Causal Mediation Analysis for Difference-in-Difference Design and Panel Data

Advantages of panel data, i.e., difference in difference (DID) design data, are a large sample size and easy availability. Therefore, panel data are widely used in epidemiology and in all social science fields. The literatures on causal inferences of panel data setting or DID design are growing, but no theory or mediation analysis method has been proposed for such settings. In this study, we propose a methodology for conducting causal mediation analysis in DID design and panel data setting. We provide formal counterfactual definitions for controlled direct effect and natural direct and indirect effect in panel data setting and DID design, including the identification and required assumptions. We also demonstrate that, under the assumptions of linearity and additivity, controlled direct effects can be estimated by contrasting marginal and conditional DID estimators whereas natural indirect effects can be estimated by calculating the product of the exposure-mediator DID estimator and the mediator-outcome DID estimator. A panel regression-based approach is also proposed. The proposed method is then used to investigate mechanisms of the effects of the Covid 19 pandemic on the mental health status of the population. The results revealed that mobility restrictions mediated approximately 45 % of the causal effect of Covid 19 on mental health status

Causal Mediation Analysis with Multiple Time-Varying Mediators

In longitudinal studies with time-varying exposures and mediators, the mediational g-formula is an important method for the assessment of direct and indirect effects. However, current methodologies based on the mediational g-formula can deal with only one mediator. This limitation makes these methodologies inapplicable to many scenarios. Hence, we develop a novel methodology by extending the mediational g-formula to cover cases with multiple time-varying mediators. We formulate two variants of our approach that are each suited to a distinct set of assumptions and effect definitions and present nonparametric identification results of each variant. We further show how complex causal mechanisms (whose complexity derives from the presence of multiple time-varying mediators) can be untangled. A parametric method along with a user-friendly algorithm was implemented in R software. We illustrate our method by investigating the complex causal mechanism underlying the progression of chronic obstructive pulmonary disease. We found that the effects of lung function impairment mediated by dyspnea symptoms and mediated by physical activity accounted for 13.7% and 10.8% of the total effect, respectively. Our analyses thus illustrate the power of this approach, providing evidence for the mediating role of dyspnea and physical activity on the causal pathway from lung function impairment to health status

Optimizing Human Synovial Fluid Preparation for Two-Dimensional Gel Electrophoresis

<p>Abstract</p> <p>Background</p> <p>Proteome analysis is frequently applied in identifying the proteins or biomarkers in knee synovial fluids (SF) that are associated with osteoarthritis and other arthritic disorders. The 2-dimensional gel electrophoresis (2-DE) is the technique of choice in these studies. Disease biomarkers usually appear in low concentrations and may be masked by high abundant proteins. Therefore, the main aim of this study was to find the most suitable sample preparation method that can optimize the expression of proteins on 2-DE gels that can be used to develop a reference proteome picture for non-osteoarthritic knee synovial fluid samples. Proteome pictures obtained from osteoarthritic knee synovial fluids can then be compared with the reference proteome pictures obtained in this study to assist us in identifying the disease biomarkers more correctly.</p> <p>Results</p> <p>The proteomic tool of 2-DE with immobilized pH gradients was applied in this study. A total of 12 2-DE gel images were constructed from SF samples that were free of osteoarthritis. In these samples, 3 were not treated with any sample preparation methods, 3 were treated with acetone, 3 were treated with 2-DE Clean-Up Kit, and 3 were treated with the combination of acetone and 2-D Clean-Up Kit prior to 2-DE analysis. Gel images were analyzed using the PDQuest Basic 8.0.1 Analytical software. Protein spots that were of interest were excised from the gels and sent for identification by mass spectrometry. Total SF total protein concentration was calculated to be 21.98 ± 0.86 mg/mL. The untreated SF samples were detected to have 456 ± 33 protein spots on 2-DE gel images. Acetone treated SF samples were detected to have 320 ± 28 protein spots, 2-D Clean-Up Kit treated SF samples were detected to have 413 ± 31 protein spots, and the combined treatment method of acetone and 2-D Clean-Up Kit was detected to have 278 ± 26 protein spots 2-DE gel images. SF samples treated with 2-D Clean-Up Kit revealed clearer presentation of the isoforms and increased intensities of the less abundant proteins of haptoglobin, apolipoprotein A-IV, prostaglandin-D synthase, alpha-1B-glycoprotein, and alpha-2-HS-glycoprotein on 2-DE gel images as compared with untreated SF samples and SF samples treated with acetone.</p> <p>Conclusions</p> <p>The acetone precipitation method and the combined treatment effect of acetone and 2-DE Clean-Up Kit are not preferred in preparing SF samples for 2-DE analysis as both protein intensities and numbers decrease significantly. On the other hand, 2-D Clean-Up Kit treated SF samples revealed clearer isoforms and higher intensities for the less abundant proteins of haptoglobin, apolipoprotein A-IV, prostaglandin-D synthase, alpha-1B-glycoprotein, and alpha-2-HS-glycoprotein on 2-DE gels. As a result, it is recommended that SF samples should be treated with protein clean up products such as 2-D Clean-Up Kit first before conducting proteomic research in searching for the relevant biomarkers associated with knee osteoarthritis.</p

