Robust and Flexible Estimation of Stochastic Mediation Effects: A Proposed Method and Example in a Randomized Trial Setting

Causal mediation analysis can improve understanding of the mechanisms underlying epidemiologic associations. However, the utility of natural direct and indirect effect estimation has been limited by the assumption of no confounder of the mediator-outcome relationship that is affected by prior exposure---an assumption frequently violated in practice. We build on recent work that identified alternative estimands that do not require this assumption and propose a flexible and double robust semiparametric targeted minimum loss-based estimator for data-dependent stochastic direct and indirect effects. The proposed method treats the intermediate confounder affected by prior exposure as a time-varying confounder and intervenes stochastically on the mediator using a distribution which conditions on baseline covariates and marginalizes over the intermediate confounder. In addition, we assume the stochastic intervention is given, conditional on observed data, which results in a simpler estimator and weaker identification assumptions. We demonstrate the estimator's finite sample and robustness properties in a simple simulation study. We apply the method to an example from the Moving to Opportunity experiment. In this application, randomization to receive a housing voucher is the treatment/instrument that influenced moving to a low-poverty neighborhood, which is the intermediate confounder. We estimate the data-dependent stochastic direct effect of randomization to the voucher group on adolescent marijuana use not mediated by change in school district and the stochastic indirect effect mediated by change in school district. We find no evidence of mediation. Our estimator is easy to implement in standard statistical software, and we provide annotated R code to further lower implementation barriers.Comment: 24 pages, 2 tables, 2 figure

How to observe a coherent superposition of an atom and a molecule

We demonstrate that it is possible, in principle, to perform a Ramsey-type interference experiment to exhibit a coherent superposition of a single atom and a diatomic molecule. This gedanken experiment, based on the techniques of Aharonov and Susskind [Phys. Rev. 155, 1428 (1967)], explicitly violates the commonly-accepted superselection rule that forbids coherent superpositions of eigenstates of differing atom number. This interference experiment makes use of a Bose-Einstein condensate as a reference frame with which to perform the coherent operations analogous to Ramsey pulses. We also investigate an analogous gedanken experiment to exhibit a coherent superposition of a single boson and a fermion, violating the commonly-accepted superselection rule forbidding coherent superpositions of states of differing particle statistics; in this case, the reference frame is realized by a multi-mode state of many fermions. This latter case reproduces all of the relevant features of Ramsey interferometry, including Ramsey fringes over many repetitions of the experiment. However, the apparent inability of this proposed experiment to produce well-defined relative phases between two distinct systems each described by a coherent superposition of a boson and a fermion demonstrates that there are additional, outstanding requirements to fully ``lift'' the univalence superselection rule.Comment: 17 pages, 1 figure, comments welcome, published version (minor changes

The Alzheimer's Disease-Associated Amyloid β-Protein Is an Antimicrobial Peptide

Background: The amyloid $\beta$-protein (A$\beta$) is believed to be the key mediator of Alzheimer's disease (AD) pathology. A$\beta$ is most often characterized as an incidental catabolic byproduct that lacks a normal physiological role. However, A$\beta$ has been shown to be a specific ligand for a number of different receptors and other molecules, transported by complex trafficking pathways, modulated in response to a variety of environmental stressors, and able to induce pro-inflammatory activities. Methodology/Principal Findings: Here, we provide data supporting an in vivo function for A$\beta$ as an antimicrobial peptide (AMP). Experiments used established in vitro assays to compare antimicrobial activities of A$\beta$ and LL-37, an archetypical human AMP. Findings reveal that A$\beta$ exerts antimicrobial activity against eight common and clinically relevant microorganisms with a potency equivalent to, and in some cases greater than, LL-37. Furthermore, we show that AD whole brain homogenates have significantly higher antimicrobial activity than aged matched non-AD samples and that AMP action correlates with tissue A$\beta$ levels. Consistent with A$\beta$-mediated activity, the increased antimicrobial action was ablated by immunodepletion of AD brain homogenates with anti-A$\beta$ antibodies. Conclusions/Significance: Our findings suggest A$\beta$ is a hitherto unrecognized AMP that may normally function in the innate immune system. This finding stands in stark contrast to current models of A$\beta$-mediated pathology and has important implications for ongoing and future AD treatment strategies

Alterations in vascular function in primary aldosteronism - a cardiovascular magnetic resonance imaging study

