Bayesian Spatial Binary Regression for Label Fusion in Structural Neuroimaging

Many analyses of neuroimaging data involve studying one or more regions of interest (ROIs) in a brain image. In order to do so, each ROI must first be identified. Since every brain is unique, the location, size, and shape of each ROI varies across subjects. Thus, each ROI in a brain image must either be manually identified or (semi-) automatically delineated, a task referred to as segmentation. Automatic segmentation often involves mapping a previously manually segmented image to a new brain image and propagating the labels to obtain an estimate of where each ROI is located in the new image. A more recent approach to this problem is to propagate labels from multiple manually segmented atlases and combine the results using a process known as label fusion. To date, most label fusion algorithms either employ voting procedures or impose prior structure and subsequently find the maximum a posteriori estimator (i.e., the posterior mode) through optimization. We propose using a fully Bayesian spatial regression model for label fusion that facilitates direct incorporation of covariate information while making accessible the entire posterior distribution. We discuss the implementation of our model via Markov chain Monte Carlo and illustrate the procedure through both simulation and application to segmentation of the hippocampus, an anatomical structure known to be associated with Alzheimer's disease.Comment: 24 pages, 10 figure

iqLearn: Interactive Q-Learning in R

Chronic illness treatment strategies must adapt to the evolving health status of the patient receiving treatment. Data-driven dynamic treatment regimes can offer guidance for clinicians and intervention scientists on how to treat patients over time in order to bring about the most favorable clinical outcome on average. Methods for estimating optimal dynamic treatment regimes, such as Q-learning, typically require modeling non- smooth, nonmonotone transformations of data. Thus, building well-fitting models can be challenging and in some cases may result in a poor estimate of the optimal treatment regime. Interactive Q-learning (IQ-learning) is an alternative to Q-learning that only requires modeling smooth, monotone transformations of the data. The R package iqLearn provides functions for implementing both the IQ-learning and Q-learning algorithms. We demonstrate how to estimate a two-stage optimal treatment policy with iqLearn using a generated data set bmiData which mimics a two-stage randomized body mass index reduction trial with binary treatments at each stage

Control-Group Feature Normalization for Multivariate Pattern Analysis Using the Support Vector Machine

Normalization of feature vector values is a common practice in machine learning. Generally, each feature value is standardized to the unit hypercube or by normalizing to zero mean and unit variance. Classification decisions based on support vector machines (SVMs) or by other methods are sensitive to the specific normalization used on the features. In the context of multivariate pattern analysis using neuroimaging data, standardization effectively up- and down-weights features based on their individual variability. Since the standard approach uses the entire data set to guide the normalization it utilizes the total variability of these features. This total variation is inevitably dependent on the amount of marginal separation between groups. Thus, such a normalization may attenuate the separability of the data in high dimensional space. In this work we propose an alternate approach that uses an estimate of the control-group standard deviation to normalize features before training. We also show that control-based normalization provides better interpretation with respect to the estimated multivariate disease pattern and improves the classifier performance in many cases

Addressing Confounding in Predictive Models with an Application to Neuroimaging

Understanding structural changes in the brain that are caused by a particular disease is a major goal of neuroimaging research. Multivariate pattern analysis (MVPA) comprises a collection of tools that can be used to understand complex disease effects across the brain. We discuss several important issues that must be considered when analyzing data from neuroimaging studies using MVPA. In particular, we focus on the consequences of confounding by non-imaging variables such as age and sex on the results of MVPA. After reviewing current practice to address confounding in neuroimaging studies, we propose an alternative approach based on inverse probability weighting. Although the proposed method is motivated by neuroimaging applications, it is broadly applicable to many problems in machine learning and predictive modeling. We demonstrate the advantages of our approach on simulated and real data examples

Association Between State Policies Using Medicaid Exclusions to Sanction Noncompliance With Welfare Work Requirements and Medicaid Participation Among Low-Income Adults

