[Quantitative Assessment of the Impact of Climate Change on the Growing Season of Vegetation Gross Primary Productivity in the Middle and Lower Reaches of the Yangtze River]

Quantitatively determining the direct, indirect, and comprehensive effects of climatic factors on the growing season of the vegetation GPP (GPPGS) in the middle and lower reaches of the Yangtze River at the regional and vegetation type scales can provide a scientific basis for the management and restoration of regional vegetation resources under the background of global climate change. Using MODIS GPP data, meteorological data, and vegetation type data, combined with Theil-Sen Median trend analysis and the Mann-Kendall significance test, the spatiotemporal characteristics of the GPPGS in the middle and lower reaches of the Yangtze River were investigated at different temporal and spatial scales. Path analysis was used to further reveal the direct, indirect, and comprehensive effects of climate factors on GPPGS variation in different vegetation types. The results showed that:① from 2000 to 2021, the vegetation GPPGS in the middle and lower reaches of the Yangtze River showed a fluctuating upward trend, with a rising rate (in terms of C, same below) of 2.70 g·(m2·a)-1 (P<0.01). The GPPGS of different vegetation types all showed a significant upward trend (P<0.01), with shrubs having the highest upward rate of 3.31 g·(m2·a)-1 and cultivated vegetation having the lowest upward rate of 2.54 g·(m2·a)-1. ② The proportion of the area with an upward trend in GPPGS in the middle and lower reaches of the Yangtze River was 88.11%. The proportion of the area with an upward trend in GPPGS was greater than 84% for all different vegetation types, with shrubs (49.76%) and cultivated vegetation (44.36%) having significantly higher proportions of the area with an upward trend than that in other vegetation types. ③ The path analysis results showed that precipitation and the maximum temperature had a significant positive direct effect on vegetation GPPGS (P<0.05), whereas solar radiation had a non-significant positive effect (P ≥ 0.05). The indirect effects of maximum temperature, precipitation, and solar radiation on vegetation GPPGS were all non-significantly negative (P ≥ 0.05). Under the combined effects of direct and indirect influences, precipitation and maximum temperature had a non-significant positive effect on vegetation GPPGS (P ≥ 0.05), whereas solar radiation had a non-significant negative effect on vegetation GPPGS (P ≥ 0.05). Among different vegetation types, precipitation was the main climate factor affecting the changes in GPPGS of cultivated vegetation, whereas the maximum temperature was the main climate factor affecting the changes in GPPGS of coniferous forests, broad-leaved forests, shrubs, and grasslands. ④ The changes in vegetation GPPGS in the middle and lower reaches of the Yangtze River were mainly influenced by the direct effects of maximum temperature, precipitation, and solar radiation, with the direct effect of precipitation dominating 56.72% of the changes in GPPGS. The research results can provide a reference for quantifying the carbon sequestration potential of vegetation in the middle and lower reaches of the Yangtze River and formulating ecological restoration governance policies tailored to local conditions under the background of global climate change.

Identification of RNA-binding proteins' direct effects on gene expression via the degradation tag system

RNA-binding proteins (RBPs) are critical regulators of gene expression. An RBP typically binds to multiple mRNAs and modulates their expression. Although loss-of-function experiments on an RBP can infer how it regulates a specific target mRNA, the results are confounded by potential secondary effects due to the attenuation of all other interactions of the target RBP. For example, regarding the interaction between Trim71, an evolutionarily conserved RBP, and Ago2 mRNA, although Trim71 binds to Ago2 mRNA and overexpression of Trim71 represses Ago2 mRNA translation, it is puzzling that AGO2 protein levels are not altered in the Trim71 knockdown/knockout cells. To address this, we adapted the dTAG (degradation tag) system for determining the direct effects of the endogenous Trim71. Specifically, we knocked in the dTAG to the Trim71 locus, enabling inducible rapid Trim71 protein degradation. We observed that following the induction of Trim71 degradation, Ago2 protein levels first increased, confirming the Trim71-mediated repression, and then returned to the original levels after 24 h post-induction, revealing that the secondary effects from the Trim71 knockdown/knockout counteracted its direct effects on Ago2 mRNA. These results highlight a caveat in interpreting the results from loss-of-function studies on RBPs and provide a method to determine the primary effect(s) of RBPs on their target mRNAs.

Effect Measure Modification by Covariates in Mediation: Extending Regression-based Causal Mediation Analysis

Existing methods for regression-based mediation analysis assume that the exposure-mediator effect, exposure-outcome effect, and mediator-outcome effect are constant across levels of the baseline characteristics of patients. However, investigators often have insight into how these underlying effects may be modified by baseline characteristics and are interested in how the resulting mediation effects, such as the natural direct effect (NDE), the natural indirect effect. (NIE), and the proportion mediated, are modified by these baseline characteristics. Motivated by an empirical example of anti-interleukin-1 therapy's benefit on incident anemia reduction and its mediation by an early change in an inflammatory biomarker, we extended the closed-form regression-based causal mediation analysis with effect measure modification (EMM). Using a simulated numerical example, we demonstrated that naive analysis without considering EMM can give biased estimates of NDE and NIE and visually illustrated how baseline characteristics affect the presence and magnitude of EMM of NDE and NIE. We then applied the extended method to the empirical example informed by pathophysiologic insights into potential EMM by age, diabetes, and baseline inflammation. We found that the proportion modified through the early post-treatment inflammatory biomarker was greater for younger, nondiabetic patients with lower baseline level of inflammation, suggesting differential usefulness of the early post-treatment inflammatory biomarker in monitoring patients depending on baseline characteristics. To facilitate the adoption of EMM considerations in causal mediation analysis by the wider clinical and epidemiologic research communities, we developed a free- and open-source R package, regmedint.