Introduction: Excess aldosterone is associated with increased cardiovascular risk. Aldosterone has a permissive effect on vascular fibrosis. Cardiovascular magnetic resonance imaging (CMR) allows study of vascular function by measuring aortic distensibility. We compared aortic distensibility in primary aldosteronism (PA), essential hypertension (EH) and normal controls and explored the relationship between aortic distensibility and pulse wave velocity (PWV).<p></p> Methods: We studied PA (n=14) and EH (n=33) subjects and age-matched healthy controls (n=17) with CMR, including measurement of aortic distensibility, and measured PWV using applanation tonometry. At recruitment, PA and EH patients had similar blood pressure and left ventricular mass.<p></p> Results: Subjects with PA had significantly lower aortic distensibilty and higher PWV compared to EH and healthy controls. These changes were independent of other factors associated with reduced aortic distensibility, including aging. There was a significant relationship between increasing aortic stiffness and age in keeping with physical and vascular aging. As expected, aortic distensibility and PWV were closely correlated.<p></p> Conclusion: These results demonstrate that PA patients display increased arterial stiffness compared to EH, independent of vascular aging. The implication is that aldosterone invokes functional impairment of arterial function. The long-term implications of arterial stiffening in aldosterone excess require further study.<p></p&gt

Age-Associated Heterogeneity of Ty21a-Induced T Cell Responses to HLA-E Restricted Salmonella Typhi Antigen Presentation

Human-restricted Salmonella enterica serovar Typhi (S. Typhi) is the causative agent of typhoid fever—a life-threatening disease of great global health significance, particularly in the developing world. Ty21a is an oral live-attenuated vaccine that protects against the development of typhoid disease in part by inducing robust T cell responses, among which multifunctional CD8+ cytotoxic T lymphocytes (CTL) play an important role. Following Ty21a vaccination, a significant component of adult CTL have shown to be targeted to S. Typhi antigen presented by the conserved major histocompatibility complex (MHC) class Ib molecule, human leukocyte antigen-E (HLA-E). S. Typhi challenge studies have shown that baseline, multifunctional HLA-E responsive T cells are associated with protection from, and delayed onset of, typhoid disease. However, despite the overwhelming burden of typhoid fever in school-aged children, and due to limited availability of pediatric samples, incomplete information is available regarding these important HLA-E-restricted responses in children, even though studies have shown that younger children may be less likely to develop protective cell mediated immune (CMI) responses than adults following vaccination. To address this gap, we have studied this phenomenon in depth by using mass cytometry to analyze pediatric and adult T cell responses to HLA-E-restricted S. Typhi antigen presentation, before and after Ty21a vaccination. Herein, we show variable responses in all age strata following vaccination among T effector memory (TEM) and T effector memory CD45RA+ (TEMRA) cells based on conventional gating analysis. However, by utilizing the dimensionality reduction tool tSNE (t-distributed Stochastic Neighbor Embedding), we are able to identify diverse, highly multifunctional gut-homing- TEM and TEMRA clusters of cells which are more abundant in adult and older pediatric participants than in younger children. These findings highlight a potential age-associated maturation of otherwise conserved HLA-E restricted T cell responses. Such insights, coupled with the marked importance of multifunctional T cell responses to combat infection, may better inform future pediatric vaccination strategies against S. Typhi and other infectious diseases

Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth

Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full-term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate two opposing CMV-associated effects on infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full-term infant development

Antibiotic-induced perturbations in gut microbial diversity influences neuro-inflammation and amyloidosis in a murine model of Alzheimer’s disease

Severe amyloidosis and plaque-localized neuro-inflammation are key pathological features of Alzheimer’s disease (AD). In addition to astrocyte and microglial reactivity, emerging evidence suggests a role of gut microbiota in regulating innate immunity and influencing brain function. Here, we examine the role of the host microbiome in regulating amyloidosis in the APP(SWE)/PS1(ΔE9) mouse model of AD. We show that prolonged shifts in gut microbial composition and diversity induced by long-term broad-spectrum combinatorial antibiotic treatment regime decreases Aβ plaque deposition. We also show that levels of soluble Aβ are elevated and that levels of circulating cytokine and chemokine signatures are altered in this setting. Finally, we observe attenuated plaque-localised glial reactivity in these mice and significantly altered microglial morphology. These findings suggest the gut microbiota community diversity can regulate host innate immunity mechanisms that impact Aβ amyloidosis