Twenty states have pursued community engagement requirements (ie, work requirements) as a condition for Medicaid eligibility among adults considered able-bodied. Work requirements seek to improve health by incentivizing work, but may result in coverage losses. The impact of work requirements on Medicaid coverage may extend beyond qualifying beneficiaries, by increasing confusion around benefit rules or deterring individuals from applying for coverage. However, the spillover effects of work requirements on individuals not directly subject to them are difficult to study because these programs have only recently been implemented. To examine this possibility, we studied Temporary Assistance for Needy Families (TANF), the cash welfare program enacted under welfare reform in 1996. The TANF program requires able-bodied beneficiaries to fulfill work requirements, and states can elect to terminate Medicaid benefits as a sanction for nonpregnant adult TANF participants who do not comply with them. In states adopting these sanctions, Medicaid eligibility for dual TANF-Medicaid enrollees was effectively conditional on meeting work requirements. This quasi-experimental cohort study examines whether TANF-Medicaid sanctions had spillover effects on Medicaid coverage among low-income adults who were not likely to participate in TANF and, therefore, were not directly subject to these sanctions

Translation and validation of the Norwegian version of the postoperative quality of recovery score QoR-15

Background As patient-centered care gains more attention, assessing the patient's perspective on their recovery has become increasingly important. In response to the need for a reliable and valid patient reported outcome measurement tool for major surgical resections in Norway. The Norwegian Registry for Gastrointestinal Surgery (NORGAST) initiated a project to translate and evaluate QoR-15's psychometric properties for patients going through general, gastrointestinal (GI), and hepato-pancreato-biliary (HPB) resectional surgery. Methods After a translation and adaption of the original version of QoR–15 into Norwegian, the QoR–15NO was psychometrically evaluated including a confirmatory factor analysis to test for unidimensionality, as well as tests for content validity, internal consistency, measurement error, construct validity, feasibility, and responsiveness. This process included cognitive interviews using a structured interview guide. Further, patients who underwent various types of GI/HPB surgery at five hospitals in different parts of Norway completed the QoR-15NO before surgery and on the first or second day after surgery. The impact of surgery was classified according to Surgical Outcome Risk Tool v2 (SORT), in extra major/complex, major, intermediate, and minor. Results This study included 324 patients with 83% return rate with both pre- and postoperative forms. There were negative correlations between duration of surgery and postoperative QoR-15 score and the difference between post- and preoperative score (change score). Individuals who had gone through surgery with major impact had a lower postoperative mean QoR-15 score (97) than their counterparts who had experienced either medium (QoR-15: 110) or minor (QoR15: 119) impact surgery. Cronbach's alpha (0.88) and Omega Alpha Total (ωt = 0.90) indicate that the scale has good to very good internal consistency. Test–retest reliability was measured by Intra-class Correlation Coefficient to ICC = 0.70. Confirmatory factor analyses supported that a one-factor model with correlated residuals had a good fit to data. Conclusion This study supports QoR-15NO as a valid, essentially unidimensional, feasible, and responsive instrument among patients undergoing general, GI, and HPB resectional surgery in Norway. The total QoR-15NO score provides important information that can be used in an everyday clinical setting and integrated into NORGAST

Influence of Microplastics on Microbial Structure, Function, and Mechanical Properties of Stream Periphyton

Este artículo contiene 17 páginas, 5 figuras, 4 tablas.Periphyton is a freshwater biofilm composed of prokaryotic and eukaryotic communities that occupy rocks and sediments, forming the base of the food web and playing a key role in nutrient cycling. Given the large surface that periphyton comprises, it may also act as a sink for a diverse range of man-made pollutants, including microplastics (MP). Here we investigated the effect of 1–4 μm and 63–75 µm sized, spherical polyethylene MP with native and ultraviolet (UV)-weathered surface on developing natural stream periphyton communities over 28 days. In order to ensure proper particle exposure, we first tested MP suspension in water or in water containing either Tween 80, extracellular polymeric substances – EPS, fulvic acids, or protein. We found the extract of EPS from natural periphyton to be most suitable to create MP suspensions in preparation of exposure. Upon exposure, all tested types of MP were found to be associated with the periphyton, independent of their size and other properties. While biomass accrual and phenotypic community structure of the photoautotrophs remained unchanged, the prokaryotic and eukaryotic communities experienced a significant change in composition and relative abundances. Moreover, alpha diversity was affected in eukaryotes, but not in prokaryotes. The observed changes were more prominent in periphyton exposed to UV-treated as compared with native surface MP. Mechanical properties, as assessed by compression rheology, showed that MP-exposed periphyton had longer filamentous streamers, higher stiffness, lower force recovery and a higher viscoelasticity than control periphyton. Despite the observed structural and mechanical changes of periphyton, functional parameters (i.e., photosynthetic yield, respiration and nutrient uptake efficiencies) were not altered by MP, indicating the absence of MP toxicity, and suggesting functional redundancy in the communities. Together, our results provide further proof that periphyton is a sink for MP and demonstrate that MP can impact local microbial community composition and mechanical properties of the biofilms. Consequences of these findings might be a change in dislodgement behavior of periphyton, a propagation through the food chains and impacts on nutrient cycling and energy transfer. Hence, taking the omnipresence, high persistence and material and size diversity of MP in the aquatic environment into account, their ecological consequences need further investigation.The study was financially supported by the Velux foundation, project number 1039, Switzerland. Additional lab work was funded by Tailwind grant of Eawag Switzerland. Open access funding was provided by Eawag–Swiss Federal Institute of Aquatic Science And Technology.Peer reviewe

