Statistical Methods for Integrated Cancer Genomic Data Using a Joint Latent Variable Model

Inspired by the TCGA (The Cancer Genome Atlas), we explore multimodal genomic datasets with integrative methods using a joint latent variable approach. We use iCluster+, an existing clustering method for integrative data, to identify potential subtypes within TCGA sarcoma and mesothelioma tumors, and across a large cohort of 33 dierent TCGA cancer datasets. For classication, motivated to improve the prediction of platinum resistance in high grade serous ovarian cancer (HGSOC) treatment, we propose novel integrative methods, iClassify to perform classication using a joint latent variable model. iClassify provides eective data integration and classication while handling heterogeneous data types, while providing a natural framework to incorporate covariate risk factors and examine genomic driver by covariate risk factor interaction. Feature selection is performed through a thresholding parameter that combines both latent variable and feature coecients. We demonstrate increased accuracy in classication over methods that assume homogeneous data type, such as linear discriminant analysis and penalized logistic regression, and improved feature selection. We apply iClassify to a TCGA cohort of HGSOC patients with three types of genomic data and platinum response data. This methodology has broad applications beyond predicting treatment outcomes and disease progression in cancer, including predicting prognosis and diagnosis in other diseases with major public health implications

Constitutional Individualism: The Ninth Amendment and the “Natural Rights of Man”

The Ninth Amendment is not a one-off historical anachronism aimed at protecting nonexistent rights. Instead, it should be construed by the courts as a bulwark against undue governmental interference in people’s private lives. Author information: Lucas B. Drill is from La Cañada Flintridge, California. He is a rising senior in the Joint Program between Columbia University and the Jewish Theological Seminary, in which he is simultaneously pursuing Bachelor of Arts degrees in Political Science and Jewish History. Lucas is an aspiring lawyer, constitutional scholar, and judge

Healthy Work Environments: An Interprofessional Partnership Model to Promote Positive Workplace Culture

Background: Healthy work environments (HWEs) are a primary focus of leaders in health care. Many nurse- specific HWE initiatives exist to improve workplace culture; however, workplace harm persists. An interprofessional partnership model is needed to sustain healthy workplace cultures to promote engagement among providers and employees, and safe, high-quality patient care. Methods: The 5-Stage Process® is a method for teams to openly examine workplace behavior, co-creating their future using continuous quality improvement strategies of Team Building, Assessment, Implementation, Evaluation, and Sustainability. To ensure success, each stage should be completed with focused attention to the concrete strategies the team needs to take to sustain the healthy work environment. Results: The entire 5-Stage Process® was used by interprofessional teams from the specialties of Perinatology and Radiology at major health care institutions in the Midwest and Perioperative in the Northeast United States. Each team implemented one-on-one conflict resolution techniques, and one team noted improvements in employee engagement scores from 60% to 86%, patient satisfaction from 74% to 85%, safety perception scores from 70% to 79%, and teamwork perception scores from 82% to 84%. Conclusion: The interprofessional partnership 5-Stage Process® may be a successful method to continuously improve workplace cultures and ultimately improve patient safety and provider and staff satisfaction. Sustaining healthy work environments requires leaders’ constant focus and dedication to partnership techniques to ensure that new healthy behaviors persist

Bringing the Environment into the English-as-a-Second-Language Classroom

Environment and Community: Caring for Our Natural Resources is a curriculum developed by UC Cooperative Extension to teach adult immigrants about the environment in English-as-a-second-language (ESL) classrooms. It was developed with participation from ESL instructors and students. Surveys were conducted to determine knowledge of and interest in the environment among ESL students and to assess changes after participation in the program. Results indicate a high level of interest in the environment. After using the Environment and Community curriculum, students experienced a significant gain in knowledge about the environment, and 63% indicated that they had implemented pro-environment behaviors

A Multisite Hospital\u27s Transition to an Interoperable Electronic Health Records System