Examining the Relationships Among Treatment, Pain, and Physical Function in Patients With Osteoarthritis: A Mediation-Modeling Approach

OBJECTIVES

To better understand the relationships among treatment, pain, and physical function (PF).

METHODS

Data were collected from 2 published randomized clinical trials of osteoarthritis patients who received tanezumab or a placebo. PF was measured by the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) PF domain. Pain (WOMAC pain domain) was a mediator of the effect of treatment on PF. A set of mediation models were investigated. Variables were treatment (tanezumab vs placebo), WOMAC pain domain, and WOMAC PF domain. Cross-sectional mediation models were assessed separately at different weeks. Longitudinal mediation models used data from all weeks simultaneously. Results could identify a steady-state period.

RESULTS

The cross-sectional and longitudinal mediation models showed a stable indirect effect of treatment through the pain on PF across time, indicating that a pseudo-steady-state model was appropriate. Therefore, the longitudinal steady-state mediation models were used with all available data assuming relationships among variables in the model being the same at all time points; results showed that the indirect effect of the treatment on PF was 77.8% in study 1 (NCT02697773) and 74.1% in study 2 (NCT02709486), both P <0.0001, whereas the direct effect was 22.2% for study 1 ( P = 0.0003) and 25.9% for study 2 ( P = 0.0019).

DISCUSSION

At least 75% of the treatment effect of tanezumab on physical functioning can be explained by the improvements in pain. However, tanezumab had an additional effect on physical functioning (~25%) that, was independent of improvements in pain. Such independent effects are of considerable interest and require further research to determine their mechanisms.

Comparison of Inhibitory Effects of Cinnamic Acid, β-Cyclodextrin, L-Cysteine, and Ascorbic Acid on Soluble and Membrane-Bound Polyphenol Oxidase in Peach Fruit

There has been considerable interest in controlling polyphenol oxidase (PPO) activity to prevent enzymatic browning in foods. However, studies on inhibitions of different forms of PPO are very limited. Thus, this study focuses on the effects of cinnamic acid, β-cyclodextrin, L-cysteine, and ascorbic acid on soluble PPO (sPPO) and membrane-bound PPO (mPPO) in peach fruit. The activity of partially purified sPPO was 3.17 times higher than that of mPPO. However, mPPO was shown to be more stable than sPPO in the presence of inhibitors with different concentrations (i.e., 1, 3, 5 mM); activation of mPPO was found by 5 mM L-cysteine. Both sPPO and mPPO inhibitions were PPO substrate-dependent. Ascorbic acid showed the highest inhibitory effect on both sPPO and mPPO with all studied inhibitors and substrates. The inhibition of 1 mM ascorbic acid on sPPO and mPPO reached 95.42 ± 0.07% and 65.60 ± 1.16%, respectively. β-Cyclodextrin had a direct inhibitory effect only on sPPO, while the other three inhibitors had direct effects on both sPPO and mPPO. Cinnamic acid exhibited a non-competitive inhibition on sPPO and mPPO, with L-cysteine showing the same, though on sPPO. The inhibition of studied inhibitors on sPPO and mPPO is highly related to the substrate environment, type, and concentration of inhibitors. This study provides a basis for the further prevention of peach fruit browning from the perspective of different enzyme forms.

SGLT2 inhibitors protect cardiomyocytes from myocardial infarction: a direct mechanism?

SGLT2 inhibitors have been developed as a novel class of glucose-lowering drugs affecting reabsorption of glucose and metabolic processes. They have been recently identified to be remarkably favorable in treating cardiovascular diseases, especially heart failure. Preclinical experiments have shown that SGLT2 inhibitors could hinder the progression of myocardial infarction and alleviate cardiac remodeling by mechanisms of metabolism influence, autophagy induction, inflammation attenuation and fibrosis reduction. Here we summarize the direct mechanism of SGLT2 inhibitors on myocardial infarction and investigate whether it could be applied to the clinic in improving cardiac function and healing after myocardial infarction.

Realizing the Improvement of Green Total Factor Productivity of the Marine Economy-New Evidence from China's Coastal Areas

Paying attention to the mechanisms of the GTFP of the marine economy and designing a scientific and reasonable optimization path are the keys to achieving a "win-win" balance between environmental protection and high-quality marine development. Therefore, this paper considers the rigid constraints of resources and negative environmental effects to construct a multi-factor evaluation model of the GTFP of the marine economy including capital, labor, and resources to expand the evaluation method system for the sustainable development of the marine economy. On this basis, this paper determines the influencing factors of the GTFP of China's marine economy, qualitatively analyzes the mechanism of each influencing factor on the GTFP of the marine economy, uses multi-dimensional data of coastal areas, quantitatively analyzes the direct and indirect effects of the factors that influence the GTFP, and proposes practical optimization paths and safeguarding measures, which provide a decision-making reference for the implementation of China's marine development strategy. The results showed that the GTFP of China's marine economy was in a state of improvement and increased from 0.9878 in 2006 to 1.2789 in 2018. The direct effects of environmental regulations have a negative and significant impact on GTFP, whereas economic development, human capital, and technological innovations have a positive and significant impact on GTFP. In addition, environmental regulations have an "inclined N" double-threshold effect on GTFP. The impact of environmental regulations on the GTFP of the marine economy depends on the intensity of the environmental regulations, as different intensities of environmental regulations have different dominant levels of the "innovation compensation effect" and "offset effect" that affect the GTFP of the marine economy.

