Prototype-based Interpretable Breast Cancer Prediction Models:Analysis and Challenges

Deep learning models have achieved high performance in medical applications, however, their adoption in clinical practice is hindered due to their black-box nature. Self-explainable models, like prototype-based models, can be especially beneficial as they are interpretable by design. However, if the learnt prototypes are of low quality then the prototype-based models are as good as black-box. Having high quality prototypes is a pre-requisite for a truly interpretable model. In this work, we propose a prototype evaluation framework for coherence (PEF-C) for quantitatively evaluating the quality of the prototypes based on domain knowledge. We show the use of PEF-C in the context of breast cancer prediction using mammography. Existing works on prototype-based models on breast cancer prediction using mammography have focused on improving the classification performance of prototype-based models compared to black-box models and have evaluated prototype quality through anecdotal evidence. We are the first to go beyond anecdotal evidence and evaluate the quality of the mammography prototypes systematically using our PEF-C. Specifically, we apply three state-of-the-art prototype-based models, ProtoPNet, BRAIxProtoPNet++ and PIP-Net on mammography images for breast cancer prediction and evaluate these models w.r.t. i) classification performance, and ii) quality of the prototypes, on three public datasets. Our results show that prototype-based models are competitive with black-box models in terms of classification performance, and achieve a higher score in detecting ROIs. However, the quality of the prototypes are not yet sufficient and can be improved in aspects of relevance, purity and learning a variety of prototypes. We call the XAI community to systematically evaluate the quality of the prototypes to check their true usability in high stake decisions and improve such models further

Cardiac Autonomic Nervous System in Heart Failure: Imaging Technique and Clinical Implications

The autonomic nervous system interacts in the pathophysiology of heart failure. Dysfunction of the sympathetic nervous system has been identified as an important prognostic marker in patients with chronic heart failure. At present, cardiac sympathetic nerve imaging with 123-iodine metaiodobenzylguanidine [123-I MIBG] has been employed most frequently for the assessment of cardiac sympathetic innervation and activation pattern. The majority of studies have shown that cardiac sympathetic dysfunction as assessed with 123-I MIBG imaging is a powerful predictor for heart failure mortality and morbidity. Additionally, 123-I MIBG imaging can be used for prediction of potentially lethal ventricular tachyarrhythmias in heart failure patients. At present however, the lack of standardization of 123-I MIBG imaging procedures represents an evident issue. Standardized criteria on the use of 123-I MIBG imaging will further strengthen the clinical use of 123-I MIBG imaging in heart failure patients

Opportunities for personalised follow-up in breast cancer: the gap between daily practice and recurrence risk

Purpose: Follow-up guidelines barely diverge from a one-size-fits-all approach, even though the risk of recurrence differs per patient. However, the personalization of breast cancer care improves outcomes for patients. This study explores the variation in follow-up pathways in the Netherlands using real-world data to determine guideline adherence and the gap between daily practice and risk-based surveillance, to demonstrate the benefits of personalized risk-based surveillance compared with usual care.Methods: Patients with stage I–III invasive breast cancer who received surgical treatment in a general hospital between 2005 and 2020 were selected from the Netherlands Cancer Registry and included all imaging activities during follow-up from hospital-based electronic health records. Process analysis techniques were used to map patients and activities to investigate the real-world utilisation of resources and identify the opportunities for improvement. The INFLUENCE 2.0 nomogram was used for risk prediction of recurrence.Results: In the period between 2005 and 2020, 3478 patients were included with a mean follow-up of 4.9 years. In the first 12 months following treatment, patients visited the hospital between 1 and 5 times (mean 1.3, IQR 1–1) and received between 1 and 9 imaging activities (mean 1.7, IQR 1–2). Mammogram was the prevailing imaging modality, accounting for 70% of imaging activities. Patients with a low predicted risk of recurrence visited the hospital more often.Conclusions: Deviations from the guideline were not in line with the risk of recurrence and revealed a large gap, indicating that it is hard for clinicians to accurately estimate this risk and therefore objective risk predictions could bridge this gap.Keywords Breast cancer · Follow-up · Real-world data · Risk of recurrence · Process mining · Resource utilisatio

