Explainable and Interpretable Machine Learning for Antimicrobial Stewardship: Opportunities and Challenges

There is growing interest in exploiting the advances in artificial intelligence and machine learning (ML) for improving and monitoring antimicrobial prescriptions in line with antimicrobial stewardship principles. Against this background, the concepts of interpretability and explainability are becoming increasingly essential to understanding how ML algorithms could predict antimicrobial resistance or recommend specific therapeutic agents, to avoid unintended biases related to the "black box" nature of complex models. In this commentary, we review and discuss some relevant topics on the use of ML algorithms for antimicrobial stewardship interventions, highlighting opportunities and challenges, with particular attention paid to interpretability and explainability of employed models. As in other fields of medicine, the exponential growth of artificial intelligence and ML indicates the potential for improving the efficacy of antimicrobial stewardship interventions, at least in part by reducing time-consuming tasks for overwhelmed health care personnel. Improving our knowledge about how complex ML models work could help to achieve crucial advances in promoting the appropriate use of antimicrobials, as well as in preventing antimicrobial resistance selection and dissemination.

Esophageal tumors: The keys to diagnosis by pneumo-computed tomography

OBJECTIVE

To review and describe the most characteristic radiological findings of the most frequent esophageal tumor lesions, with emphasis on the esophago-gastric distention technique pneumo-computed tomography performed in our institution. To know the main advantage of this distension technique.

CONCLUSION

Malignant tumor lesions (predominantly squamous cell carcinoma in the mid esophagus and adenocarcinoma in the distal esophagus) present as asymmetric wall thickening, mucosal irregularity, or mass extending into adjacent organs with lymph node involvement. Benign tumors (mainly leiomyoma being the most frequent and others such as lipoma) present as endoluminal growth, with defined borders and homogeneous attenuation. Post-contrast enhancement is scarce or moderate. The technique of computed tomography pneumotomography technique achieves an additional distension of the esophageal lumen in all cases. It allows delimiting the superior and inferior borders of the lesions, helping the surgeon to define the therapeutic strategy.

Experimental application of Business Process Management technology to manage clinical pathways: a pediatric kidney transplantation follow up case

BACKGROUND

To test the application of Business Process Management technology to manage clinical pathways, using a pediatric kidney transplantation as case study, and to identify the benefits obtained from using this technology.

METHODS

Using a Business Process Management platform, we implemented a specific application to manage the clinical pathway of pediatric patients, and monitored the activities of the coordinator in charge of the case management during a 6-month period (from June 2015 to November 2015) using two methodologies: the traditional procedure and the one under study.

RESULTS

The application helped physicians and nurses to optimize the amount of time and resources devoted to management purposes. In particular, time reduction was close to 60%. In addition, the reduction of data duplication, the integrated event management and the efficient data collection improved the quality of the service.

CONCLUSIONS

The use of Business Process Management technology, usually related to well-defined processes with high management costs, is an established procedure in multiple environments; its use in healthcare, however, is innovative. The use of already accepted clinical pathways is known to improve outcomes. The combination of these two techniques, well established in their respective areas of application, could represent a revolution in clinical pathway management. The study has demonstrated that the use of this technology in a clinical environment, using a proper architecture and identifying a well-defined process, leads to real benefits in terms of resources optimization and quality improvement.

Optimization and planning of operating theatre activities: an original definition of pathways and process modeling

Background

The Operating Room (OR) is a key resource of all major hospitals, but it also accounts for up 40 % of resource costs. Improving cost effectiveness, while maintaining a quality of care, is a universal objective. These goals imply an optimization of planning and a scheduling of the activities involved. This is highly challenging due to the inherent variable and unpredictable nature of surgery.

Methods

A Business Process Modeling Notation (BPMN 2.0) was used for the representation of the “OR Process” (being defined as the sequence of all of the elementary steps between “patient ready for surgery” to “patient operated upon”) as a general pathway (“path”). The path was then both further standardized as much as possible and, at the same time, keeping all of the key-elements that would allow one to address or define the other steps of planning, and the inherent and wide variability in terms of patient specificity. The path was used to schedule OR activity, room-by-room, and day-by-day, feeding the process from a “waiting list database” and using a mathematical optimization model with the objective of ending up in an optimized planning.