Confounding, Mediation, or Independent Effect? Childhood Psychological Abuse, Mental Health, Mood/Psychological State, COPD, and Migraine

In some settings, it may be difficult to differentiate between a confounder and a mediator. For instance, the observed association of self-reported childhood psychological abuse (CPA) with onset of chronic obstructive pulmonary disease (COPD) and migraine may be confounded by current mood/psychological state (e.g., the subjective evaluation of one's own affective state), as well as mediated by an individual's psychopathological symptoms. In this study, we propose the "independence hypothesis," which could prove meaningful to explore in data that lack prospective or objective indices of CPA. We used cross-sectional data from wave VI (2007-2008) of the Tromsø Study, Norway (N = 12,981). The associations between CPA and COPD and migraine were assessed with Poisson regression models. CPA was associated with a 46% increased risk of COPD (relative risk [RR] = 1.46, 95% confidence interval [CI]: [1.02, 1.90]) and a 28% increased risk of migraine in adulthood (RR = 1.28, 95% CI: [1.04, 1.53]), independent of age, sex, parental history of psychiatric problems/asthma/dementia, smoking, respondent's mood/psychological state, and mental health. These findings suggest that the association between retrospectively reported CPA and COPD and migraine is not driven entirely by respondent's mood/psychological state and mental health. Assessing the independent effect of self-reported CPA on COPD and migraine in retrospective studies may prove more meaningful than exploring the mediating role of mental health. Here, we provide the analytical rationale for assessing the independent effect in settings where it is difficult to differentiate between a confounder and a mediator. Moreover, we provide a theoretical rationale for assessing the independent effect of retrospectively reported childhood adversity on health and well-being.

Elemental diet directly affects chemotherapy-induced dermatitis and raw wound areas

Elental^® is an L-glutamine-rich elemental diet (ED) that has been widely used in Japan as a nutritional supplement for malnourished patients. In addition, Elental^® has been successfully used in the management of chemotherapy-induced mucositis in cancer patients. Recently, it was also reported that Elental^® can effectively reduce chemotherapy-induced oral mucositis in patients with oral squamous cell carcinoma, and can also reduce mucositis and dermatitis in animal models. However, it is unclear whether oral intake or topical application of Elental^® can act directly on chemotherapy-induced oral mucositis or dermatitis. The aim of the present study was to investigate the possible direct healing effect of Elental^® on chemotherapy-induced dermatitis and raw wound areas in a mouse model. Dermatitis and raw wounds were induced in nude mice by administration of 5-fluorouracil (5-FU) (via gastric tube) and mechanical injury (using a metal brush or a surgical knife). We then compared the outcome following oral or topical application of Elental^® in these mice. The effect of Elental^® on the growth and migration ability of the human oral keratinocyte cell line, HOK, was also examined using MTT and migration assays, respectively. In the mouse model, both oral administration and topical application of Elental^® reduced 5-FU-induced dermatitis and healed raw wound areas more effectively compared with the topical application of saline. The MTT assay revealed that Elental^® exerted a growth-promoting effect on HOKs. In addition, Elental^® enhanced the ability of HOKs to migrate, as demonstrated by the migration assay. These findings demonstrated that the topical application as well as the oral intake of Elental^® exerted a direct healing effect on chemotherapy-induced dermatitis or raw wound areas. The data also indicated that oral intake of an ED may exert a direct healing effect on chemotherapy-induced oral mucositis.

Antimicrobial and Immunomodulatory Effect of Gum Arabic on Human and Bovine Granulocytes Against Staphylococcus aureus and Escherichia coli

Gum arabic (GA) is a traditional herbal medicine from Acacia Senegal (L.) Willdenow trees, which consist of a complex mixture of polysaccharides and glycoproteins. It is used in daily applications for several diseases and is considered to protect against bacterial infections. The detailed mechanisms behind these observations are still unclear. In this study, we investigated the direct antibacterial activity of GA water and ethanol extracts against Staphylococcus (S.) aureus or Escherichia (E.) coli and the immunomodulating properties of those extracts on granulocytes as a first line of defense against bacteria. Firstly, the direct antimicrobial effect of GA was tested on three different S. aureus strains and two E. coli strains. The growth of bacteria was analyzed in the presence of different GA concentrations over time. GA water as well as ethanol extracts showed a significant growth inhibition in a concentration-dependent manner in the case of S. aureus Newman, S. aureus Rd5, and E. coli 25922, but not in the case of S. aureus USA300 and E. coli K1. Transmission electron microscopic analysis confirmed an antibacterial effect of GA on the bacteria. Secondly, the immunomodulatory effect of GA on the antimicrobial activity of bovine or human blood-derived granulocytes was evaluated. Interestingly, water and ethanol extracts enhanced antimicrobial activity of granulocytes by the induction of intracellular ROS production. In line with these data, GA increased the phagocytosis rate of E. coli. No effect was seen on neutrophil extracellular trap (NET) formation that mediates killing of extracellular bacteria such as S. aureus. In conclusion, we show that GA exhibits a direct antibacterial effect against some S. aureus and E. coli strains. Furthermore, GA boosts the antimicrobial activities of granulocytes and increases intracellular ROS production, which may lead to more phagocytosis and intracellular killing. These data might explain the described putative antimicrobial activity of GA used in traditional medicine.

