Shapley Computations Using Surrogate Model-Based Trees

Shapley-related techniques have gained attention as both global and local interpretation tools because of their desirable properties. However, their computation using conditional expectations is computationally expensive. Approximation methods suggested in the literature have limitations. This paper proposes the use of a surrogate model-based tree to compute Shapley and SHAP values based on conditional expectation. Simulation studies show that the proposed algorithm provides improvements in accuracy, unifies global Shapley and SHAP interpretation, and the thresholding method provides a way to trade-off running time and accuracy

The candidate tumor suppressor gene ECRG4 inhibits cancer cells migration and invasion in esophageal carcinoma

<p>Abstract</p> <p>Background</p> <p>The esophageal cancer related gene 4 (ECRG4) was initially identified and cloned in our laboratory from human normal esophageal epithelium (GenBank accession no.<ext-link ext-link-id="AF325503" ext-link-type="gen">AF325503</ext-link>). ECRG4 was a new tumor suppressor gene in esophageal squamous cell carcinoma (ESCC) associated with prognosis. In this study, we investigated the novel tumor-suppressing function of ECRG4 in cancer cell migration, invasion, adhesion and cell cycle regulation in ESCC.</p> <p>Methods</p> <p>Transwell and Boyden chamber experiments were utilized to examined the effects of ECRG4 expression on ESCC cells migration, invasion and adhesion. And flow cytometric analysis was used to observe the impact of ECRG4 expression on cell cycle regulation. Finally, the expression levels of cell cycle regulating proteins p53 and p21 in human ESCC cells transfected with ECRG4 gene were evaluated by Western blotting.</p> <p>Results</p> <p>The restoration of ECRG4 expression in ESCC cells inhibited cancer cells migration and invasion (<it>P </it>< 0.05), which did not affect cell adhesion capacity (<it>P </it>> 0.05). Furthermore, ECRG4 could cause cell cycle G1 phase arrest in ESCC (<it>P </it>< 0.05), through inducing the increased expression of p53 and p21 proteins.</p> <p>Conclusion</p> <p>ECRG4 is a candidate tumor suppressor gene which suppressed tumor cells migration and invasion without affecting cell adhesion ability in ESCC. Furthermore, ECRG4 might cause cell cycle G1 phase block possibly through inducing the increased expression of p53 and p21 proteins in ESCC.</p

Exotic electronic states in gradient-strained untwisted graphene bilayers

Many exotic electronic states were discovered in moire superlattices hosted in twisted homo-bilayers in the past decade, including unconventional superconductivity and correlated insulating states. However, it is technically challenging to precisely and orderly stack two or more layers into certain twisting angles. Here, we presented a theoretical strategy that introduces moire superlattices in untwisted homo-bilayers by applying different in-plane strains on the two layers of a graphene homo-bilayer, respectively. Our density functional theory calculations indicate that the graphene bilayer exhibits substantial out-of-plane corrugations that form a coloring-triangular structure in each moire supercell under gradient in-plane strains. Such structure leads to a set of kagome bands, namely one flat-band and, at least, one Dirac band, developing along the M-K path after band-folding. For comparison, uniformly applied in-plane strain only yields a nearly flat band within path K-G, which is originated from local quantum confinement. These findings highlight the gradient strain as a route to feasibly fabricate exotic electronic states in untwisted flexible homo-bilayers.Comment: 15 pages, 4 figure

Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization.

Soil types heavily influence ecological dynamics. It remains controversial to what extent soil types shape microbial responses to land management changes, largely due to lack of in-depth comparison across various soil types. Here, we collected samples from three major zonal soil types spanning from cold temperate to subtropical climate zones. We examined bacterial and fungal community structures, as well as microbial functional genes. Different soil types had distinct microbial biomass levels and community compositions. Five years of maize cropping (growing corn or maize) changed the bacterial community composition of the Ultisol soil type and the fungal composition of the Mollisol soil type but had little effect on the microbial composition of the Inceptisol soil type. Meanwhile, 5 years of fertilization resulted in soil acidification. Microbial compositions of the Mollisol and Ultisol, but not the Inceptisol, were changed and correlated (P &lt; 0.05) with soil pH. These results demonstrated the critical role of soil type in determining microbial responses to land management changes. We also found that soil nitrification potentials correlated with the total abundance of nitrifiers and that soil heterotrophic respiration correlated with the total abundance of carbon degradation genes, suggesting that changes in microbial community structure had altered ecosystem processes. IMPORTANCE Microbial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial and fungal community structures using Illumina sequencing, microbial functional genes using GeoChip, microbial biomass using phospholipid fatty acid analysis, as well as functional processes of soil nitrification potential and CO2 efflux. We demonstrated the critical role of soil type in determining microbial responses to land use changes at the continental level. Our findings underscore the inherent difficulty in generalizing ecosystem responses across landscapes and suggest that assessments of community feedback must take soil types into consideration. Author Video: An author video summary of this article is available

Characteristics of High Risk People with Cardiovascular Disease in Chinese Rural Areas: Clinical Indictors, Disease Patterns and Drug Treatment

Background and Aims: Current cardiovascular disease (CVD) prevention is based on diagnosis and treatment of specific disease. Little is known for high risk people with CVD at the community level. In rural China, health records of all residents were established after the recent health reforms. This study aims to describe the characters of the rural population with high CVD risk regarding their clinical indicators, disease patterns, drug treatment and adherence. Methods and Results: 17042 (87%) of all the 19500 rural residents in the two townships had valid health records in 2009. We employed a validated tool, the Asian Equation, to screen 8182 (48%) resident health records of those aged between 40-75 years in 2010. Those who were identified with a CVD risk of 20% or higher were selected for a face-to-face questionnaire survey regarding their diagnosed disease and drug treatment. 453 individuals were identified as high risk of CVD, with an average age of 53 years, 62% males, 50% smoking rate and average systolic blood pressure of 161 mmHg. 386 (85%) participated in the survey, while 294 (76%) were diagnosed with and 88 (23%) were suspects of CVD, hypertension, diabetes or hyperlipidaemia. 75 (19%) took drug regularly and 125 (32%) either stopped treatment or missed drugs. The most often used drugs were calcium channel blockers (20%). Only 2% used aspirins and 0.8% used statins. The median costs of drugs were 17 RMB (USD2.66) per month. Conclusion: The majority of the high risk population in our setting of rural China had already been diagnosed with a CVD related disease, but very few took any drugs, and less still took highly effective drugs to prevent CVD. A holistic strategy focused on population with high risk CVD and based on the current China public health reform is suggested in the context of primary care. © 2013 Wei et al.published_or_final_versio