Ordinal SuStaIn: Subtype and Stage Inference for Clinical Scores, Visual Ratings, and Other Ordinal Data

Subtype and Stage Inference (SuStaIn) is an unsupervised learning algorithm that uniquely enables the identification of subgroups of individuals with distinct pseudo-temporal disease progression patterns from cross-sectional datasets. SuStaIn has been used to identify data-driven subgroups and perform patient stratification in neurodegenerative diseases and in lung diseases from continuous biomarker measurements predominantly obtained from imaging. However, the SuStaIn algorithm is not currently applicable to discrete ordinal data, such as visual ratings of images, neuropathological ratings, and clinical and neuropsychological test scores, restricting the applicability of SuStaIn to a narrower range of settings. Here we propose 'Ordinal SuStaIn', an ordinal version of the SuStaIn algorithm that uses a scored events model of disease progression to enable the application of SuStaIn to ordinal data. We demonstrate the validity of Ordinal SuStaIn by benchmarking the performance of the algorithm on simulated data. We further demonstrate that Ordinal SuStaIn out-performs the existing continuous version of SuStaIn (Z-score SuStaIn) on discrete scored data, providing much more accurate subtype progression patterns, better subtyping and staging of individuals, and accurate uncertainty estimates. We then apply Ordinal SuStaIn to six different sub-scales of the Clinical Dementia Rating scale (CDR) using data from the Alzheimer's disease Neuroimaging Initiative (ADNI) study to identify individuals with distinct patterns of functional decline. Using data from 819 ADNI1 participants we identified three distinct CDR subtype progression patterns, which were independently verified using data from 790 ADNI2 participants. Our results provide insight into patterns of decline in daily activities in Alzheimer's disease and a mechanism for stratifying individuals into groups with difficulties in different domains. Ordinal SuStaIn is broadly applicable across different types of ratings data, including visual ratings from imaging, neuropathological ratings and clinical or behavioural ratings data

Self-interested service-oriented agents based on trust and QoS for dynamic reconfiguration

Progressively increasing complexity of dynamic environments, in which services and applications are demanded by potential clients, requires a high level of reconfiguration of the offer to better match that ever changing demand. In particular, the dynamic change of the client’s needs, leading to higher exigency, may require a smart and flexible automatic composition of more elementary services. By leveraging the service-oriented architectures and multi-agent system benefits, the paper proposes a method to explore the flexibility of the decision support for the services’ reconfiguration based on several pillars, such as trust, reputation and QoS models, which allows the selection based on measuring the expected performance of the agents. Preliminary experimental results, extracted from a real case scenario, allow highlighting the benefits of the proposed distributed and flexible solution to balance the workload of service providers in a simple and fast manner. The proposed solution includes the agents’ intelligent decision-making capability to dynamically and autonomously change services selection on the fly, towards more trustworthy services with better quality when unexpected events happen, e.g. broken machines. We then propose the use of competitive self-interested agents to provide services that best suits to the client through dynamic service composition.info:eu-repo/semantics/publishedVersio

Occupational exposure and markers of genetic damage, systemic inflammation and lung function: a Danish cross-sectional study among air force personnel

Air force ground crew personnel are potentially exposed to fuels and lubricants, as raw materials, vapours and combustion exhaust emissions, during operation and maintenance of aircrafts. This study investigated exposure levels and biomarkers of effects for employees at a Danish air force military base. We enrolled self-reported healthy and non-smoking employees (n = 79) and grouped them by exposure based on job function, considered to be potentially exposed (aircraft engineers, crew chiefs, fuel operators and munition specialists) or as reference group with minimal occupational exposure (avionics and office workers). We measured exposure levels to polycyclic aromatic hydrocarbons (PAHs) and organophosphate esters (OPEs) by silicone bands and skin wipes (PAHs only) as well as urinary excretion of PAH metabolites (OH-PAHs). Additionally, we assessed exposure levels of ultrafine particles (UFPs) in the breathing zone for specific job functions. As biomarkers of effect, we assessed lung function, plasma levels of acute phase inflammatory markers, and genetic damage levels in peripheral blood cells. Exposure levels of total PAHs, OPEs and OH-PAHs did not differ between exposure groups or job functions, with low correlations between PAHs in different matrices. Among the measured job functions, the UFP levels were higher for the crew chiefs. The exposure level of the PAH fluorene was significantly higher for the exposed group than the reference group (15.9 +/- 23.7 ng/g per 24 h vs 5.28 +/- 7.87 ng/g per 24 h, p = 0.007), as was the OPE triphenyl phosphate (305 +/- 606 vs 19.7 +/- 33.8 ng/g per 24 h, p = 0.011). The OPE tris(1, 3-dichlor-2-propyl)phosphate had a higher mean in the exposed group (60.7 +/- 135 ng/g per 24 h) compared to the reference group (8.89 +/- 15.7 ng/g per 24 h) but did not reach significance. No evidence of effects for biomarkers of systemic inflammation, genetic damage or lung function was found. Overall, our biomonitoring study show limited evidence of occupational exposure of air force ground crew personnel to UFPs, PAHs and OPEs. Furthermore, the OH-PAHs and the assessed biomarkers of early biological effects did not differ between exposed and reference groups

