Methodology for Good Machine Learning with Multi-Omics Data.

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio-genomics-based prognostic and predictive factors for HR+/HER- metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi-omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as "maintaining effective communication" and "following good data science practices," followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

Pectoralis Muscle Dosimetry and Posttreatment Rehabilitation Utilization for Patients With Early-Stage Breast Cancer.

PURPOSE: Up to 50% of women treated for localized breast cancer will experience some degree of arm or shoulder morbidity. Although radiation is thought to contribute to this morbidity, the mechanism remains unclear. Prior studies have shown biologic and radiographic changes in the pectoralis muscles after radiation. This study thus aimed to investigate the relationship between radiation to the pectoralis muscles and referrals for rehabilitation services posttreatment for arm and shoulder morbidity. METHODS AND MATERIALS: A retrospective 1:1 matched case-control study was conducted for patients with breast cancer who were and were not referred for breast or shoulder rehabilitation services between 2014 and 2019 at a single academic institution. Patients were included if they had a lumpectomy and adjuvant radiation. Patients who underwent an axillary lymph node dissection were excluded. Cohorts were matched based on age, axillary surgery, and use of radiation boost. Muscle doses were converted to equivalent dose in 2 Gy fractions assuming an α:ß ratio of 2.5 and were compared between the 2 groups. RESULTS: In our cohort of 50 patients of a median age 60 years (interquartile range, 53-68 years), 36 patients (72%) underwent a sentinel lymph node biopsy in addition to a lumpectomy. Although pectoralis muscle doses were generally higher in those receiving rehabilitation services, this was not statistically significant. Pectoralis major V20-40 Gy reached borderline significance, as did pectoralis major mean dose (17.69 vs 20.89 Gy; P = .06). CONCLUSIONS: In this limited cohort of patients, we could not definitively conclude a relationship between pectoralis muscle doses and use of rehabilitation services. Given the borderline significant findings, this should be further investigated in a larger cohort.

Clinical Considerations in Returning Pediatric and Young Adults With Cancer to Physical Activity.

ABSTRACT: There is a gap in the literature on the best treatment of clinical sequelae within adolescent and young adult pediatric cancer populations. Children, adolescents, and young adults are at risk for a multitude of immediate and late effects of their disease and treatment that warrant a comprehensive, multidisciplinary team approach to optimize care. Sports medicine providers are well-equipped with their background to join the oncology rehabilitation team in diagnosing and managing cancer-related impairments to help these populations live a healthier and more active lifestyle. In this manuscript, four essential clinical components to consider when returning children, adolescents, and young adults with cancer history to physical activity are discussed: chemotherapy-induced peripheral neuropathy, cardiotoxicity, nutritional deficiencies, and deconditioning.

Anomalous Left Coronary Artery from the Pulmonary Artery: How to Diagnose and Treat.

Anomalous origin of the left coronary artery from the pulmonary artery (ALCAPA) is a rare coronary anomaly that can present in childhood or adulthood with a multitude of symptoms depending on the age of presentation. It should be suspected in infants presenting with heart failure in the setting of left ventricular systolic dysfunction and associated mitral regurgitation from papillary muscle ischemia. Adults with ALCAPA may present with cardiac ischemic symptoms. Prompt diagnosis with echocardiography and cross-sectional chest imaging is important to guide surgical intervention and improve the patients' survival and prognosis. The goal of surgery is to establish a dual-coronary system with mid-term results revealing progressive recovery of left ventricular function and improvement in mitral regurgitation. Patients with ALCAPA should maintain life-long follow-up with a cardiologist with congenital heart disease expertise for surveillance of post-operative complications.

Function in Cancer Patients: Disease and Clinical Determinants.

Patients with cancer often experience changes in function during and after treatment but it is not clear what cancer types, and associated clinical factors, affect function. This study evaluated patient-reported functional impairments between specific cancer types and risk factors related to disease status and non-cancer factors. A cross-sectional study evaluating 332 individuals referred to cancer rehabilitation clinics was performed at six U.S. hospitals. The PROMIS Cancer Function Brief 3D Profile was used to assess functional outcomes across the domains of physical function, fatigue, and social participation. Multivariable modeling showed an interaction between cancer type and cancer status on the physical function and social participation scales. Subset analyses in the active cancer group showed an effect by cancer type for physical function (p < 0.001) and social participation (p = 0.008), but no effect was found within the non-active cancer subset analyses. Brain, sarcoma, prostate, and lymphoma were the cancers associated with lower function when disease was active. Premorbid neurologic or musculoskeletal impairments were found to be predictors of lower physical function and social participation in those with non-active cancer; cancer type did not predict low function in patients with no evidence of disease. There was no differential effect of cancer type on fatigue, but increased fatigue was significantly associated with lower age (0.027), increased body mass index (p < 0.001), premorbid musculoskeletal impairment (p < 0.015), and active cancer status (p < 0.001). Anticipatory guidance and education on the common impairments observed with specific cancer types and during specific stages of cancer care may help improve/support patients and their caregivers as they receive impairment-driven cancer rehabilitation care.

