SCOUT: Signal Correction and Uncertainty Quantification Toolbox in MATLAB

This manuscript describes the software package SCOUT, which analyzes, characterizes, and corrects one-dimensional random signals. Specifically, it allows to check and correct for stationarity, detect spurious samples, check for normality, check for periodicity, filter, perform spectral analysis, determine the integral time scale, and perform uncertainty analysis on individual and on propagated signals. The novelty of SCOUT lies in combining these various methods into one compact and easy-to-use toolbox, which enables students and professionals alike to analyze, characterize, and correct for signals without expert knowledge. The program is oriented towards time traces, but an easy adaptation to spatial distributions can be performed by the user. SCOUT is available in two variants: a graphical user interface (GUI) and a script-based version

Cluster-based network modeling: From snapshots to complex dynamical systems

We propose a universal method for data-driven modeling of complex nonlinear dynamics from time-resolved snapshot data without prior knowledge. Complex nonlinear dynamics govern many fields of science and engineering. Data-driven dynamic modeling often assumes a low-dimensional subspace or manifold for the state. We liberate ourselves from this assumption by proposing cluster-based network modeling (CNM) bridging machine learning, network science, and statistical physics. CNM describes short- and long-term behavior and is fully automatable, as it does not rely on application-specific knowledge. CNM is demonstrated for the Lorenz attractor, ECG heartbeat signals, Kolmogorov flow, and a high-dimensional actuated turbulent boundary layer. Even the notoriously difficult modeling benchmark of rare events in the Kolmogorov flow is solved. This automatable universal data-driven representation of complex nonlinear dynamics complements and expands network connectivity science and promises new fast-track avenues to understand, estimate, predict, and control complex systems in all scientific fields

xROM: A Toolkit for Reduced-Order Modeling of Fluid Flows

This book initiates the new Series `Machine Learning Tools in Fluid Mechanics' published by the Technische Universität Braunschweig. The series focuses on machine learning tools for fluid mechanics tasks, like analysis, dynamic modeling, response modeling, control and closures. The tools comprise documentations of publicly available software packages, of good practices and of application studies. Our book introduces the software platform xROM, which is a freely available package for spectral analysis and reduced-order modeling. Initially, xROM was developed as a tool to quickly derive dynamic POD models from snapshot data and Galerkin projection using the Navier-Stokes equations. This purpose has since expanded, and xROM has become a platform that allows easy modular expansions and collaborations with partners worldwide. In this book, however, we focus on POD-based Galerkin modeling for reasons of simplicity

Metric for attractor overlap

We present the first general metric for attractor overlap (MAO) facilitating an unsupervised comparison of flow data sets. The starting point is two or more attractors, i.e., ensembles of states representing different operating conditions. The proposed metric generalizes the standard Hilbert-space distance between two snapshots to snapshot ensembles of two attractors. A reduced-order analysis for big data and many attractors is enabled by coarse-graining the snapshots into representative clusters with corresponding centroids and population probabilities. For a large number of attractors, MAO is augmented by proximity maps for the snapshots, the centroids, and the attractors, giving scientifically interpretable visual access to the closeness of the states. The coherent structures belonging to the overlap and disjoint states between these attractors are distilled by few representative centroids. We employ MAO for two quite different actuated flow configurations: (1) a two-dimensional wake of the fluidic pinball with vortices in a narrow frequency range and (2) three-dimensional wall turbulence with broadband frequency spectrum manipulated by spanwise traveling transversal surface waves. MAO compares and classifies these actuated flows in agreement with physical intuition. For instance, the first feature coordinate of the attractor proximity map correlates with drag for the fluidic pinball and for the turbulent boundary layer. MAO has a large spectrum of potential applications ranging from a quantitative comparison between numerical simulations and experimental particle-image velocimetry data to the analysis of simulations representing a myriad of different operating conditions.Comment: 33 pages, 20 figure

Electromagnetic navigation transthoracic needle aspiration for the diagnosis of pulmonary nodules: A safety and feasibility pilot study