Exploring the Impact of the Rational Antibiotic Use System on Hospital Performance: The Direct Effect and the Spillover Effect

Irrational antibiotic usage not only causes an increase in antibiotic-borne diseases, but also inflicts pain on patients, as a result of inappropriate treatment. In order to resolve the hazards caused by irrational antibiotic usage, a kind of e-health service, the Rational Antibiotic Use System (RAUS), has been incorporated into the hospital information system. The RAUS provides doctors and patients with the functions of antibiotic usage monitoring, antibiotic information consultation and antibiotic prescription support. Though existing literature has already proved the usefulness of the RAUS on monitoring doctors’ behavior, the effects on hospital performance from an organizational perspective has rarely been measured by empirical data. Therefore, our study has explored the effects of the RAUS on the performance of a large Chinese hospital, which has implemented the RAUS since March 2014. Through empirical research, we quantified the effects of the implementation of the RAUS on a hospital’s performance from both the direct effects on the “drug income” and the spillover effect on the “treatment income”. The results indicate a significant positive spillover effect on the treatment incomes of a hospital in its inpatient activities (seen as significant in the long term) and in its outpatient activities (seen as significant in both the short and long terms). In addition, this research provides certain theoretical and practical implications for the dilemma of e-health services application in irrational antibiotic usage.

Direct or Spillover Effect: The Impact of Pure Technical and Scale Efficiencies of Water Use on Water Scarcity in China

The spatial relationship between water use efficiency and water scarcity has been widely discussed, but little attention has been paid to the impact of the pure technical and scale efficiencies of water use on water scarcity. Using input-oriented data envelopment analysis (DEA) and panel spatial Durbin models (SDM), the direct and spillover effects of different water use efficiencies on water scarcity from 2007 to 2016 in China were examined at the regional scale. The results show that the water use pure technical efficiency had significantly negative direct effects on water scarcity; however, the water use scale efficiency did not have a similar effect. The improvement in water use pure technical efficiency in one region could aggravate the water scarcity in neighboring regions through spatial spillover effects, but the same effect was not observed between the water use scale efficiency and water scarcity. Finally, we propose solutions to improve the water use efficiency to reduce the water scarcity.

MODIMA, a Method for Multivariate Omnibus Distance Mediation Analysis, Allows for Integration of Multivariate Exposure-Mediator-Response Relationships

Many important exposure-response relationships, such as diet and weight, can be influenced by intermediates, such as the gut microbiome. Understanding the role of these intermediates, the mediators, is important in refining cause-effect theories and discovering additional medical interventions (e.g., probiotics, prebiotics). Mediation analysis has been at the heart of behavioral health research, rapidly gaining popularity with the biomedical sciences in the last decade. A specific analytic challenge is being able to incorporate an entire 'omics assay as a mediator. To address this challenge, we propose a hypothesis testing framework for multivariate omnibus distance mediation analysis (MODIMA). We use the power of energy statistics, such as partial distance correlation, to allow for analysis of multivariate exposure-mediator-response triples. Our simulation results demonstrate the favorable statistical properties of our approach relative to the available alternatives. Finally, we demonstrate the application of the proposed methods in two previously published microbiome datasets. Our framework adds a new tool to the toolbox of approaches to the integration of 'omics big data.

High dimensional mediation analysis with latent variables

We propose a model for high dimensional mediation analysis that includes latent variables. We describe our model in the context of an epidemiologic study for incident breast cancer with one exposure and a large number of biomarkers (i.e., potential mediators). We assume that the exposure directly influences a group of latent, or unmeasured, factors which are associated with both the outcome and a subset of the biomarkers. The biomarkers associated with the latent factors linking the exposure to the outcome are considered "mediators." We derive the likelihood for this model and develop an expectation-maximization algorithm to maximize an L1-penalized version of this likelihood to limit the number of factors and associated biomarkers. We show that the resulting estimates are consistent and that the estimates of the nonzero parameters have an asymptotically normal distribution. In simulations, procedures based on this new model can have significantly higher power for detecting the mediating biomarkers compared with the simpler approaches. We apply our method to a study that evaluates the relationship between body mass index, 481 metabolic measurements, and estrogen-receptor positive breast cancer.

Diagnostics for Pleiotropy in Mendelian Randomization Studies: Global and Individual Tests for Direct Effects

Diagnosing pleiotropy is critical for assessing the validity of Mendelian randomization (MR) analyses. The popular MR-Egger method evaluates whether there is evidence of bias-generating pleiotropy among a set of candidate genetic instrumental variables. In this article, we propose a statistical method-global and individual tests for direct effects (GLIDE)-for systematically evaluating pleiotropy among the set of genetic variants (e.g., single nucleotide polymorphisms (SNPs)) used for MR. As a global test, simulation experiments suggest that GLIDE is nearly uniformly more powerful than the MR-Egger method. As a sensitivity analysis, GLIDE is capable of detecting outliers in individual variant-level pleiotropy, in order to obtain a refined set of genetic instrumental variables. We used GLIDE to analyze both body mass index and height for associations with colorectal cancer risk in data from the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry (multiple studies). Among the body mass index-associated SNPs and the height-associated SNPs, several individual variants showed evidence of pleiotropy. Removal of these potentially pleiotropic SNPs resulted in attenuation of respective estimates of the causal effects. In summary, the proposed GLIDE method is useful for sensitivity analyses and improves the validity of MR.

