Data Format Standardization and DICOM Integration for Hyperpolarized C MRI.

Hyperpolarized (HP) C MRI has shown promise as a valuable modality for measurements of metabolism and is currently in human trials at 15 research sites worldwide. With this growth it is important to adopt standardized data storage practices as it will allow sites to meaningfully compare data. In this paper we (1) describe data that we believe should be stored and (2) demonstrate pipelines and methods that utilize the Digital Imaging and Communications in Medicine (DICOM) standard.

Data Format Standardization and DICOM Integration for Hyperpolarized C MRI.

Hyperpolarized (HP) C MRI has shown promise as a valuable modality for in vivo measurements of metabolism and is currently in human trials at 15 research sites worldwide. With this growth, it is important to adopt standardized data storage practices as it will allow sites to meaningfully compare data. In this paper, we (1) describe data that we believe should be stored and (2) demonstrate pipelines and methods that utilize the Digital Imaging and Communications in Medicine (DICOM) standard.

Implementation and prospective real-time evaluation of a generalized system for in-clinic deployment and validation of machine learning models in radiology.

The medical imaging community has embraced Machine Learning (ML) as evidenced by the rapid increase in the number of ML models being developed, but validating and deploying these models in the clinic remains a challenge. The engineering involved in integrating and assessing the efficacy of ML models within the clinical workflow is complex. This paper presents a general-purpose, end-to-end, clinically integrated ML model deployment and validation system implemented at UCSF.

How do we operate a large monthly red blood cell exchange program.

Background: Red blood cell (RBC) exchange for sickle cell disease presents unique difficulties due to RBC phenotyping, complex antibody work-ups, large number of RBC units required, and vascular access considerations, any of which can delay the procedure. Multidisciplinary coordination and systemic processes ensure that monthly appointments remain on schedule.

Study Design And Methods: A high-volume chronic RBC exchange program is described, highlighting the importance of multidisciplinary coordination and process improvement strategies involving initial referral, vascular access, order sets, and allocation of antigen-negative or phenotypically matched RBCs.

Interactive Effects of Molecular, Therapeutic, and Patient Factors on Outcome of Diffuse Low-Grade Glioma.

Purpose: In patients with diffuse low-grade glioma (LGG), the extent of surgical tumor resection (EOR) has a controversial role, in part because a randomized clinical trial with different levels of EOR is not feasible.

Methods: In a 20-year retrospective cohort of 392 patients with IDH-mutant grade 2 glioma, we analyzed the combined effects of volumetric EOR and molecular and clinical factors on overall survival (OS) and progression-free survival by recursive partitioning analysis. The OS results were validated in two external cohorts (n = 365).

Utilizing a Digital Swarm Intelligence Platform to Improve Consensus Among Radiologists and Exploring Its Applications.

Radiologists today play a central role in making diagnostic decisions and labeling images for training and benchmarking artificial intelligence (AI) algorithms. A key concern is low inter-reader reliability (IRR) seen between experts when interpreting challenging cases. While team-based decisions are known to outperform individual decisions, inter-personal biases often creep up in group interactions which limit nondominant participants from expressing true opinions.

Improving the Automatic Classification of Brain MRI Acquisition Contrast with Machine Learning.

Automated quantification of data acquired as part of an MRI exam requires identification of the specific acquisition of relevance to a particular analysis. This motivates the development of methods capable of reliably classifying MRI acquisitions according to their nominal contrast type, e.g.

Aurora-A kinase is differentially expressed in the nucleus and cytoplasm in normal Müllerian epithelium and benign, borderline and malignant serous ovarian neoplasms.

Background: Aurora-A kinase is important for cellular proliferation and is implicated in the tumorigenesis of several malignancies, including of the ovary. Information regarding the expression patterns of Aurora-A in normal Müllerian epithelium as well as benign, borderline and malignant epithelial ovarian neoplasms is limited.

Methods: We investigated Aurora-A expression by immunohistochemistry in 15 benign, 19 borderline and 17 malignant ovarian serous tumors, and 16 benign, 8 borderline, and 2 malignant ovarian mucinous tumors.

Federated learning for predicting clinical outcomes in patients with COVID-19.

Federated learning (FL) is a method used for training artificial intelligence models with data from multiple sources while maintaining data anonymity, thus removing many barriers to data sharing. Here we used data from 20 institutes across the globe to train a FL model, called EXAM (electronic medical record (EMR) chest X-ray AI model), that predicts the future oxygen requirements of symptomatic patients with COVID-19 using inputs of vital signs, laboratory data and chest X-rays. EXAM achieved an average area under the curve (AUC) >0.