Layer-by-layer interleukin-12 nanoparticles drive a safe and effective response in ovarian tumors.

Ovarian cancer is especially deadly, challenging to treat, and has proven refractory to known immunotherapies. Cytokine therapy is an attractive strategy to drive a proinflammatory immune response in immunologically cold tumors such as many high grade ovarian cancers; however, this strategy has been limited in the past due to severe toxicity. We previously demonstrated the use of a layer-by-layer (LbL) nanoparticle (NP) delivery vehicle in subcutaneous flank tumors to reduce the toxicity of interleukin-12 (IL-12) therapy upon intratumoral injection. However, ovarian cancer cannot be treated by local injection as it presents as dispersed metastases. Herein, we demonstrate the use of systemically delivered LbL NPs using a cancer cell membrane-binding outer layer to effectively target and engage the adaptive immune system as a treatment in multiple orthotopic ovarian tumor models, including immunologically cold tumors. IL-12 therapy from systemically delivered LbL NPs shows reduced severe toxicity and maintained anti-tumor efficacy compared to carrier-free IL-12 or layer-free liposomal NPs leading to a 30% complete survival rate.

Developing an Echocardiography-Based, Automatic Deep Learning Framework for the Differentiation of Increased Left Ventricular Wall Thickness Etiologies.

AIMS: Increased left ventricular (LV) wall thickness is frequently encountered in transthoracic echocardiography (TTE). While accurate and early diagnosis is clinically important, given the differences in available therapeutic options and prognosis, an extensive workup is often required to establish the diagnosis. We propose the first echo-based, automated deep learning model with a fusion architecture to facilitate the evaluation and diagnosis of increased left ventricular (LV) wall thickness. METHODS AND RESULTS: Patients with an established diagnosis of increased LV wall thickness (hypertrophic cardiomyopathy (HCM), cardiac amyloidosis (CA), and hypertensive heart disease (HTN)/others) between 1/2015 and 11/2019 at Mayo Clinic Arizona were identified. The cohort was divided into 80%/10%/10% for training, validation, and testing sets, respectively. Six baseline TTE views were used to optimize a pre-trained InceptionResnetV2 model. Each model output was used to train a meta-learner under a fusion architecture. Model performance was assessed by multiclass area under the receiver operating characteristic curve (AUROC). A total of 586 patients were used for the final analysis (194 HCM, 201 CA, and 191 HTN/others). The mean age was 55.0 years, and 57.8% were male. Among the individual view-dependent models, the apical 4-chamber model had the best performance (AUROC: HCM: 0.94, CA: 0.73, and HTN/other: 0.87). The final fusion model outperformed all the view-dependent models (AUROC: HCM: 0.93, CA: 0.90, and HTN/other: 0.92). CONCLUSION: The echo-based InceptionResnetV2 fusion model can accurately classify the main etiologies of increased LV wall thickness and can facilitate the process of diagnosis and workup.

A new label-free optical imaging method for the lymphatic system enhanced by deep learning.

Our understanding of the lymphatic vascular system lags far behind that of the blood vascular system, limited by available imaging technologies. We present a label-free optical imaging method that visualizes the lymphatic system with high contrast. We developed an orthogonal polarization imaging (OPI) in the shortwave infrared range (SWIR) and imaged both lymph nodes and lymphatic vessels of mice and rats in vivo through intact skin, as well as human mesenteric lymph nodes in colectomy specimens. By integrating SWIR-OPI with U-Net, a deep learning image segmentation algorithm, we automated the lymph node size measurement process. Changes in lymph nodes in response to cancer progression were monitored in two separate mouse cancer models, through which we obtained insights into pre-metastatic niches and correlation between lymph node masses and many important biomarkers. In a human pilot study, we demonstrated the effectiveness of SWIR-OPI to detect human lymph nodes in real time with clinical colectomy specimens. One Sentence Summary: We develop a real-time high contrast optical technique for imaging the lymphatic system, and apply it to anatomical pathology gross examination in a clinical setting, as well as real-time monitoring of tumor microenvironment in animal studies.