Comparative effectiveness of less commonly used systemic monotherapies and common combination therapies for moderate to severe psoriasis in the clinical setting.

BACKGROUND: The effectiveness of psoriasis therapies in real-world settings remains relatively unknown. OBJECTIVE: We sought to compare the effectiveness of less commonly used systemic therapies and commonly used combination therapies for psoriasis. METHODS: This was a multicenter cross-sectional study of 203 patients with plaque psoriasis receiving less common systemic monotherapy (acitretin, cyclosporine, or infliximab) or common combination therapies (adalimumab, etanercept, or infliximab and methotrexate) compared with 168 patients receiving methotrexate evaluated at 1 of 10 US outpatient dermatology sites participating in the Dermatology Clinical Effectiveness Research Network. RESULTS: In adjusted analyses, patients on acitretin (relative response rate 2.01; 95% confidence interval [CI] 1.18-3.41), infliximab (relative response rate 1.93; 95% CI 1.26-2.98), adalimumab and methotrexate (relative response rate 3.04; 95% CI 2.12-4.36), etanercept and methotrexate (relative response rate 2.22; 95% CI 1.25-3.94), and infliximab and methotrexate (relative response rate 1.72; 95% CI 1.10-2.70) were more likely to have clear or almost clear skin compared with patients on methotrexate. There were no differences among treatments when response rate was defined by health-related quality of life. LIMITATIONS: Single time point assessment may result in overestimation of effectiveness. CONCLUSIONS: The efficacy of therapies in clinical trials may overestimate their effectiveness as used in clinical practice. Although physician-reported relative response rates were different among therapies, absolute differences were small and did not correspond to differences in patient-reported outcomes

Influence of Microplastics on Microbial Structure, Function, and Mechanical Properties of Stream Periphyton

Periphyton is a freshwater biofilm composed of prokaryotic and eukaryotic communities that occupy rocks and sediments, forming the base of the food web and playing a key role in nutrient cycling. Given the large surface that periphyton comprises, it may also act as a sink for a diverse range of man-made pollutants, including microplastics (MP). Here we investigated the effect of 1-4 mu m and 63-75 mu m sized, spherical polyethylene MP with native and ultraviolet (UV)-weathered surface on developing natural stream periphyton communities over 28 days. In order to ensure proper particle exposure, we first tested MP suspension in water or in water containing either Tween 80, extracellular polymeric substances - EPS, fulvic acids, or protein. We found the extract of EPS from natural periphyton to be most suitable to create MP suspensions in preparation of exposure. Upon exposure, all tested types of MP were found to be associated with the periphyton, independent of their size and other properties. While biomass accrual and phenotypic community structure of the photoautotrophs remained unchanged, the prokaryotic and eukaryotic communities experienced a significant change in composition and relative abundances. Moreover, alpha diversity was affected in eukaryotes, but not in prokaryotes. The observed changes were more prominent in periphyton exposed to UV-treated as compared with native surface MP. Mechanical properties, as assessed by compression rheology, showed that MP-exposed periphyton had longer filamentous streamers, higher stiffness, lower force recovery and a higher viscoelasticity than control periphyton. Despite the observed structural and mechanical changes of periphyton, functional parameters (i.e., photosynthetic yield, respiration and nutrient uptake efficiencies) were not altered by MP, indicating the absence of MP toxicity, and suggesting functional redundancy in the communities. Together, our results provide further proof that periphyton is a sink for MP and demonstrate that MP can impact local microbial community composition and mechanical properties of the biofilms. Consequences of these findings might be a change in dislodgement behavior of periphyton, a propagation through the food chains and impacts on nutrient cycling and energy transfer. Hence, taking the omnipresence, high persistence and material and size diversity of MP in the aquatic environment into account, their ecological consequences need further investigation