Spatial organization acts on cell signaling: how physical force contributes to the development of cancer

Cells constantly encounter physical forces and respond to neighbors and circulating factors by triggering intracellular signaling cascades that in turn affect their behavior. The mechanisms by which cells transduce mechanical signals to downstream biochemical changes are not well understood. In their work, Salaita and coworkers show that the spatial organization of cell surface receptors is crucial for mechanotransduction. Consequently, force modulation that disrupts the mechanochemical coupling may represent a critical step in cancerogenesis

Variation in Prices Charged to Patients for Specialty Intraocular Lenses Inserted during Universally Covered Cataract Surgery

Patients often pay for specialty intraocular lenses (IOLs) for cataract surgery covered by universal insurance. This practice creates the potential for inequitable pricing where the medical service provider is also the retailer. We measured the variation in prices between cataract surgeons for the same IOL and associated testing.We telephoned every cataract surgeon in Ontario, Canada, and asked their price for the most common type of specialty IOL as a prospective patient. We measured the total prices quoted and variation between providers.We contacted 404 ophthalmologists. There were 256 that performed cataract surgery but 127 offered the most commonly employed specialty IOL and would provide a price to patients over the telephone. We obtained prices from all 127 ophthalmologists. Prices for the same lens and associated testing varied substantially between ophthalmologists from $358 to$2790 (median $615, interquartile range$528-$915). There was variation in all components of the total out-of-pocket price, including the price for the IOL itself, charges for uninsured eye measurements, and non-specific supplemental fees.Although cataract surgery is covered by public health insurance, some ophthalmologists charge much more than others for the same specialty IOL and associated testing. Greater access to price information and better regulatory control could help ensure patients receive fair value for out-of-pocket health expenses

Tailoring communications to the evolving needs of patients throughout the cancer care trajectory: a qualitative exploration with breast cancer patients

Background: Doctor-patient communication is a crucial aspect of patient care. This study explored the communication experience of patients in a cancer consultation over the course of the cancer continuum. Methods: In-depth interviews with seven breast cancer patients were carried out. Results: Themes related to communication experiences across the five phases of cancer consultation, from diagnosis to recurrence, were identified. The most salient issue is that patients also perceived cancer as 'a disease of the mind', which is not adequately cared for in consultation. This highlights the notion that cancer care providers should provide appropriate care for the psychological dimensions of the cancer experience with an empathic and sincere attitude during consultations. To this end, non-verbal aspects of communication that convey caring, support, and respect seem important. Furthermore, patients perceived that the consultation time was far shorter then they needed and reported that they felt pressured for time. Moreover, the stance taken by patients and the needs and preferences of patients varied across the phases of the cancer trajectory. As patients progressed through the phases of their treatment, they assumed more active roles in the course of their care and the need for more detailed information and questioning increased. Thus, ensuring that patients have opportunities to ask questions in the consultation is important. Conclusion: Current findings suggest that the efficacy of communication varies depending on which phase patients are in and that effective communication should be tailored to these evolving needs and preferences of breast cancer patients. Also, patients perceived that the consultation did not adequately address their need for information related to their care or their emotional issues associated with the cancer experience. It is therefore important to address their needs by paying particular attention to non-verbal aspects of communication that convey empathy and respect toward patients, as well as allowing patients to ask questionsope

Therapeutic DNA vaccine induces broad T cell responses in the gut and sustained protection from viral rebound and AIDS in SIV-infected rhesus macaques.