Graft-Versus-Host Disease: an Update on Functional Implications and Rehabilitation Interventions.

PURPOSE OF REVIEW: Despite advances in treatment, chronic graft-versus-host disease (cGVHD) remains a highly morbid complication of allogeneic hematopoietic stem cell transplantation. Due to direct effects of the disease on specific body sites, and its treatment, patients lose function. This review summarizes the latest evidence surrounding how cGVHD affects function, and restorative interventions. RECENT FINDINGS: Different body sites of cGVHD carry a higher risk of functional decline, including pulmonary and sclerotic/fascial. Support should be comprehensive and individualized, with precautions taken to avoid worsening fibrosis, offloading painful joints and fractures, and utilizing function-directed skilled therapies. Inpatient rehabilitation improves function in hospitalized people with cGVHD. For people with cGVHD, rehabilitation addresses different aspects of impaired function across the spectrum of disease. Given the dynamic nature of the disease process, routine assessment may be warranted. Rehabilitation may also improve deleterious effects of anti-cGVHD medication including glucocorticoids and tyrosine kinase inhibitors.

Risk factors for reduced function in women with a history of breast cancer.

PURPOSE: People with a history of breast cancer are at risk of losing function during and after treatment. Unfortunately, little is known about the individual and additive effects of specific treatment, disease-related, and demographic factors that may contribute to functional decline. This manuscript reports the results of a multi-center study to evaluate the effects of these factors on function. METHODS: In this cross-sectional study, women with a history of breast cancer referred to physical medicine and rehabilitation cancer rehabilitation clinics were administered the PROMIS® Cancer Function Brief 3D Profile to evaluate function in the domains of physical function, fatigue, and social participation. Clinical and demographic information, including treatment history and disease status, was recorded by clinicians. Patients were analyzed in two groups: those with active disease on antineoplastic treatment, and those with no evidence of disease (NED). A multivariable model was constructed to detect associations between clinical and demographic factors. RESULTS: In patients with NED, the presence of chemotherapy-induced peripheral neuropathy (CIPN) was strongly associated with reduced function in all three domains. In those with active disease, having brain metastases was significantly associated with reduced function in all domains and CIPN with reduced physical function. Radiation was associated with improved function in both cohorts. CONCLUSIONS: Among women seeking rehabilitative care, CIPN and the presence of brain metastases were most strongly associated with a decline in function. The effects of radiation on function were unexpected and may be partially explained by the treatment's role in symptom management. Clinicians who treat breast cancer should consider a patient's functional status when providing supportive care.

IMPACT the Brain: A Team-Based Approach to Management of Metastatic Breast Cancer With CNS Metastases.

PURPOSE: CNS metastases are associated with decreased survival and quality of life for patients with metastatic breast cancer (MBC). Team-based care can optimize outcomes. IMPACT the Brain is a care coordination program that aims to improve access to team-based care for patients with MBC and CNS metastases. MATERIALS AND METHODS: Patients with MBC and CNS metastases were eligible for enrollment in this care coordination program. A team of specialists supported a dedicated program coordinator who provided navigation, education, specialty referral, and clinical trial screening. A unique intake form developed for the program created personalized, coordinated, and expedited specialty referrals. Patient-reported outcomes and caregiver burden assessments were collected on a voluntary basis throughout enrollment. Data were analyzed using descriptive statistics. RESULTS: Sixty patients were referred, and 53 were enrolled (88%). The median time to program enrollment was 1 day (range, 0-11) and to first visit was 5 days (range, 0-25). On the basis of the program intake form, 47 referrals were made across six specialties, most commonly physical medicine and rehabilitation (n = 10), radiation oncology (n = 10), and neuropsychology (n = 10). Nineteen patients (36%) consented to enroll in clinical trials. CONCLUSION: A tailored team-based care coordination program for patients with MBC and CNS metastases is feasible. Use of a unique intake screening form by a dedicated program coordinator resulted in faster time to first patient visit, enabled access to subspecialist care, and supported enrollment in clinical trials. Future research should focus on intervention development using PRO data collected in this care coordination program.

Responsiveness and interpretation of the PROMIS Cancer Function Brief 3D Profile.