Vegetation growth enhancement in urban environments of the Conterminous United States

Cities are natural laboratories for studying vegetation responses to global environmental changes because of their climate, atmospheric, and biogeochemical conditions. However, few holistic studies have been conducted on the impact of urbanization on vegetation growth. We decomposed the overall impacts of urbanization on vegetation growth into direct (replacement of original land surfaces by impervious built-up) and indirect (urban environments) components, using a conceptual framework and remotely sensed data for 377 metropolitan statistical areas (MSAs) in the conterminous United States (CONUS) in 2001, 2006, and 2011. Results showed that urban pixels are often greener than expected given the amount of paved surface they contain. The vegetation growth enhancement due to indirect effects occurred in 88.4%, 90.8%, and 92.9% of urban bins in 2001, 2006, and 2011, respectively. By defining offset value as the ratio of the absolute indirect and direct impact, we obtained that growth enhancement due to indirect effects compensated for about 29.2%, 29.5%, and 31.0% of the reduced productivity due to loss of vegetated surface area on average in 2001, 2006, and 2011, respectively. Vegetation growth responses to urbanization showed little temporal variation but large regional differences with higher offset value in the western CONUS than in the eastern CONUS. Our study highlights the prevalence of vegetation growth enhancement in urban environments and the necessity of differentiating various impacts of urbanization on vegetation growth, and calls for tailored field experiments to understand the relative contributions of various driving forces to vegetation growth and predict vegetation responses to future global change using cities as harbingers.

Understanding Power Anomalies in Mediation Analysis

Previous studies have found some puzzling power anomalies related to testing the indirect effect of a mediator. The power for the indirect effect stagnates and even declines as the size of the indirect effect increases. Furthermore, the power for the indirect effect can be much higher than the power for the total effect in a model where there is no direct effect and therefore the indirect effect is of the same magnitude as the total effect. In the presence of direct effect, the power for the indirect effect is often much higher than the power for the direct effect even when these two effects are of the same magnitude. In this study, the limiting distributions of related statistics and their non-centralities are derived. Computer simulations are conducted to demonstrate their validity. These theoretical results are used to explain the observed anomalies.

Two-step estimation in ratio-of-mediator-probability weighted causal mediation analysis

This study investigates appropriate estimation of estimator variability in the context of causal mediation analysis that employs propensity score-based weighting. Such an analysis decomposes the total effect of a treatment on the outcome into an indirect effect transmitted through a focal mediator and a direct effect bypassing the mediator. Ratio-of-mediator-probability weighting estimates these causal effects by adjusting for the confounding impact of a large number of pretreatment covariates through propensity score-based weighting. In step 1, a propensity score model is estimated. In step 2, the causal effects of interest are estimated using weights derived from the prior step's regression coefficient estimates. Statistical inferences obtained from this 2-step estimation procedure are potentially problematic if the estimated standard errors of the causal effect estimates do not reflect the sampling uncertainty in the estimation of the weights. This study extends to ratio-of-mediator-probability weighting analysis a solution to the 2-step estimation problem by stacking the score functions from both steps. We derive the asymptotic variance-covariance matrix for the indirect effect and direct effect 2-step estimators, provide simulation results, and illustrate with an application study. Our simulation results indicate that the sampling uncertainty in the estimated weights should not be ignored. The standard error estimation using the stacking procedure offers a viable alternative to bootstrap standard error estimation. We discuss broad implications of this approach for causal analysis involving propensity score-based weighting.

Estimating and testing direct genetic effects in directed acyclic graphs using estimating equations

In genetic association studies, it is important to distinguish direct and indirect genetic effects in order to build truly functional models. For this purpose, we consider a directed acyclic graph setting with genetic variants, primary and intermediate phenotypes, and confounding factors. In order to make valid statistical inference on direct genetic effects on the primary phenotype, it is necessary to consider all potential effects in the graph, and we propose to use the estimating equations method with robust Huber-White sandwich standard errors. We evaluate the proposed causal inference based on estimating equations (CIEE) method and compare it with traditional multiple regression methods, the structural equation modeling method, and sequential G-estimation methods through a simulation study for the analysis of (completely observed) quantitative traits and time-to-event traits subject to censoring as primary phenotypes. The results show that CIEE provides valid estimators and inference by successfully removing the effect of intermediate phenotypes from the primary phenotype and is robust against measured and unmeasured confounding of the indirect effect through observed factors. All other methods except the sequential G-estimation method for quantitative traits fail in some scenarios where their test statistics yield inflated type I errors. In the analysis of the Genetic Analysis Workshop 19 dataset, we estimate and test genetic effects on blood pressure accounting for intermediate gene expression phenotypes. The results show that CIEE can identify genetic variants that would be missed by traditional regression analyses. CIEE is computationally fast, widely applicable to different fields, and available as an R package.

On the Mechanics of Immediate Corrections and Aftereffects in Prism Adaptation

Prisms laterally shifting the perceived visual world cause arm movements to deviate from intended targets. The resulting error—the direct effect—both for pointing and throwing movements, usually corresponds to only around half of the prism’s optical power due to an “immediate correction effect”. We investigated the mechanisms of this immediate correction effect. In three experiments with 73 healthy subjects we find that the immediate correction effect is associated with a head and/or eye rotation. Since these rotations are subconscious they are not taken into account by the participants. These subconscious rotations compensate for a large portion of the prism’s optical effect and change the subjective straight ahead. These movements seem to be induced only in a rich visual environment and hence do not take place in the dark. They correspond to the difference between the direct effect and the optical power of the prisms and seem to cause the immediate correction effect. Hence, eye-hand adaptation only adapts to the prism’s optical power minus unconscious head rotation and hence is much smaller than the optical power of the prisms.

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

BACKGROUND

Causal mediation analysis can improve understanding of the mechanism s 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 (which we call an intermediate confounder)--an assumption frequently violated in practice.