Immunotherapies that induce durable immune control of chronic HIV infection may eliminate the need for life-long dependence on drugs. We investigated a DNA vaccine formulated with a novel genetic adjuvant that stimulates immune responses in the blood and gut for the ability to improve therapy in rhesus macaques chronically infected with SIV. Using the SIV-macaque model for AIDS, we show that epidermal co-delivery of plasmids expressing SIV Gag, RT, Nef and Env, and the mucosal adjuvant, heat-labile E. coli enterotoxin (LT), during antiretroviral therapy (ART) induced a substantial 2-4-log fold reduction in mean virus burden in both the gut and blood when compared to unvaccinated controls and provided durable protection from viral rebound and disease progression after the drug was discontinued. This effect was associated with significant increases in IFN-γ T cell responses in both the blood and gut and SIV-specific CD8+ T cells with dual TNF-α and cytolytic effector functions in the blood. Importantly, a broader specificity in the T cell response seen in the gut, but not the blood, significantly correlated with a reduction in virus production in mucosal tissues and a lower virus burden in plasma. We conclude that immunizing with vaccines that induce immune responses in mucosal gut tissue could reduce residual viral reservoirs during drug therapy and improve long-term treatment of HIV infection in humans

Application of circulating cell-free tumor DNA profiles for therapeutic monitoring and outcome prediction in genetically heterogeneous metastatic melanoma

PURPOSE Circulating cell-free tumor DNA (ctDNA) reflects the heterogeneousspectrum of tumor-specific mutations, especially in systemic disease. We validated plasma-based assays that allow the dynamic quantitative detection of ctDNA as a prognostic biomarker for tumor load and prediction of therapy response in melanoma. MATERIALS and METHODS We analyzed plasma-derived ctDNA from a large training cohort (n = 96) of patients with advanced-stage melanoma, with assays for the BRAFV600E and NRASQ61 driver mutations as well as TERTC250T and TERTC228T promoter mutations. An independent patient cohort (n = 35) was used to validate the utility of ctDNA monitoring under mitogen-activated protein kinase–targeted or immune checkpoint therapies. RESULTS Elevated plasma ctDNA level at baseline was an independent prognostic factor of disease progression when compared with serum S100 and lactate dehydrogenase levels in multivariable analyses (hazard ratio [HR], 7.43; 95% CI, 1.01 to 55.19; P = .05). The change in ctDNA levels during therapy correlated with treatment response, where increasing ctDNA was predictive for shorter progression-free survival (eg, for BRAFV600EctDNA, HR, 3.70; 95% CI, 1.86 to 7.34; P < .001). Increasing ctDNA levels predicted disease progression significantly earlier than did routine radiologic scans (P < .05), with a mean lead time of 3.5 months. NRAS-mutant ctDNA was detected in a significant proportion of patients with BRAF-mutant tumors under therapy, but unexpectedly also at baseline. In vitro sensitivity studies suggested that this represents higher-than-expected intratumoral heterogeneity. The detection of NRASQ61 ctDNA in baseline samples of patients with BRAFV600E mutation who were treated with mitogen-activated protein kinase inhibitors significantly correlated with shorter progression-free survival (HR, 3.18; 95% CI, 1.31 to 7.68; P = .03) and shorter overall survival (HR, 4.08; 95% CI, 1.57 to 10.58; P = .01). CONCLUSION Our results show the potential role of ctDNA measurement as a sensitive monitoring and prediction tool for the early assessment of disease progression and therapeutic response in patients with metastaticmelanoma

The price of tumor control: an analysis of rare side effects of anti-CTLA-4 therapy in metastatic melanoma from the ipilimumab network

Background: Ipilimumab, a cytotoxic T-lymphocyte antigen-4 (CTLA-4) blocking antibody, has been approved for the treatment of metastatic melanoma and induces adverse events (AE) in up to 64% of patients. Treatment algorithms for the management of common ipilimumab-induced AEs have lead to a reduction of morbidity, e.g. due to bowel perforations. However, the spectrum of less common AEs is expanding as ipilimumab is increasingly applied. Stringent recognition and management of AEs will reduce drug-induced morbidity and costs, and thus, positively impact the cost-benefit ratio of the drug. To facilitate timely identification and adequate management data on rare AEs were analyzed at 19 skin cancer centers. Methods and Findings: Patient files (n = 752) were screened for rare ipilimumab-associated AEs. A total of 120 AEs, some of which were life-threatening or even fatal, were reported and summarized by organ system describing the most instructive cases in detail. Previously unreported AEs like drug rash with eosinophilia and systemic symptoms (DRESS), granulomatous inflammation of the central nervous system, and aseptic meningitis, were documented. Obstacles included patientś delay in reporting symptoms and the differentiation of steroid-induced from ipilimumab-induced AEs under steroid treatment. Importantly, response rate was high in this patient population with tumor regression in 30.9% and a tumor control rate of 61.8% in stage IV melanoma patients despite the fact that some patients received only two of four recommended ipilimumab infusions. This suggests that ipilimumab-induced antitumor responses can have an early onset and that severe autoimmune reactions may reflect overtreatment. Conclusion: The wide spectrum of ipilimumab-induced AEs demands doctor and patient awareness to reduce morbidity and treatment costs and true ipilimumab success is dictated by both objective tumor responses and controlling severe side effects