Orthogonalized Residuals for Estimation of Marginally Specified Association Parameters in Multivariate Binary Data: Orthogonalized residuals

This paper focuses on marginal regression models for correlated binary responses when estimation of the association structure is of primary interest. A new estimating function approach based on orthogonalized residuals is proposed. A special case of the proposed procedure allows a new representation of the alternating logistic regressions method through marginal residuals. The connections between second-order generalized estimating equations, alternating logistic regressions, pseudo-likelihood and other methods are explored. Eficiency comparisons are presented, with emphasis on variable cluster size and on the role of higher-order assumptions. The new method is illustrated with an analysis of data on impaired pulmonary function

Pretty Picky for a Generalist: Impacts of Toxicity and Nutritional Quality on Mantid Prey Processing

Prey have evolved a number of defenses against predation, and predators have developed means of countering these protective measures. Although caterpillars of the monarch butterfly, Danaus plexippus L., are defended by cardenolides sequestered from their host plants, the Chinese mantid Tenodera sinensis Saussure guts the caterpillar before consuming the rest of the body. We hypothesized that this gutting behavior might be driven by the heterogeneous quality of prey tissue with respect to toxicity and/or nutrients. We conducted behavioral trials in which mantids were offered cardenolide-containing and cardenolide-free D. plexippus caterpillars and butterflies. In addition, we fed mantids starved and unstarved D. plexippus caterpillars from each cardenolide treatment and nontoxic Ostrinia nubilalis Hübner caterpillars. These trials were coupled with elemental analysis of the gut and body tissues of both D. plexippus caterpillars and corn borers. Cardenolides did not affect mantid behavior: mantids gutted both cardenolide-containing and cardenolide-free caterpillars. In contrast, mantids consumed both O. nubilalis and starved D. plexippus caterpillars entirely. Danaus plexippus body tissue has a lower C:N ratio than their gut contents, while O. nubilalis have similar ratios; gutting may reflect the mantid’s ability to regulate nutrient uptake. Our results suggest that post-capture prey processing by mantids is likely driven by a sophisticated assessment of resource quality

Deletion Diagnostics for Alternating Logistic Regressions

Deletion diagnostics are introduced for the regression analysis of clustered binary outcomes estimated with alternating logistic regressions, an implementation of generalized estimating equations (GEE) that estimates regression coefficients in a marginal mean model and in a model for the intracluster association given by the log odds ratio. The diagnostics are developed within an estimating equations framework that recasts the estimating functions for association parameters based upon conditional residuals into equivalent functions based upon marginal residuals. Extensions of earlier work on GEE diagnostics follow directly, including computational formulae for one-step deletion diagnostics that measure the influence of a cluster of observations on the estimated regression parameters and on the overall marginal mean or association model fit. The diagnostic formulae are evaluated with simulations studies and with an application concerning an assessment of factors associated with health maintenance visits in primary care medical practices. The application and the simulations demonstrate that the proposed cluster-deletion diagnostics for alternating logistic regressions are good approximations of their exact fully iterated counterparts

Log-linear models for mutations in the HIV genome

We discuss a general application of categorical data analysis to mutations along the HIV genome. We consider a multidimensional table for several positions at the same time. Due to the complexity of the multidimensional table, we may collapse it by pooling some categories. However, the association between the remaining variables may not be the same as before collapsing. We discuss the collapsibility of tables and the change in the meaning of parameters after collapsing categories. We also address this problem with a log-linear model. We present a parameterization with the consensus output as the reference cell as is appropriate to explain genomic mutations in HIV. We also consider five null hypotheses and some classical methods to address them. We illustrate methods for six positions along the HIV genome, through consideration of all triples of positions

A Potential Biofilm Metabolite Signature for Caries Activity - A Pilot Clinical Study