METHODS

We build on recent work that identified alternative estimands that do not require this assumption and propose a flexible and double robust targeted minimum loss-based estimator for stochastic direct and indirect effects. The proposed method intervenes stochastically on the mediator using a distribution which conditions on baseline covariates and marginalizes over the intermediate confounder.

RESULTS

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 with the voucher out of public housing, which is the intermediate confounder. We estimate the 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.

CONCLUSIONS

Our estimator is easy to implement in standard statistical software, and we provide annotated R code to further lower implementation barriers.

On the Interpretation and Use of Mediation: Multiple Perspectives on Mediation Analysis

Mediation analysis has become a very popular approach in psychology, and it is one that is associated with multiple perspectives that are often at odds, often implicitly. Explicitly discussing these perspectives and their motivations, advantages, and disadvantages can help to provide clarity to conversations and research regarding the use and refinement of mediation models. We discuss five such pairs of perspectives on mediation analysis, their associated advantages and disadvantages, and their implications: with vs. without a mediation hypothesis, specific effects vs. a global model, directness vs. indirectness of causation, effect size vs. null hypothesis testing, and hypothesized vs. alternative explanations. Discussion of the perspectives is facilitated by a small simulation study. Some philosophical and linguistic considerations are briefly discussed, as well as some other perspectives we do not develop here.

Dissecting Causal Pathways Using Mendelian Randomization with Summarized Genetic Data: Application to Age at Menarche and Risk of Breast Cancer

Mendelian randomization is the use of genetic variants as instrumental variables to estimate causal effects of risk factors on outcomes. The total causal effect of a risk factor is the change in the outcome resulting from intervening on the risk factor. This total causal effect may potentially encompass multiple mediating mechanisms. For a proposed mediator, the direct effect of the risk factor is the change in the outcome resulting from a change in the risk factor, keeping the mediator constant. A difference between the total effect and the direct effect indicates that the causal pathway from the risk factor to the outcome acts at least in part via the mediator (an indirect effect). Here, we show that Mendelian randomization estimates of total and direct effects can be obtained using summarized data on genetic associations with the risk factor, mediator, and outcome, potentially from different data sources. We perform simulations to test the validity of this approach when there is unmeasured confounding and/or bidirectional effects between the risk factor and mediator. We illustrate this method using the relationship between age at menarche and risk of breast cancer, with body mass index (BMI) as a potential mediator. We show an inverse direct causal effect of age at menarche on risk of breast cancer (independent of BMI), and a positive indirect effect via BMI. In conclusion, multivariable Mendelian randomization using summarized genetic data provides a rapid and accessible analytic strategy that can be undertaken using publicly available data to better understand causal mechanisms.

Unpacking Direct and Indirect Relationships of Short-Term Memory to Word Reading: Evidence From Korean-Speaking Children

We examined the relations of short-term memory (STM), metalinguistic awareness (phonological, morphological, and orthographic awareness), and rapid automatized naming (RAN) to word reading in Korean, a language with a relatively transparent orthography. STM, metalinguistic awareness, and RAN have been shown to be important to word reading, but the nature of the relations of STM, metalinguistic awareness, and RAN to word reading has rarely been investigated. Two alternative models were fitted. In the indirect relation model, STM was hypothesized to be indirectly related to word reading via metalinguistic awareness and RAN. In the direct and indirect relations model, STM was hypothesized to be directly and indirectly related to word reading. Results from 207 beginning readers in South Korea showed that STM was directly related to word reading as well as indirectly via metalinguistic awareness and RAN. Although the direct effect of STM was relatively small (.16), the total effect incorporating the indirect effect was substantial (.42). These results suggest that STM is an important, foundational cognitive capacity that underpins metalinguistic awareness and RAN as well as word reading, and further indicate the importance of considering both direct and indirect effects of language and cognitive skills on word reading.

Confounding and Statistical Significance of Indirect Effects: Childhood Adversity, Education, Smoking, and Anxious and Depressive Symptomatology

The life course perspective, the risky families model, and stress-and-coping models provide the rationale for assessing the role of smoking as a mediator in the association between childhood adversity and anxious and depressive symptomatology (ADS) in adulthood. However, no previous study has assessed the independent mediating role of smoking in the association between childhood adversity and ADS in adulthood. Moreover, the importance of mediator-response confounding variables has rarely been demonstrated empirically in social and psychiatric epidemiology. The aim of this paper was to (i) assess the mediating role of smoking in adulthood in the association between childhood adversity and ADS in adulthood, and (ii) assess the change in estimates due to different mediator-response confounding factors (education, alcohol intake, and social support). The present analysis used data collected from 1994 to 2008 within the framework of the Tromsø Study (N = 4,530), a representative prospective cohort study of men and women. Seven childhood adversities (low mother's education, low father's education, low financial conditions, exposure to passive smoke, psychological abuse, physical abuse, and substance abuse distress) were used to create a childhood adversity score. Smoking status was measured at a mean age of 54.7 years (Tromsø IV), and ADS in adulthood was measured at a mean age of 61.7 years (Tromsø V). Mediation analysis was used to assess the indirect effect and the proportion of mediated effect (%) of childhood adversity on ADS in adulthood via smoking in adulthood. The test-retest reliability of smoking was good (Kappa: 0.67, 95% CI: 0.63; 0.71) in this sample. Childhood adversity was associated with a 10% increased risk of smoking in adulthood (Relative risk: 1.10, 95% CI: 1.03; 1.18), and both childhood adversity and smoking in adulthood were associated with greater levels of ADS in adulthood (p < 0.001). Smoking in adulthood did not significantly mediate the association between childhood adversity and ADS in adulthood. However, when education was excluded as a mediator-response confounding variable, the indirect effect of childhood adversity on ADS in adulthood was statistically significant (p < 0.05). This study shows that a careful inclusion of potential confounding variables is important when assessing mediation.

