Topological Structures in the Space of Treatment-Naïve Patients with Chronic Lymphocytic Leukemia.

Patients are complex and heterogeneous; clinical data sets are complicated by noise, missing data, and the presence of mixed-type data. Using such data sets requires understanding the high-dimensional "space of patients", composed of all measurements that define all relevant phenotypes. The current state-of-the-art merely defines spatial groupings of patients using cluster analyses.

Diffuse large B-cell lymphoma and red cell autoimmunity: clinical role and pathogenesis.

Diffuse large B-cell lymphoma (DLBCL) is the most common form of B-cell non-Hodgkin lymphoma (B-NHL) with significant morbidity and mortality despite advancements in treatment. Lymphoma and autoimmune disease both result from breakdowns in normal cell regulatory pathways, and epidemiological studies have confirmed both that B-NHL is more likely to develop in the setting of autoimmune diseases and vice versa. Red cell immunity, as evidenced by direct antiglobulin test (DAT) positivity, has been linked to DLBCL and more recently the pathogenic causes of this association have begun to be better understood using molecular techniques.

Sequences of Events from the Electronic Medical Record and the Onset of Infection.

We present a novel model of time-series analysis to learn from electronic health record (EHR) data when infection occurred in the intensive care unit (ICU) by translating methods from proteomics and Bayesian statistics. Using 48,536 patients hospitalized in an ICU, we describe each hospital course as an 'alphabet' of 23 physician actions ('events') in temporal order. We analyze these as k-mers of length 3-12 events and apply a Bayesian model of (cumulative) relative risk (RR).

Multifocal pupillographic objective perimetry for assessment of early diabetic retinopathy and generalised diabetes-related tissue injury in persons with type 1 diabetes.

Background: To examine the potential utility of five multifocal pupillographic objective perimetry (mfPOP) protocols, in the assessment of early diabetic retinopathy (DR) and generalised diabetes-related tissue injury in subjects with type 1 diabetes (T1D).

Methods: Twenty-five T1D subjects (age 41.8 ± 12.

Simulation-derived best practices for clustering clinical data.

Introduction: Clustering analyses in clinical contexts hold promise to improve the understanding of patient phenotype and disease course in chronic and acute clinical medicine. However, work remains to ensure that solutions are rigorous, valid, and reproducible. In this paper, we evaluate best practices for dissimilarity matrix calculation and clustering on mixed-type, clinical data.

A novel model to label delirium in an intensive care unit from clinician actions.

Background: In the intensive care unit (ICU), delirium is a common, acute, confusional state associated with high risk for short- and long-term morbidity and mortality. Machine learning (ML) has promise to address research priorities and improve delirium outcomes. However, due to clinical and billing conventions, delirium is often inconsistently or incompletely labeled in electronic health record (EHR) datasets.

Pattern recognition in lymphoid malignancies using CytoGPS and Mercator.

Background: There have been many recent breakthroughs in processing and analyzing large-scale data sets in biomedical informatics. For example, the CytoGPS algorithm has enabled the use of text-based karyotypes by transforming them into a binary model. However, such advances are accompanied by new problems of data sparsity, heterogeneity, and noisiness that are magnified by the large-scale multidimensional nature of the data.

Mercator: a pipeline for multi-method, unsupervised visualization and distance generation.

Summary: Unsupervised machine learning provides tools for researchers to uncover latent patterns in large-scale data, based on calculated distances between observations. Methods to visualize high-dimensional data based on these distances can elucidate subtypes and interactions within multi-dimensional and high-throughput data. However, researchers can select from a vast number of distance metrics and visualizations, each with their own strengths and weaknesses.

High proportion of anergic B cells in the bone marrow defined phenotypically by CD21(-/low)/CD38- expression predicts poor survival in diffuse large B cell lymphoma.

Background: Diffuse large B cell lymphoma (DLBCL) is the commonest lymphoma that is highly aggressive where one-third of the patients relapse despite effective treatment. Interaction between the lymphoma cells and the non-clonal immune cells within the bone marrow microenvironment is thought to play a critical role in the pathogenesis of DLBCL.

Methods: We used flow cytometry to characterize the proportion of B cell subpopulations in the bone marrow (N = 47) and peripheral blood (N = 54) of 75 DLBCL patients at diagnosis and study their impact on survival.

CytoGPS: A large-scale karyotype analysis of CML data.

Karyotyping, the practice of visually examining and recording chromosomal abnormalities, is commonly used to diagnose diseases of genetic origin, including cancers. Karyotypes are recorded as text written in the International System for Human Cytogenetic Nomenclature (ISCN). Downstream analysis of karyotypes is conducted manually, due to the visual nature of analysis and the linguistic structure of the ISCN.

Unsupervised machine learning and prognostic factors of survival in chronic lymphocytic leukemia.

Objective: Unsupervised machine learning approaches hold promise for large-scale clinical data. However, the heterogeneity of clinical data raises new methodological challenges in feature selection, choosing a distance metric that captures biological meaning, and visualization. We hypothesized that clustering could discover prognostic groups from patients with chronic lymphocytic leukemia, a disease that provides biological validation through well-understood outcomes.

Prognostic significance of translocations in the presence of mutated IGHV and of cytogenetic complexity at diagnosis of chronic lymphocytic leukemia.

Mutations of the IGH variable region in patients with chronic lymphocytic leukemia (CLL) are associated with a favorable prognosis. Cytogenetic complexity (>3 unrelated aberrations) and translocations have been associated with an unfavorable prognosis. While mutational status of IGHV is stable, cytogenetic aberrations frequently evolve.

The Current and Future Use of Telemedicine in Infectious Diseases Practice.

Purpose Of Review: Novel technologies, such as high-definition cameras, encryption software, electronic stethoscopes, microfluidic diagnostic systems, and widely available broadband Internet have expanded the potential for telemedicine. This narrative review presents current and future uses of telemedicine in the prevention, diagnosis, treatment, stewardship, and management of infectious disease.

Recent Findings: Beginning in the 1990s, early approaches to telemedicine in infectious disease focused largely on treatment of HIV/AIDS, hepatitis C, and tuberculosis.

Outcomes of synchronous systemic and central nervous system (CNS) involvement of diffuse large B-cell lymphoma are dictated by the CNS disease: a collaborative study of the Australasian Lymphoma Alliance.

De novo diffuse large B-cell lymphoma (DLBCL) presenting with synchronous central nervous system (CNS) and systemic disease (synDLBCL) is not well described and is excluded from clinical trials. We performed a retrospective analysis of 80 synDLBCL patients treated across 10 Australian and UK centres. Of these patients, 96% had extranodal systemic disease.

A Survey of Australian Dysphagia Practice Patterns.

Dysphagia assessment and rehabilitation practice is complex, and significant variability in speech-language pathology approaches has been documented internationally. The aim of this study was to evaluate swallowing-related assessment and rehabilitation practices of SLPs currently working in Australia. One hundred and fifty-four SLPs completed an online questionnaire administered via QuickSurveys from May to July 2015.