The health care industry is transforming into an industry that requires health information technology, yet many health care organizations are reluctant to implement new technology. The purpose of this case study was to explore strategies that led to a successful transition from an older electronic health record (EHR) system to a compliant EHR system at a multisite hospital system (MHS). The study included face-to-face and phone interviews with 12 managers who worked on the transition of an MHS\u27s EHR system in the Pacific Northwest region of the United States. The technology acceptance model was used to frame the study. Audio recordings with these managers were transcribed and analyzed along with interview notes and publicly available documents to identify themes regarding strategies used by managers to successfully upgrade to a compliant EHR system at an MHS. Three major themes emerged: hybrid implementation strategy, training strategy, and social pressure strategy. Results may be used to facilitate the adoption of information technology systems in any industry. Results may directly benefit other MHSs by facilitating successful EHR system transitions. Implications for social change include improved care coordination, reductions in duplicated medical procedures, and more timely and relevant tests for patients through the full use of EHRs

Ichthyofauna of the Los Angeles River

The Los Angeles River is a highly modified urban system. Upper tributaries of the watershed are located in Angeles National Forest and are in a relatively natural state, but below the forest boundary the tributaries and the mainstem consist of a series of completely channelized sections with a concrete bottom that includes a low-flow channel and vertical walls, sections where there are graded berms and a substrate that was either not stabilized with a concrete substrate, or where enough sediment has accumulated to provide a “soft-bottom” with vegetation, boulders, and variation in flow, and off-channel impoundments. Here we provide the results of fish surveys and both professional and community-contributed citizen science observations collected from 2007-2020 that document the presence of 29 species, of which six, found either in upper reaches (sections of the river with similar habitat and hydrologic characteristics) or in the estuary, are native to the river. To accompany these data, we also provide a novel classification schema identifying the unique reaches of the LA River

Assessment of Clinical Information: Comparison of the Validity of a Structured Clinical Interview (the Scid) and the Clinical Diagnostic Interview

Adaptive functioning is a key aspect of psychiatric diagnosis and assessment in research and practice. This study compared adaptive functioning validity ratings from Structured Clinical Interviews (SCIDs, symptom-focused structured diagnostic interviews), and Clinical Diagnostic Interviews (CDIs, systematic diagnostic interviews modeling naturalistic clinical interactions focusing on relational narratives). Two hundred forty-five patients (interviewed by two independent interviewers) and their interviewers completed the Clinical Data Form which assesses adaptive functioning and clinical information. Both interviews converged strongly with patient-reports, with no significant differences in validity of the interviews in measuring global and specific domains of adaptive functioning variables. Findings suggest that CDIs provide adaptive functioning data comparable to SCIDs (often considered gold standard for assessment but difficult to use in practice) and have important implications for bridging the research-practice gap. By incorporating clinicians\u27 everyday methods, CDIs yield information that is psychometrically sound for empirical investigation, diagnostically practical, and clinically meaningful and valid

Agreement Between Clinician and Patient Ratings of Adaptive Functioning and Developmental History

Objective: Psychiatric researchers rely heavily on patient report data for clinical research. However, patient reports are prone to defensive and self-presentation biases. Recent research using practice networks has relied on clinician reports, and both forensic and personality disorder researchers have recently turned to quantified data from clinically expert observers as well. However, critics have raised legitimate concerns about the reliability and validity of data from clinician informants. The aim of this study was to assess the validity and diagnostic efficiency of clinician reports of their patients\u27 adaptive functioning and developmental histories, using patient reports as the comparative standard traditionally used in psychiatric research. Method: Eighty-four clinicians and their patients completed a clinical data form designed to assess a range of patient functioning, clinical history, and developmental relationship variables used in multiple clinician report studies. The authors correlated clinician and patient reports across a number of clinically relevant adaptive functioning variables and calculated diagnostic efficiency statistics for a range of clinical history variables, including suicide attempts, hospitalizations, arrests, interpersonal conflicts affecting employment, and childhood physical and sexual abuse. Results: Across variables, patient-therapist correlations (0.40-0.66) and overall correct classification statistics (0.74-0.96) were high. Conclusions: The data demonstrate that clinicians\u27 judgments about their patients\u27 functioning and histories agree with patients\u27 self-reports and that in areas of discrepancy, clinicians tend to make appropriately conservative judgments in the absence of clear data. These findings suggest that quantified clinical judgment provides a vast untapped potential for large-sample research on psychopathology and treatment