Genetic variability, associations, and path analysis of chemical and morphological traits in Indian ginseng [Withania somnifera (L.) Dunal] for selection of higher yielding genotypes

Background

The study was carried out to assess the genetic variability present in ashwagandha and to examine the nature of associations of various traits to the root yield of the plant.

Methods

Fifty-three diverse genetic stocks of ashwagandha (Withania somnifera) were evaluated for 14 quantitative characteristics. Analysis of variance, correlation, and path coefficient analysis were performed using the mean data of 2 years.

Results

Analysis of variance revealed that the genotypes differed significantly for all characteristics studied. High heritability in conjunction with high genetic advance was observed for fresh root weight, 12 deoxywithastramonolide in roots, and plant height, which indicated that selection could be effective for these traits. Dry root weight has a tight linkage with plant height and fresh root weight. Further, in path coefficient analysis, fresh root weight, total alkaloid (%) in leaves, and 12 deoxywithastramonolide (%) in roots had the highest positive direct effect on dry root weight.

Conclusion

Therefore, these characteristics can be exploited to improve dry root weight in ashwagandha genotypes and there is also scope for the selection of promising and specific chemotypes (based on the alkaloid content) from the present germplasm.

Identification of the Unstable Human Postural Control System

Maintaining upright bipedal posture requires a control system that continually adapts to changing environmental conditions, such as different support surfaces. Behavioral changes associated with different support surfaces, such as the predominance of an ankle or hip strategy, is considered to reflect a change in the control strategy. However, tracing such behavioral changes to a specific component in a closed loop control system is challenging. Here we used the joint input–output (JIO) method of closed-loop system identification to identify the musculoskeletal and neural feedback components of the human postural control loop. The goal was to establish changes in the control loop corresponding to behavioral changes observed on different support surfaces. Subjects were simultaneously perturbed by two independent mechanical and two independent sensory perturbations while standing on a normal or short support surface. The results show a dramatic phase reversal between visual input and body kinematics due to the change in surface condition from trunk leads legs to legs lead trunk with increasing frequency of the visual perturbation. Through decomposition of the control loop, we found that behavioral change is not necessarily due to a change in control strategy, but in the case of different support surfaces, is linked to changes in properties of the plant. The JIO method is an important tool to identify the contribution of specific components within a closed loop control system to overall postural behavior and may be useful to devise better treatment of balance disorders.

Educational Tracking and Juvenile Deviance in Taiwan: Direct Effect, Indirect Effect, or Both

Educational tracking in Chinese society is quite different from that in Western society, in that the allocation to either the vocational or academic track is based on a national entrance examination, which happens at ninth grade (age 14-15). Hence, students in many Asian countries (e.g., China and Taiwan) have to face academic tracking in early adolescence. Because of cultural emphasis on education in Taiwan, the impact of tracking on deviance is profound and can be seen as a crucial life-event. With this concept in mind, we examine how educational tracking influences adolescent deviance during high school. In addition, we also examine how educational tracking may indirectly influence deviance through other life domains, including depression, delinquent peer association, and school attachment. By using longitudinal data (the Taiwan Youth Project), we find that educational tracking increases deviance not only directly but also indirectly through delinquent peers and low school attachment. Some implications and limitations are also discussed.

How to Get the Full Prism Effect

We investigate how the immediate correction effect decreases mispointing under prisms. Subjects performed rhythmic pointing movements under different conditions with horizontally shifting prisms. Even the first (initial) pointing error is much smaller than the prismatic shift, a phenomenon called the immediate correction effect. Knowledge about the structure of the room and of objects in the room obtained before the prisms were worn may limit the amount of the prismatic displacement perceived. We therefore compared the direct prism effect as well as prismatic adaptation with room illumination switched on versus switched off. Our 44 subjects participated in two experiments, with varying amounts of information about room structure available. The results show a direct effect corresponding to the optical power of the prisms in the dark condition, when in addition body position was slightly rotated in direction of the prismatic shift. But even in the dark, a significant immediate correction effect arises with the fixed body position. The largest immediate correction amounting to almost half of optical displacement arose in the standard condition of bright light and fixed body position.

Network Mendelian randomization: using genetic variants as instrumental variables to investigate mediation in causal pathways

BACKGROUND

Mendelian randomization uses genetic variants, assumed to be instrumental variables for a particular exposure, to estimate the causal effect of that exposure on an outcome. If the instrumental variable criteria are satisfied, the resulting estimator is consistent even in the presence of unmeasured confounding and reverse causation.

METHODS

We extend the Mendelian randomization paradigm to investigate more complex networks of relationships between variables, in particular where some of the effect of an exposure on the outcome may operate through an intermediate variable (a mediator). If instrumental variables for the exposure and mediator are available, direct and indirect effects of the exposure on the outcome can be estimated, for example using either a regression-based method or structural equation models. The direction of effect between the exposure and a possible mediator can also be assessed. Methods are illustrated in an applied example considering causal relationships between body mass index, C-reactive protein and uric acid.