Results

The OR process was defined with special attention paid to flows, timing and resource involvement. Standardization involved a dynamics operation and defined an expected operating time for each operation. The optimization model has been implemented and tested on real clinical data. The comparison of the results reported with the real data, shows that by using the optimization model, allows for the scheduling of about 30 % more patients than in actual practice, as well as to better exploit the OR efficiency, increasing the average operating room utilization rate up to 20 %.

Conclusions

The optimization of OR activity planning is essential in order to manage the hospital’s waiting list. Optimal planning is facilitated by defining the operation as a standard pathway where all variables are taken into account. By allowing a precise scheduling, it feeds the process of planning and, further up-stream, the management of a waiting list in an interactive and bi-directional dynamic process.

Dissimilar expression of multidrug resistance mdr1 and bcrp by the replication of hepatitis C virus: role of the nonstructural 5A protein

Multidrug resistance associated with the overexpression of ATP-dependent binding cassette (ABC) proteins is widely accepted as an important cause of treatment failure in patients with neoplastic or infectious diseases. Some of them play also a pivotal role in detoxification processes. Herein, we investigated the effect of hepatitis C virus (HCV) replication and nonstructural 5A (NS5A) protein on the expression and functional activity of two ABC transport proteins: MDR1 and BCRP. RT-quantitative real-time polymerase chain reaction (qPCR) was carried out for mdr1 and bcrp mRNAs in both Huh7 cells expressing NS5A and Huh7.5 cells containing either full-length- or subgenomic-HCV replicon systems. The functional activity of these pumps was studied by performing a dye efflux assay with DiOC2 and Rhodamine 123. A dose-dependent down-regulation of mdr1 expression was documented in Huh7 cells expressing the NS5A protein, as well as in both replicon systems. In contrast, a significant increase of bcrp expression in both systems was recorded, which were in full agreement with the dye efflux assay results. These results warrant further in vivo studies in HCV patients with cholestasis and/or patients that are refractive to the pharmacotherapy due to the activity of these pumps.

Dissimilar expression of multidrug resistance mdr1 and bcrp by the replication of hepatitis C virus: role of the nonstructural 5A protein

Multidrug resistance associated with the overexpression of ATP-dependent binding cassette (ABC) proteins is widely accepted as an important cause of treatment failure in patients with neoplastic or infectious diseases. Some of them play also a pivotal role in detoxification processes. Herein, we investigated the effect of hepatitis C virus (HCV) replication and nonstructural 5A (NS5A) protein on the expression and functional activity of two ABC transport proteins: MDR1 and BCRP. RT-quantitative real-time polymerase chain reaction (qPCR) was carried out for mdr1 and bcrp mRNAs in both Huh7 cells expressing NS5A and Huh7.5 cells containing either full-length- or subgenomic-HCV replicon systems. The functional activity of these pumps was studied by performing a dye efflux assay with DiOC2 and Rhodamine 123. A dose-dependent down-regulation of mdr1 expression was documented in Huh7 cells expressing the NS5A protein, as well as in both replicon systems. In contrast, a significant increase of bcrp expression in both systems was recorded, which were in full agreement with the dye efflux assay results. These results warrant further in vivo studies in HCV patients with cholestasis and/or patients that are refractive to the pharmacotherapy due to the activity of these pumps.