Sunram 7: An MR Safe Robotic System for Breast Biopsy

In breast cancer patients, some nodules are only visible on MRI, thus, requiring MRI-guidance to perform the biopsy. MRI interventions are cumbersome due to the magnetic field and the constrained working space. An MR safe robotic system actuated by pneumatic stepper motors may enable these procedures, improving both accuracy and image-guided navigation. A compact multipurpose pneumatic stepper motor has been designed with outer dimensions $(45 \times 40\times 15)\mathbf{mm}^{\mathbf{3}}$. This is configurable as a linear, rotational or curved stepper motor with a customizable step size and radius of curvature. Five copies of these motors actuate the Sunram 7 biopsy robot, of which the moving part (without protruding racks and tubes) measures $(130 \times 65\times 55)\mathbf{mm}^{\mathbf{3}}$. After manually choosing the target location and angle of approach, the needle is robotically inserted into the breast and the integrated pneumatic biopsy gun is fired to sample tissue from the lesion. The maximum torque of the presented motor is 0.61 N m at 6 bar which can be achieved using 13-teeth polycarbonate gears. Using 17-teeth gears for higher accuracy and a more convenient working pressure of 2 bar the maximum torque is 0.28 N m. The accuracy in free air of the Sunram 7 robot is 1.69mm and 1.72mm in X and Z-direction respectively, with a resulting 2-D error of 2.54 mm. The workspace volume is 4.1 L. When targeting 10 mm-sized lesions in phantoms under MRI guidance, Sunram 7 achieved a success rate of 68%. The minimum interval between two successive biopsies was 5:47 minutes. The presented multipurpose stepper motor has distinct advantages over previous designs in terms of robustness, customizability, printability and ease of integration in MR safe robotics. The Sunram 7 is able to perform accurate MRI-guided biopsies in a large workspace volume while reducing the intervention time when compared to the gold standard (i.e., MRI-guided free-hand biopsy)

Orbitofrontal gray matter relates to early morning awakening: a neural correlate of insomnia complaints?

Sleep complaints increase profoundly with age; prevalence estimates of insomnia in elderly people reach up to 37%. The three major types of nocturnal complaints are difficulties initiating sleep (DIS), difficulties maintaining sleep (DMS) and early morning awakening (EMA), of which the latter appears most characteristic for aging. The neural correlates associated with these complaints have hardly been investigated, hampering the development of rational treatment and prevention. A recent study on structural brain correlates of insomnia showed that overall severity, but not duration, of insomnia complaints is associated with lower gray matter (GM) density in part of the left orbitofrontal cortex. Following up on this, we investigated, in an independent sample of people not diagnosed with insomnia, whether individual differences in GM density are associated with differences in DIS, DMS and EMA.65 healthy participants filled out questionnaires and underwent structural magnetic resonance imaging. Three compound Z-scores were computed for questionnaire items relating to DIS, DMS and EMA. Whole-brain voxel-based morphometry was used to investigate their association with GM density. Results show that participants with lower GM density in a region where the left inferior orbitofrontal cortex borders the insula report more EMA, but not DIS or DMS.This is the first study to investigate structural brain correlates of specific sleep characteristics that can translate into complaints in insomniacs. The selective association of EMA with orbitofrontal GM density makes our findings particularly relevant to elderly people, where EMA represents the most characteristic complaint. It is hypothesized that low GM density in aforementioned orbitofrontal area affects its role in sensing comfort. An intact ability to evaluate comfort may be crucial to maintain sleep, especially at the end of the night when sleep is vulnerable because homeostatic sleep propensity has dissipated

Trends in incidence, treatment, survival and subsequent breast cancer in lobular carcinoma in situ in the Netherlands:A population-based analysis

Purpose: We analysed incidence, treatment, survival, occurrence of ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC) after lobular carcinoma in situ (LCIS) in the Netherlands. Methods: All women diagnosed with classic LCIS between 1989 and 2017 were identified from the Netherlands Cancer Registry. We calculated overall (OS), relative survival (RS) and cumulative incidence functions (CIF, accounting for competing risks) of mortality, DCIS and IBC. For IBC, standardised incidence ratios (SIR) of IBC were calculated. Analyses were stratified for surgical treatment. Results: We included 1890 patients. Median age was 51 years. Median follow-up was 8.5 years. In 1989–2017, LCIS incidence increased from 41 to 124, surgical treatment decreased from 100% to 41.1 % – mostly BCS. 10-year OS and 20-year RS exceeded 90 % in all subgroups. Overall, 48 (2.5 %) and 270 (14.3 %) patients were diagnosed with DCIS and IBC. IBCs were mostly early-stage. After mastectomy, 13 of 14 IBCs presented contralaterally. In the other groups, 64.8–70.9 % of IBCs presented ipsilaterally, 34.5–53.9 % of these were lobular. The SIR of ipsilateral IBC was highest after no surgery (6.9, 95%CI:4.9–9.4), lowest after mastectomy (0.2, 95%CI:0.4–0.8). Conclusion: LCIS incidence increased, surgical treatment decreased. The low mortality risks support consideration of active surveillance. However, the increased IBC incidence suggests careful monitoring

Adherence to the Dutch Breast Cancer Guidelines for Surveillance in Breast Cancer Survivors:Real-World Data from a Pooled Multicenter Analysis