RESULTS

These estimators are consistent in the presence of unmeasured confounding if, in addition to the instrumental variable assumptions, the effects of both the exposure on the mediator and the mediator on the outcome are homogeneous across individuals and linear without interactions. Nevertheless, a simulation study demonstrates that even considerable heterogeneity in these effects does not lead to bias in the estimates.

CONCLUSIONS

These methods can be used to estimate direct and indirect causal effects in a mediation setting, and have potential for the investigation of more complex networks between multiple interrelated exposures and disease outcomes.

Natural direct and indirect effects on the exposed: effect decomposition under weaker assumptions

We define natural direct and indirect effects on the exposed. We show that these allow for effect decomposition under weaker identification conditions than population natural direct and indirect effects. When no confounders of the mediator-outcome association are affected by the exposure, identification is possible under essentially the same conditions as for controlled direct effects. Otherwise, identification is still possible with additional knowledge on a nonidentifiable selection-bias function which measures the dependence of the mediator effect on the observed exposure within confounder levels, and which evaluates to zero in a large class of realistic data-generating mechanisms. We argue that natural direct and indirect effects on the exposed are of intrinsic interest in various applications. We moreover show that they coincide with the corresponding population natural direct and indirect effects when the exposure is randomly assigned. In such settings, our results are thus also of relevance for assessing population natural direct and indirect effects in the presence of exposure-induced mediator-outcome confounding, which existing methodology has not been able to address.

Partially hidden Markov model for time-varying principal stratification in HIV prevention trials

It is frequently of interest to estimate the intervention effect that adjusts for post-randomization variables in clinical trials. In the recently completed HPTN 035 trial, there is differential condom use between the three microbicide gel arms and the No Gel control arm, so that intention to treat (ITT) analyses only assess the net treatment effect that includes the indirect treatment effect mediated through differential condom use. Various statistical methods in causal inference have been developed to adjust for post-randomization variables. We extend the principal stratification framework to time-varying behavioral variables in HIV prevention trials with a time-to-event endpoint, using a partially hidden Markov model (pHMM). We formulate the causal estimand of interest, establish assumptions that enable identifiability of the causal parameters, and develop maximum likelihood methods for estimation. Application of our model on the HPTN 035 trial reveals an interesting pattern of prevention effectiveness among different condom-use principal strata.

Principal stratification--a goal or a tool?

Principal stratification has recently become a popular tool to address certain causal inference questions, particularly in dealing with post-randomization factors in randomized trials. Here, we analyze the conceptual basis for this framework and invite response to clarify the value of principal stratification in estimating causal effects of interest.

Mediation and moderation: Testing relationships between symptom status, functional health, and quality of life in HIV patients

We extended Wilson and Cleary's (1995) health-related quality of life model to examine the relationships among symptoms status (Symptoms), functional health (Disability), and quality of life (QOL). Using a community sample (N = 956) of male HIV positive patients, we tested a mediation model in which the relationship between Symptoms and QOL is partially mediated by Disability. Common and unique ideas from three approaches to examining moderation of effects in mediational models (Edwards & Lambert, 2007; Preacher, Rucker, & Hayes, 2007; MacKinnon, 2008) were used to test whether (a) the direct relationship of Symptoms to QOL and (b) the relationship of Disability to QOL are moderated by age. In the mediation model, both the direct and the indirect (mediated) effects were significant. The direct relationship of Symptoms to QOL was significantly moderated by age, but the relationship of Disability to QOL was not. High Symptoms were associated with lower QOL at all ages, but that this relationship became stronger at older ages. We compare the three approaches and consider their advantages over traditional approaches to combining mediation and moderation.

Cyclophosphamide and abrogation of tumor-induced suppressor T cell activity

Previously we have demonstrated that the in vitro generation of P815-specific anti-tumor cytotoxic T lymphocytes (CTL) was suppressed by splenic suppressor T cells from late tumor-bearing hosts (TBH). Suppression is not caused by in vitro growth of P815 from splenic metastases, since suppression was also seen with spleen cells from late TBH mice bearing a hypoxanthine/aminopterin/thymidine-sensitive subline (PHS-5) of P815 in the presence of HAT. Cyclophosphamide has been shown to inhibit the induction of suppressor cells selectively in a number of immune responses, but evidence that it can inhibit active tumor-induced suppressor T cells is limited. We have found that suppressor T cells already induced by P815 in syngeneic late TBH are sensitive to low doses of cyclophosphamide (50 mg/kg) given 1 day before spleen harvest, but the in vitro CTL response of late TBH spleen cells could not be restored by pretreating the mice with cyclophosphamide, even when exogenous interleukin-2 was added to the cultures. Although 50 mg/kg cyclophosphamide did not inhibit the CTL response of spleen cells from mice immunized with P815 + Corynebacterium parvum, the same dose of cyclophosphamide eliminated the CTL response of spleen cells from early TBH. Interleukin-2 (IL-2) did not overcome this effect of cyclophosphamide, suggesting a direct effect on CTL. "Ultra-low" -dose cyclophosphamide (10 mg/kg) did not adversely effect early TBH CTL but was still able to eliminate suppressor T cell activity from late TBH. Nevertheless, late TBH CTL remained unresponsive after pretreatment of mice with ultra-low-dose cyclophosphamide, even when exogenous IL-2 was added in vitro. CTL precursor frequency analyses demonstrated that cyclophosphamide pretreatment had little or no effect on the numbers of CTL precursors from early TBH. Late TBH CTL precursor cells were not detectable in these studies, with or without suppressor T cell inhibition by cyclophosphamide pretreatment. Thus, it appears that most CTL precursor cells may be lost or irretrievably inactivated in the spleens of late TBH mice.