The expression levels of the translational factors eEF1A 1/2 correlate with cell growth but not apoptosis in hepatocellular carcinoma cell lines with different differentiation grade

Despite the involvement of the elongation factors eEF1A (eEF1A1 and eEF1A2) in the development of different cancers no information is available on their possible contribution to the biology of hepatocellular carcinoma (HCC). We investigated the expression of both forms of eEF1A in HepG2 and JHH6 cell lines considered to be a good in vitro model of HCC at different stage of differentiation. Our data indicate that the mRNA amount of eEF1A1 is increased in both cell lines as compared to normal liver tissue, but eEF1A2 mRNA level is markedly increased only in JHH6. Moreover, the less differentiated cell line JHH6 displays higher EEF1A1 and EEF1A2 mRNAs levels and an higher nuclear-enriched/cytoplasm ratio of EEF1A protein compared to the better differentiated HepG2 cell line. Over-expression depends only partially on gene amplification. The more abundant mRNA levels and the higher nuclear-enriched/cytoplasm ratio of eEF1A in JHH6 neither correlate with apoptosis resistance nor with proliferation rate in sub-confluent cells. However, in confluent cells, a clear tendency to maintain JHH6 into the cell cycle was observed. In conclusion, we document the increased mRNA levels of EEF1A genes in HCC cell lines compared to normal liver. Additionally, we show the increased nuclear-enriched/cytoplasmic protein ratio of eEF1A and the marked raise of the expression of both eEF1A forms in JHH6 compared to HepG2, suggesting the possibility that eEF1A forms might become a relevant markers related to HCC tumor phenotype.

Development of ISFET array-based microsystems for bioelectrochemical measurements of cell populations

Monitoring the bioelectrochemical activity of living cells with sensor array-based microsystems represents an emerging technique in a large area of biomedical applications, ranging from basic research to various fields of pharmacological analyses. The main appeal is the ability of these miniaturised microsystems to perform, in real time, non-invasive in-vitro investigations of the physiological state of a cell population. In this paper, we present two different microsystems designed for multisite monitoring of the physiological state of a cell population. The first microsystem, intended for cellular metabolism monitoring, consists of an array of 12 spatially distributed ISFETs to detect small pH variations induced by the cell population. The second microsystem consists of an array of 40 ISFETs and 20 gold microelectrodes and it has been designed to monitor the electrical activity of neurons. This is achieved by direct coupling of the neuronal culture with the ISFET sensitive layer and by utilising gold microelectrodes for neuronal electrical stimulation.

[Follicular conjunctivitis due to Chlamydia trachomatis]

During two years (1997-1999) an investigation of possible infections of chlamydial etiology in outpatients with follicular conjunctivitis was carried out, through the use of specific assays. Fifty-seven selected patients with presumptive inclusion conjunctivitis were diagnosed by means of ophthalmoscopic examination and bilateral tarsal-conjunctiva swabbing for microorganisms. The possible presence of Chlamydia trachomatis was tested by immunofluorescence microscopy and isolation in cell culture of McCoy line. Of the 57 conjunctivitis patients screened, 37 (65%) proved to be positive by cell culture (CC) and 27 (47%) by direct immunofluorescence (IFD). A good agreement between the two assays was observed, where the CC was more sensitive than IFD. Of these 37 patients with chlamydial conjunctivitis, 23 (62%) were women, with over one-third of them ranging in age from 45 to 65 years. Their clinical records revealed an evolution period of 1 to 12 months. Eighteen (78%) of these women reported previous genital pathology, while 4 (29%) of the 14 men had a history of urethritis by Chlamydia trachomatis. A high frequency of follicular conjunctivitis by Chlamydia (65%) in the screened patients was observed, without any evidence of urogenital signs and symptoms at the moment of the study.

The use of carbon dioxide laser in pit and fissure caries prevention: clinical evaluation

In this 4-year follow-up in vivo controlled study, 112 human permanent first molars from children between 6 and 11 years old were used to investigate the viability of the carbon dioxide (CO2) laser in promoting caries-free occlusal surfaces in permanent molars as an isolated form of treatment or associated with conventional fissure sealants. The findings suggest that occlusal caries prevention only by means of CO2 laser irradiation is not effective; that the utilization of photoactivated sealants, as well as its association with CO2 laser, applied over the occlusal fissures, are effective means of preventing occlusal caries, and that the application of CO2 laser over occlusal fissures prior to the application of a photoactivated fissure sealant improves the retention of the sealant.