BACKGROUND: This study's aim was to compare the dental biofilm metabolite-profile of caries-active (N=11) or caries-free (N=4) children by gas chromatography-mass spectrometry (GC/MS) analyses. METHODS: Samples collected after overnight fasting, with or without a previous glucose rinse, were combined for each child based on the caries status of the site, re-suspended in ethanol and analyzed by GC/MS. RESULTS: Biofilm from caries-active sites exhibited a different chromatographic profile compared to caries-free sites. Qualitative and quantitative analysis suggested a special cluster of branched alcohols and esters present at substantially higher intensity in biofilms of caries-active sites. CONCLUSIONS: This pilot study indicates that there are metabolites present in the biofilm which have the potential to provide a characteristic metabolomics signature for caries activity

Chronic impacts of invasive herbivores on a foundational forest species: a whole‐tree perspective

Forests make up a large portion of terrestrial plant biomass, and the long‐lived woody plants that dominate them possess an array of traits that deter consumption by forest pests. Although often extremely effective against native consumers, invasive species that avoid or overcome these defenses can wreak havoc on trees and surrounding ecosystems. This is especially true when multiple invasive species co‐occur, since interactions between invasive herbivores may yield non‐additive effects on the host. While the threat posed by invasive forest pests is well known, long‐term field experiments are necessary to explore these consumer‐host interactions at appropriate spatial and temporal scales. Moreover, it is important to measure multiple variables to get a “whole‐plant” picture of their combined impact. We report the results of a 4‐yr field experiment addressing the individual and combined impacts of two invasive herbivores, the hemlock woolly adelgid (Adelges tsugae) and elongate hemlock scale (Fiorinia externa), on native eastern hemlock (Tsuga canadensis) in southern New England. In 2011, we planted 200 hemlock saplings into a temperate forest understory and experimentally manipulated the presence/absence of both herbivore species; in 2015, we harvested the 88 remaining saplings and assessed plant physiology, growth, and resource allocation. Adelgids strongly affected hemlock growth: infested saplings had lower above/belowground biomass ratios, more needle loss, and produced fewer new needles than control saplings. Hemlock scale did not alter plant biomass allocation or growth, and its co‐occurrence did not alter the impact of adelgid. While both adelgid and scale impacted the concentrations of primary metabolites, adelgid effects were more pronounced. Adelgid feeding simultaneously increased free amino acids local to feeding sites and a ~30% reduction in starch. The cumulative impact of adelgid‐induced needle loss, manipulation of nitrogen pools, and the loss of stored resources likely accelerates host decline through disruption of homeostatic source‐sink dynamics occurring at the whole‐plant level. Our research stresses the importance of considering long‐term impacts to predict how plants will cope with contemporary pressures experienced in disturbed forests

Sample Size Considerations for GEE Analyses of Three-Level Cluster Randomized Trials

Cluster randomized trials in health care may involve three instead of two levels, for instance, in trials where different interventions to improve quality of care are compared. In such trials, the intervention is implemented in health care units (“clusters”) and aims at changing the behavior of health care professionals working in this unit (“subjects”), while the effects are measured at the patient level (“evaluations”). Within the generalized estimating equations (GEE) approach, we derive a sample size formula that accounts for two levels of clustering: that of subjects within clusters and that of evaluations within subjects. The formula reveals that sample size is inflated, relative to a design with completely independent evaluations, by a multiplicative term that can be expressed as a product of two variance inflation factors, one that quantifies the impact of within-subject correlation of evaluations on the variance of subject-level means and the other that quantifies the impact of the correlation between subject level means on the variance of the cluster means. Power levels as predicted by the sample size formula agreed well with the simulated power for more than 10 clusters in total, when data was analyzed using bias-corrected estimating equations for the correlation parameters in combination with the model-based covariance estimator or the sandwich estimator with a finite sample correction