BACKGROUND: Pulmonary nodules remain a diagnostic challenge for physicians. Minimally invasive biopsy methods include bronchoscopy and CT guided transthoracic needle aspiration (TTNA). A novel electromagnetic guidance transthoracic needle aspiration (ETTNA) procedure which can be combined with navigational bronchoscopy (NB) and endobronchial ultrasound (EBUS) in a single setting has become available. METHODS: A prospective pilot study examining the safety, feasibility and diagnostic yield of ETTNA in a single procedural setting. All patients enrolled underwent EBUS for lung cancer staging followed by NB and ETTNA. Feasibility of performing ETTNA and a safety assessment by recording procedural related complications including pneumothorax or bleeding was performed. Diagnostic yield of ETTNA defined by a definitive pathologic tissue diagnosis was recorded. An additional diagnostic yield analysis was performed using a cohort analysis of combined interventions (EBUS + NB + ETTNA). All non-diagnostic biopsies were either followed with radiographic imaging or a surgical biopsy was performed. RESULTS: Twenty-four subjects were enrolled. ETTNA was feasible in 96% of cases. No bleeding events occurred. There were five pneumothoraces (21%) of which only two (8%) subjects required drainage. The diagnostic yield for ETTNA alone was 83% and increased to 87% (P=0.0016) when ETTNA was combined with NB. When ETTNA and NB were performed with EBUS for complete staging, the diagnostic yield increased further to 92% (P=0.0001). CONCLUSIONS: This is the first human pilot study demonstrating an acceptable safety and feasibility profile with a novel ETTNA system. Further studies are needed to investigate the increased diagnostic yield from this pilot study

A randomized controlled trial evaluating airway inspection effectiveness during endobronchial ultrasound bronchoscopy

Endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) has revolutionized the evaluation of patients with mediastinal and hilar adenopathy. Limitations of conventional endobronchial ultrasound (C-EBUS) bronchoscopes include the inability to perform a complete airway inspection, low definition optics, and limited maneuverability. These limitations require the use of a standard bronchoscope to perform an airway examination prior to the EBUS procedure. Recently, a hybrid endobronchial ultrasound (H-EBUS) bronchoscope with high definition optics and increased maneuverability has been introduced. Our objective was to assess the ability of H-EBUS to perform a full airway inspection and TBNA

Formative Assessment of ARM-U: A Modular Intervention for Decreasing Risk Behaviors Among HIV-Positive and HIV-Negative Methamphetamine-Using MSM

BACKGROUND: Methamphetamine is a major contributor to HIV transmission among men who have sex with men (MSM). Recent studies show that up to one-third of methamphetamine-using MSM (MUMSM) inject the drug. We developed a behavioral intervention for MUMSM to decrease unprotected anal intercourse and increase awareness of parenteral HIV transmission risk. This 6-session (3 in-person, 3 by telephone) modular intervention was designed to be tailored to participants' HIV (+/-) and injection drug user ([IDU] yes/no) status. We present results of formative research used to evaluate the content and to assess feasibility and acceptability of this individual-level HIV risk-reduction intervention. SETTING: HIV research clinic in a high MSM and methamphetamine prevalence neighborhood. PROJECT: Avoiding Risks from Methamphetamine-Use (ARM-U) is a brief toolbox intervention that allows counselors to select modules that suit a client's individual risk profile and intervention needs employing motivational interviewing and cognitive behavioral theory. We evaluated the format and content of the intervention through focus groups and pre-testing of the entire intervention using volunteers from the target population stratified into four groups (HIV+/IDU, HIV-/IDU, HIV+/non-IDU, HIV-/non-IDU). Four individuals in each stratum were recruited to undergo the intervention and complete a satisfaction survey at the end of each in-person session. RESULTS: In total, 25 MUMSM attended one of five focus groups. Participants thought all proposed intervention topics were important and could aid in reducing sexual risk behaviors among MUMSM. However, the neurocognitive effects of methamphetamine were reported to be a barrier to practicing safer sex, condom use negotiation or HIV status disclosure. Fifteen (94%) of 16 participants completed all 6 sessions and the satisfaction survey. On average, participants felt the intervention was useful for MUMSM, made them contemplate and move toward behavior change, and would recommend the program to their peers. LESSONS LEARNED: Based on our formative research, we revised the ARM-U intervention to emphasize pre-planning to avoid combining methamphetamine use and sex or develop strategies to avoid sex risk following methamphetamine use. We also increased emphasis on referrals for care and other requested services. Future efficacy trials are needed to evaluate the intervention's ability to reduce HIV-associated risk behaviors