Federated Learning used for predicting outcomes in SARS-COV-2 patients.

'Federated Learning' (FL) is a method to train Artificial Intelligence (AI) models with data from multiple sources while maintaining anonymity of the data thus removing many barriers to data sharing. During the SARS-COV-2 pandemic, 20 institutes collaborated on a healthcare FL study to predict future oxygen requirements of infected patients using inputs of vital signs, laboratory data, and chest x-rays, constituting the "EXAM" (EMR CXR AI Model) model. EXAM achieved an average Area Under the Curve (AUC) of over 0.

Hyperpolarized C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco.

Based on the expanding set of applications for hyperpolarized carbon-13 (HP- C) MRI, this work aims to communicate standardized methodology implemented at the University of California, San Francisco, as a primer for conducting reproducible metabolic imaging studies of the prostate and brain. Current state-of-the-art HP- C acquisition, data processing/reconstruction and kinetic modeling approaches utilized in patient studies are presented together with the rationale underpinning their usage. Organized around spectroscopic and imaging-based methods, this guide provides an extensible framework for handling a variety of HP- C applications, which derives from two examples with dynamic acquisitions: 3D echo-planar spectroscopic imaging of the human prostate and frequency-specific 2D multislice echo-planar imaging of the human brain.

Rhythmic Interventions, Musical Returns: The Health Benefits of Music as an Embodied, Everyday Practice.

In this essay, I explore the intermodal nature of well-being by considering the health benefits of music as an embodied, everyday practice in the unrelenting tempo of contemporary society. I draw from Henri Lefebvre's concept of rhythmanalysis to perform an embodied appraisal of neoliberal ideology as I experience it within the everyday spaces of higher education, and to promote an appreciation for, and utilization of musical and rhythmic interventions that restore balance and well-being amid the compressing agenda of the doctoral-degree chase. I weave together autoethnographic accounts of my own experience as I alternate between the challenges of graduate school and my involvement in various musical projects.

Association of Maximal Extent of Resection of Contrast-Enhanced and Non-Contrast-Enhanced Tumor With Survival Within Molecular Subgroups of Patients With Newly Diagnosed Glioblastoma.

Importance: Per the World Health Organization 2016 integrative classification, newly diagnosed glioblastomas are separated into isocitrate dehydrogenase gene 1 or 2 (IDH)-wild-type and IDH-mutant subtypes, with median patient survival of 1.2 and 3.6 years, respectively.

Kinetic Modeling of Hyperpolarized Carbon-13 Pyruvate Metabolism in the Human Brain.

Kinetic modeling of the in vivo pyruvate-to-lactate conversion is crucial to investigating aberrant cancer metabolism that demonstrates Warburg effect modifications. Non-invasive detection of alterations to metabolic flux might offer prognostic value and improve the monitoring of response to treatment. In this clinical research project, hyperpolarized [1-C] pyruvate was intravenously injected in a total of 10 brain tumor patients to measure its rate of conversion to lactate ( k ) and bicarbonate ( k ) via echo-planar imaging.

Hemostasis testing and therapeutic plasma exchange: Results of a practice survey.

Introduction: Performing therapeutic plasma exchange (TPE) with albumin replacement decreases coagulation factor and platelet levels. No defined guidelines exist regarding laboratory testing to assess hemostasis in patients undergoing TPE.

Materials And Methods: A survey to evaluate hemostasis testing with TPE was distributed using online survey software.

Hemostasis management and therapeutic plasma exchange: Results of a practice survey.

Background: Patients undergoing therapeutic plasma exchange (TPE) may present with risks for hemorrhage or thrombosis. Use of replacement fluids devoid of coagulation factors will decrease factor levels and platelet levels. There are no established guidelines for hemostasis management in these situations.

Reliable and Reproducible GABA Measurements Using Automated Spectral Prescription at Ultra-High Field.

To evaluate spectral acquisition processes important for obtaining reliable and reproducible γ-aminobutyric acid (GABA) signals from volunteers in brain regions that are frequently used for neuroimaging studies [anterior cingulate cortex (ACC), superior temporal gyrus, and caudate] at ultra-high field. Ten healthy volunteers were studied using a single-voxel Point-RESolved Spectrosocpy (PRESS) sequence with band selective inversion with gradient dephasing pulses (BASING). The editing pulse was designed to be symmetrically placed at 2.

Fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging: Toward robust and reproducible metabolite measurements in human brain.

Purpose: To implement a fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging (MRSI).

Methods: The PRESS selected volume and outer-volume suppression bands were predefined on the MNI152 standard template image. The template image was aligned to the subject T -weighted image during a scan, and the resulting transformation was then applied to the predefined prescription.

Metabolic Profiling of IDH Mutation and Malignant Progression in Infiltrating Glioma.

Infiltrating low grade gliomas (LGGs) are heterogeneous in their behavior and the strategies used for clinical management are highly variable. A key factor in clinical decision-making is that patients with mutations in the isocitrate dehydrogenase 1 and 2 (IDH1/2) oncogenes are more likely to have a favorable outcome and be sensitive to treatment. Because of their relatively long overall median survival, more aggressive treatments are typically reserved for patients that have undergone malignant progression (MP) to an anaplastic glioma or secondary glioblastoma (GBM).

Serial analysis of 3D H-1 MRSI for patients with newly diagnosed GBM treated with combination therapy that includes bevacizumab.

Interpretation of changes in the T1- and T2-weighted MR images from patients with newly diagnosed glioblastoma (GBM) treated with standard of care in conjunction with anti-angiogenic agents is complicated by pseudoprogression and pseudoresponse. The hypothesis being tested in this study was that 3D H-1 magnetic resonance spectroscopic imaging (MRSI) provides estimates of levels of choline, creatine, N-acetylaspartate (NAA), lactate and lipid that change in response to treatment and that metrics describing these characteristics are associated with survival. Thirty-one patients with newly diagnosed GBM and being treated with radiation therapy (RT), temozolomide, erlotinib and bevacizumab were recruited to receive serial MR scans that included 3-D lactate edited MRSI at baseline, mid-RT, post-RT and at specific follow-up time points.

Association of early changes in 1H MRSI parameters with survival for patients with newly diagnosed glioblastoma receiving a multimodality treatment regimen.

Background: The heterogeneous biology of glioblastoma (GBM) emphasizes the need for imaging methods to assess tumor burden and assist in evaluating individual patients. The purpose of this study was to investigate early changes in metrics from 3D 1H magnetic resonance spectroscopic imaging (MRSI) data, compare them with anatomic lesion volumes, and determine whether they were associated with survival for patients with newly diagnosed GBM receiving a multimodality treatment regimen.

Methods: Serial MRI and MRSI scans provided estimates of anatomic lesion volumes and levels of choline, creatine, N-acetylaspartate, lactate, and lipid.

Detection of localized changes in the metabolism of hyperpolarized gluconeogenic precursors C-lactate and C-pyruvate in kidney and liver.

Purpose: The purpose of this study was to characterize tissue-specific alterations in metabolism of hyperpolarized (HP) gluconeogenic precursors C-lactate and C-pyruvate by rat liver and kidneys under conditions of fasting or insulin-deprived diabetes.

Methods: Seven normal rats were studied by MR spectroscopic imaging of both HP C-lactate and C-pyruvate in both normal fed and 24 h fasting states, and seven additional rats were scanned after induction of diabetes by streptozotocin (STZ) with insulin withdrawal. Phosphoenolpyruvate carboxykinase (PEPCK) expression levels were also measured in liver and kidney tissues of the STZ-treated rats.

Power estimation for non-standardized multisite studies.

A concern for researchers planning multisite studies is that scanner and T1-weighted sequence-related biases on regional volumes could overshadow true effects, especially for studies with a heterogeneous set of scanners and sequences. Current approaches attempt to harmonize data by standardizing hardware, pulse sequences, and protocols, or by calibrating across sites using phantom-based corrections to ensure the same raw image intensities. We propose to avoid harmonization and phantom-based correction entirely.

Precision medicine in chronic disease management: The multiple sclerosis BioScreen.

We present a precision medicine application developed for multiple sclerosis (MS): the MS BioScreen. This new tool addresses the challenges of dynamic management of a complex chronic disease; the interaction of clinicians and patients with such a tool illustrates the extent to which translational digital medicine-that is, the application of information technology to medicine-has the potential to radically transform medical practice. We introduce 3 key evolutionary phases in displaying data to health care providers, patients, and researchers: visualization (accessing data), contextualization (understanding the data), and actionable interpretation (real-time use of the data to assist decision making).