BACKGROUND: Regular follow-up after treatment for breast cancer is crucial to detect potential recurrences and second contralateral breast cancer in an early stage. However, information about follow-up patterns in the Netherlands is scarce. PATIENTS AND METHODS: Details concerning diagnostic procedures and policlinic visits in the first 5 years following a breast cancer diagnosis were gathered between 2009 and 2019 for 9916 patients from 4 large Dutch hospitals. This information was used to analyze the adherence of breast cancer surveillance to guidelines in the Netherlands. Multivariable logistic regression was used to relate the average number of a patient’s imaging procedures to their demographics, tumor–treatment characteristics, and individual locoregional recurrence risk (LRR), estimated by a risk-prediction tool, called INFLUENCE. RESULTS: The average number of policlinic contacts per patient decreased from 4.4 in the first to 2.0 in the fifth follow-up year. In each of the 5 follow-up years, the share of patients without imaging procedures was relatively high, ranging between 31.4% and 33.6%. Observed guidelines deviations were highly significant (P < .001). A higher age, lower UICC stage, and having undergone radio- or chemotherapy were significantly associated with a higher chance of receiving an imaging procedure. The estimated average LRR-risk was 3.5% in patients without any follow-up imaging compared with 2.3% in patients with the recommended number of 5 imagings. CONCLUSION: Compared to guidelines, more policlinic visits were made, although at inadequate intervals, and fewer imaging procedures were performed. The frequency of imaging procedures did not correlate with the patients’ individual risk profiles for LRR

Preparing children with a mock scanner training protocol results in high quality structural and functional MRI scans

We evaluated the use of a mock scanner training protocol as an alternative for sedation and for preparing young children for (functional) magnetic resonance imaging (MRI). Children with severe mental retardation or developmental disorders were excluded. A group of 90 children (median age 6.5 years, range 3.65–14.5 years) participated in this study. Children were referred to the actual MRI investigation only when they passed the training. We assessed the pass rate of the mock scanner training sessions. In addition, the quality of both structural and functional MRI (fMRI) scans was rated on a semi-quantitative scale. The overall pass rate of the mock scanner training sessions was 85/90. Structural scans of diagnostic quality were obtained in 81/90 children, and fMRI scans with sufficient quality for further analysis were obtained in 30/43 of the children. Even in children under 7 years of age, who are generally sedated, the success rate of structural scans with diagnostic quality was 53/60. FMRI scans with sufficient quality were obtained in 23/36 of the children in this younger age group. The association between age and proportion of children with fMRI scans of sufficient quality was not statistically significant. We conclude that a mock MRI scanner training protocol can be useful to prepare children for a diagnostic MRI scan. It may reduce the need for sedation in young children undergoing MRI. Our protocol is also effective in preparing young children to participate in fMRI investigations

Prognostic value of coronary vessel dominance in relation to significant coronary artery disease determined with non-invasive computed tomography coronary angiography

Aims Limited information is available regarding the relationship between coronary vessel dominance and prognosis. Therefore, the purpose of this study was to determine the prognostic value of coronary vessel dominance in relation to significant coronary artery disease (CAD) in patients referred for computed tomography coronary angiography (CTA). Methods and results The study population consisted of 1425 patients (869 men, 57 ± 12 years) referred for CTA. To evaluate the impact of vessel dominance and significant CAD on CTA on outcome, patients were followed during a median period of 24 months for the occurrence of non-fatal myocardial infarction and all-cause mortality. The presence of a left dominant system was identified as a significant predictor for non-fatal myocardial infarction and all-cause mortality (HR: 3.20; 95% CI: 1.67-6.13, P < 0.001) and had incremental value over baseline risk factors and severity of CAD on CTA. In addition, in the subgroup of patients with significant CAD on CTA, patients with a left dominant system had a worse outcome compared with patients with a right dominant system (cumulative event rates: 9.5% and 35% at 3-year follow-up for a right and left dominant coronary artery system, respectively, log-rank P < 0.001). Conclusions The presence of a left dominant system was identified as an independent predictor of non-fatal myocardial infarction and all-cause mortality, especially in patients with significant CAD on CTA. Therefore, the assessment of coronary vessel dominance on CTA may further enhance risk stratification beyond the assessment of significant CAD on CT

High throughput identification of human monoclonal antibodies and heavy-chain-only antibodies to treat snakebite

Snakebite envenoming is a priority Neglected Tropical Disease that causes an estimated 81,000-135,000 fatalities each year. The development of a new generation of safer, affordable, and accessible antivenom therapies is urgently needed. With this goal in mind, rigorous characterisation of the specific toxins in snake venom is key to generating novel therapies for snakebite. Monoclonal antibodies directed against venom toxins are emerging as potentially strong candidates in the development of new snakebite diagnostics and treatment. Venoms comprise many different toxins of which several are responsible for their pathological effects. Due to the large variability of venoms within and between species, formulations of combinations of human antibodies are proposed as the next generation antivenoms. Here a high-throughput screening method employing antibody-based ligand fishing of venom toxins in 384 filter-well plate format has been developed to determine the antibody target/s The approach uses Protein G beads for antibody capture followed by exposure to a full venom or purified toxins to bind their respective ligand toxin(s). This is followed by a washing/centrifugation step to remove non-binding toxins and an in-well tryptic digest. Finally, peptides from each well are analysed by nanoLC-MS/MS and subsequent Mascot database searching to identify the bound toxin/s for each antibody under investigation. The approach was successfully validated to rapidly screen antibodies sourced from hybridomas, derived from venom-immunised mice expressing either regular human antibodies or heavy-chain-only human antibodies (HCAbs)