BACKGROUND: Measuring function with valid and responsive tools in patients with cancer is essential for driving clinical decision-making and for the end points of clinical trials. Current patient-reported outcome measurements of function fall short for many reasons. This study evaluates the responsiveness of the Patient-Reported Outcomes Measurement Information System (PROMIS) Cancer Function Brief 3D Profile, a novel measure of function across multiple domains. METHODS: Two hundred nine participants across five geographically distinct tertiary care centers completed the assessment and pain rating at two outpatient cancer rehabilitation clinic visits. Patients and providers completed a global rating of change measure at the second visit to indicate whether the patient was improving or worsening in function. Multiple response indices and linear models measured whether the measure was responsive to self-reported and clinician-rated changes over time. Correlations between changes in function and changes in anchors (pain rating and performance status) were also calculated. RESULTS: Function as measured by the PROMIS Cancer Function Brief 3D Profile changed appropriately as both patients and clinicians rated change. Small to moderate effect sizes supported the tool's responsiveness. Function was moderately correlated with pain and more strongly correlated with performance status, and changes in function corresponded with changes in anchor variables. No floor/ceiling effect was found. CONCLUSIONS: The PROMIS Cancer Function Brief 3D Profile is sensitive to changes over time in patients with cancer. The measure may be useful in clinical practice and as an end point in clinical trials. LAY SUMMARY: We gave patients a questionnaire by which they told their physicians how well they were functioning, including how fatigued they were. This study tested that questionnaire to see whether the scores would change if patients got better or worse.

Integrating Palliative Care Into Physiatric Care: Perspective of the Association of Academic Physiatrists Physiatry Palliative Care Task Force.

ABSTRACT: There are opportunities for physiatrists to apply a palliative care lens within clinical encounters across rehabilitation settings. The expanding population of patients with serious illness and injury cared for by physiatrists and the anticipated shortage of specialty palliative care clinicians make it important that physiatrists hone and apply basic palliative care skills as part of comprehensive physiatric care. In this article, four clinical vignettes highlight relevant palliative care communication skills and demonstrate the value of integrating these skills within physiatry encounters. Resources to support physiatrists in applying basic palliative skills are provided throughout.

Passerini chemistries for synthesis of polymer pro-drug and polymersome drug delivery nanoparticles.

New materials chemistries are urgently needed to overcome the limitations of existing biomedical materials in terms of preparation, functionality and versatility, and also in regards to their compatibility with biological environments. Here, we show that Passerini reactions are especially suited for the preparation of drug delivery materials, as with relatively few steps, polymers can be synthesized with functionality installed enabling drug conjugation and encapsulation, self-assembly into micellar or vesicular architectures, and with facile attachment triggerable chemistries. The polymers can be made with a variety of building blocks and assemble into nanoparticles, which are rapidly internalized in triple negative breast cancer (TNBC) cells. In addition, the polymers transport drug molecules efficiently through 3D cell cultures, and when designed with chemistries allowing pH-mediated release, exhibit greater efficacy against TNBC cells compared to the parent drug.

Electronic Regulation of Nickel Single Atoms by Confined Nickel Nanoparticles for Energy-Efficient CO2 Electroreduction.

Modulating the electronic structure of atomically dispersed active sites is promising to boost catalytic activity but is challenging to achieve. Here we show a cooperative Ni single-atom-on-nanoparticle catalyst (NiSA/NP) prepared via direct solid-state pyrolysis, where Ni nanoparticles donate electrons to Ni(i)-N-C sites via a network of carbon nanotubes, achieving a high CO current density of 346 mA cm-2 at -0.5 V vs RHE in an alkaline flow cell. When coupled with a NiFe-based anode in a zero-gap membrane electrolyzer, the catalyst delivers an industrially relevant CO current density of 310 mA cm-2 at a low cell voltage of -2.3 V, corresponding to an overall energy efficiency of 57 %. The superior CO2 electroreduction performance is attributed to the enhanced adsorption of key intermediate COOH* on the electron-rich Ni single atoms, as well as a high density of active sites.

Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample.

BACKGROUND: Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based somatic mutation detection approach, and demonstrated performance advantages on in silico data. RESULTS: In this study, we use the first comprehensive and well-characterized somatic reference data sets from the SEQC2 consortium to investigate best practices for using a deep learning framework in cancer mutation detection. Using the high-confidence somatic mutations established for a cancer cell line by the consortium, we identify the best strategy for building robust models on multiple data sets derived from samples representing real scenarios, for example, a model trained on a combination of real and spike-in mutations had the highest average performance. CONCLUSIONS: The strategy identified in our study achieved high robustness across multiple sequencing technologies for fresh and FFPE DNA input, varying tumor/normal purities, and different coverages, with significant superiority over conventional detection approaches in general, as well as in challenging situations such as low coverage, low variant allele frequency, DNA damage, and difficult genomic regions.