Magnetosheath jet occurrence rate in relation to CMEs and SIRs

Magnetosheath jets constitute a significant coupling effect between the solar wind (SW) and the magnetosphere of the Earth. In order to investigate the effects and forecasting of these jets, we present the first-ever statistical study of the jet production during large-scale SW structures like coronal mass ejections (CMEs), stream interaction regions (SIRs) and high speed streams (HSSs). Magnetosheath data from Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft between January 2008 and December 2020 serve as measurement source for jet detection. Two different jet definitions were used to rule out statistical biases induced by our jet detection method. For the CME and SIR + HSS lists, we used lists provided by literature and expanded on incomplete lists using OMNI data to cover the time range of May 1996 to December 2020. We find that the number and total time of observed jets decrease when CME-sheaths hit the Earth. The number of jets is lower throughout the passing of the CME-magnetic ejecta (ME) and recovers quickly afterward. On the other hand, the number of jets increases during SIR and HSS phases. We discuss a few possibilities to explain these statistical results

Limitations of selective deltamethrin application for triatomine control in central coastal Ecuador

<p>Abstract</p> <p>Background</p> <p>This year-long study evaluated the effectiveness of a strategy involving selective deltamethrin spraying and community education for control of Chagas disease vectors in domestic units located in rural communities of coastal Ecuador.</p> <p>Results</p> <p>Surveys for triatomines revealed peridomestic infestation with <it>Rhodnius ecuadoriensis </it>and <it>Panstrongylus howardi</it>, with infestation indices remaining high during the study (13%, 17%, and 10%, at initial, 6-month, and 12-month visits, respectively), which indicates a limitation of this strategy for triatomine population control. Infestation was found 6 and 12 months after spraying with deltamethrin. In addition, a large number of previously vector-free domestic units also were found infested at the 6- and 12-month surveys, which indicates new infestations by sylvatic triatomines. The predominance of young nymphs and adults suggests new infestation events, likely from sylvatic foci. In addition, infection with <it>Trypanosoma cruzi </it>was found in 65%, 21% and 29% at initial, 6-month and 12-month visits, respectively. All parasites isolated (n = 20) were identified as TcI.</p> <p>Conclusion</p> <p>New vector control strategies need to be devised and evaluated for reduction of <it>T. cruzi </it>transmission in this region.</p

Comparison of perioperative outcomes between open and robotic radical cystectomy: a population based analysis

Introduction: Radical cystectomy represents the standard of care for muscle-invasive bladder cancer (MIBC). Due to its novelty the use of robotic radical cystectomy (RARC) is still under debate. We examined intraoperative and postoperative morbidity and mortality in addition to impact on length of stay (LOS) and total hospital charges (THCGs) of RARC compared with open radical cystectomy (ORC). Materials and Methods: Within National Inpatient Sample (2008-2013), we identified patients with nonmetastatic bladder cancer treated with either ORC or RARC. We relied on inverse probability of treatment weighting to reduce the effect of inherent differences between ORC vs RARC. Multivariable logistic regression (MLR) and multivariable Poisson regression (MPR) models were used. Results: Of all 10,027 patients, 12.6% underwent RARC. Between 2008 and 2013, RARC rates increased from 0.8% to 20.4% [estimated annual percentage change (EAPC): +26.5%, 95% confidence interval (CI): +11.1 to +48.3; p=0.035] and RARC THCGs decreased from 45,981 to 31,749 United States dollars (EAPC: -6.8%, 95% CI: -9.6 to -3.9; p=0.01). In MLR models RARC resulted in lower rates of overall complications [odds ratio (OR): 0.6; p&lt;0.001] and transfusions (OR: 0.44; p&lt;0.001). In MPR models, RARC was associated with shorter LOS (relative risk 0.91; p&lt;0.001). Finally, higher THCGs (OR: 1.09; p&lt;0.001) were recorded for RARC. Data are retrospective and no tumor characteristics were available. Conclusion: RARC is related to lower rates of overall complications and transfusions rates. In consequence, RARC is a safe and feasible technique in select MIBC patients. Moreover, RARC is associated with shorter LOS, although higher THCGs