Interaction between Thymidylate Synthase and Its Cognate mRNA in Zebrafish Embryos

Thymidylate synthase (TS), which catalyzes the de novo synthesis of dUMP, is an important target for cancer therapy. In this report, the effects of 5-fluorouracil (5-FU) and ZD1694 on the regulation of TS gene expression were evaluated in zebrafish embryos. Our results revealed that the expression of TS was increased by about six-fold when embryos were treated with 1.0 µM 5-FU and there was a greater than 10-fold increase in the TS protein level after treatment with 0.4 µM ZD1694. Northern blot analysis confirmed that expression of TS mRNA was identical in treated or untreated embryos. Gel shift and immunoprecipitation assays revealed that zebrafish TS was specifically bound with its cognate mRNA in vitro and in vivo. We identified a 20 nt RNA sequence, TS:N20, localized to the 5′-UTR of TS mRNA, which corresponded to nt 13–32; TS:N20 bound to the TS protein with an affinity similar to that of the full-length TS mRNA. The MFold program predicted that TS:N20 formed a stable stem-loop structure similar to that of the cis-acting element found in human TS mRNA. Variant RNAs with either a deletion or mutation in the core motif of TS:N20 were unable to bind to the TS protein. In vitro translation experiments, using the rabbit lysate system, confirmed that zebrafish TS mRNA translation was significantly repressed when an excess amount of TS protein was included in the system. Additionally, a TS stability experiment confirmed that treatment of zebrafish embryos with 5-FU could increase the TS stability significantly, and the half life of TS protein was about 2.7 times longer than in untreated embryos. Our study revealed a structural requirement for the interaction of TS RNA with TS protein. These findings also demonstrated that the increase in TS protein induced by 5-FU occurs at the post-transcriptional level and that increased stability and translation efficiency both contributed to the increase in TS protein levels induced by TS inhibitors

Characteristics of chronic hepatitis B patients who underwent liver biopsies

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87030/1/j.1365-2893.2010.01364.x.pd

The Effectiveness of Cupping Therapy on Relieving Chronic Neck and Shoulder Pain: A Randomized Controlled Trial

