respondents were unaware of the guidelines and 89% felt comfortable discussing and carrying out an HIV test themselves; of the 11% that did not, all but one were from low prevalence areas (P = 0.037). Respondents felt that main barrier to HIV testing was patient acceptability. Having read the guidelines, 70% believed it would be feasible to follow them in practice. Those who disagreed felt that time implications were the most important reason not to adopt the guidelines. Almost half the respondents were not aware of the guidelines; having read them, the majority felt that implementation is feasible. This demonstrates the necessity for better dissemination of these guidelines. This study found that the main barrier to performing an HIV test was felt to be patient acceptance, a contradiction to findings from recent pilot studies.

Using social cognitive theory to explain discretionary, "leisure-time" physical exercise among high school students.

PURPOSE: To examine whether knowledge of high school students' actions of self-regulation, and perceptions of self-efficacy to overcome exercise barriers, social situation, and outcome expectation will predict non-school related moderate and vigorous physical exercise. METHODS: High school students enrolled in introductory Physical Education courses completed questionnaires that targeted selected Social Cognitive Theory variables. They also self-reported their typical "leisure-time" exercise participation using a standardized questionnaire. Bivariate correlation statistic and hierarchical regression were conducted on reports of moderate and vigorous exercise frequency. RESULTS: Each predictor variable was significantly associated with measures of moderate and vigorous exercise frequency. All predictor variables were significant in the final regression model used to explain vigorous exercise. After controlling for the effects of gender, the psychosocial variables explained 29% of variance in vigorous exercise frequency. Three of four predictor variables were significant in the final regression equation used to explain moderate exercise. The final regression equation accounted for 11% of variance in moderate exercise frequency. CONCLUSIONS: Professionals who attempt to increase the prevalence of physical exercise through educational methods should focus on the psychosocial variables utilized in this study.