The research aimed to investigate the effectiveness of cupping therapy (CT) in changes on skin surface temperature (SST) for relieving chronic neck and shoulder pain (NSP) among community residents. A single-blind experimental design constituted of sixty subjects with self-perceived NSP. The subjects were randomly allocated to two groups. The cupping group received CT at SI 15, GB 21, and LI 15 acupuncture points, and the control group received no intervention. Pain was assessed using the SST, visual analog scale (VAS), and blood pressure (BP). The main results were SST of GB 21 acupuncture point raised from 30.6°C to 32.7°C and from 30.7°C to 30.6°C in the control group. Neck pain intensity (NPI) severity scores were reduced from 9.7 to 3.6 in the cupping group and from 9.7 to 9.5 in the control group. The SST and NPI differences between the groups were statistically significant (P < 0.001). One treatment of CT is shown to increase SST. In conjunction with the physiological effect the subjective experience of NSP is reduced in intensity. Further studies are required to improve the understanding and potential long-term effects of CT

Time-dependent supergravity solutions in null dilaton background

A class of time dependent pp-waves with NS-NS flux in type IIA string theory is considered. The background preserves 1/4 supersymmetry and may provide a toy model of Big Bang cosmology with non trivial flux. At the Big Bang singularity in early past, the string theory is strongly coupled and Matrix string model can be used to describe the dynamics. We also construct some time dependent supergravity solutions for D-branes and analyze their supersymmetry properties.Comment: 11 pages, a typo is fixed in eqn 20. To appear in Phys. Lett.

Optimizing Fresh Agricultural Product Distribution Paths Under Demand Uncertainty

Consumers' demand for fresh agricultural products (FAPs) and their quality requirements are increasing in the current agricultural-product consumption market. FAPs' unique perishability and short shelf-life features mean a high level of delivery efficiency is required to ensure their freshness and quality. However, consumers' demand for FAPs is contingent and geographically dispersed. Therefore, the conflicting relationship between the costs associated with the logistics distribution and the level of delivery quality is important to consider. In this paper, the authors consider a fresh agricultural-product distribution path planning problem with time windows (FAPDPPPTW). To address the FAPDPPPTW under demand uncertainty, a mixed-integer linear programming model based on robust optimization is proposed. Moreover, a particle swarm optimization algorithm combined with a variable neighborhood search is designed to solve the proposed mathematical model. The numerical experiment results show the robustness and fast convergence of the algorithm.</p

Postchallenge responses of nitrotyrosine and TNF-alpha during 75-g oral glucose tolerance test are associated with the presence of coronary artery diseases in patients with prediabetes

<p>Abstract</p> <p>Background</p> <p>Meta-analysis has demonstrated an exponential relationship between 2-hr postchallenge hyperglycemia and coronary artery disease (CAD). Pulsatile hyperglycemia can acutely increase proinflammatory cytokines by oxidative stress. We hypothesized that postchallenge proinflammatory and nitrosative responses after 75 g oral glucose tolerance tests (75 g-OGTT) might be associated with CAD in patients without previously recognized type 2 diabetes mellitus (T2DM).</p> <p>Methods</p> <p>Serial changes of plasma glucose (PG), tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6) and nitrotyrosine levels were analyzed during 75 g-OGTT in 120 patients (81 male; age 62 ± 11 years) before coronary angiography. Patients were classified as normal (NGT; 42%), impaired (IGT; 34%) and diabetic (T2DM; 24%) glucose tolerance by 75 g-OGTT.</p> <p>Results</p> <p>Postchallenge hyperglycemia elicited TNF-α, IL-6 and nitrotyrosine levels time-dependently, and 2-hr median levels of TNF-α (7.1 versus 6.4 pg/ml; <it>P </it>< 0.05) and nitrotyrosine (1.01 versus 0.83 <it>μ</it>mol/l; <it>P </it>< 0.05), but not IL-6 or PG, were significantly higher in patients with CAD in either IGT or T2DM groups. After adjusting risk factors and glucose tolerance status, 2-hr nitrotyrosine in highest quartiles (OR: 3.1, <it>P </it>< 0.05) remained an independent predictor of CAD by logistic regression analysis.</p> <p>Conclusions</p> <p>These results highlight postchallenge proinflammatory and nitrosative responses by 75 g-OGTT, rather than hyperglycemia <it>per se</it>, are associated with CAD in patients without previous recognized diabetes.</p