Adaptive Finite Element Approximations for Kohn-Sham Models

The Kohn-Sham equation is a powerful, widely used approach for computation of ground state electronic energies and densities in chemistry, materials science, biology, and nanosciences. In this paper, we study the adaptive finite element approximations for the Kohn-Sham model. Based on the residual type a posteriori error estimators proposed in this paper, we introduce an adaptive finite element algorithm with a quite general marking strategy and prove the convergence of the adaptive finite element approximations. Using D{\" o}rfler's marking strategy, we then get the convergence rate and quasi-optimal complexity. We also carry out several typical numerical experiments that not only support our theory,but also show the robustness and efficiency of the adaptive finite element computations in electronic structure calculations.Comment: 38pages, 7figure

dugksFoam : An open source OpenFOAM solver for the Boltzmann model equation

A deterministic Boltzmann model equation solver called dugksFoam has been developed in the framework of the open source CFD toolbox OpenFOAM. The solver adopts the discrete unified gas kinetic scheme (Guo et al., 2015) with the Shakhov collision model. It has been validated by simulating several test cases covering different flow regimes including the one dimensional shock tube problem, a two dimensional thermal induced flow and the three dimensional lid-driven cavity flow. The solver features a parallel computing ability based on the velocity space decomposition, which is different from the physical space decomposition based approach provided by the OpenFOAM framework. The two decomposition approaches have been compared in both two and three dimensional cases. The parallel performance improves significantly using the newly implemented approach. A speed up by two orders of magnitudes has been observed using 256 cores on a small cluster. Program summary Program Title: dugksFoam Program Files doi:http://dx.doi.org/10.17632/zwn7t9cf5w.1 Licensing provisions: The MIT License Programming language: C++ External routines/libraries: OpenFOAM (http://www.openfoam.org) Nature of problem: Solving the Boltzmann equation with Shakhov model explicitly. Solution method: Discrete unified gas kinetic scheme (DUGKS) Restrictions: Symmetric boundary condition can only be applied at walls parallel to axis directions

Optimization of a Decellularization/Recellularization Strategy for Transplantable Bioengineered Liver

The liver is a complex organ that requires constant perfusion for the delivery of nutrients and oxygen and the removal of waste in order to survive. Efforts to recreate or mimic the liver microstructure via a ground-up approach are essential for liver tissue engineering. A decellularization/recellularization strategy is one of the approaches aiming at the possibility of producing a fully functional organ with in vitro-developed construction for clinical applications to replace failed livers, such as end-stage liver disease (ESLD). However, the complexity of the liver microarchitecture along with the limited suitable hepatic component, such as the optimization of the extracellular matrix (ECM) of the biomaterials, the selection of the seed cells, and development of the liver-specific three-dimensional (3D) niche settings, pose numerous challenges. In this chapter, we have provided a comprehensive outlook on how the physiological, pathological, and spatiotemporal aspects of these drawbacks can be turned into the current challenges in the field, and put forward a few techniques with the potential to address these challenges, mainly focusing on a decellularization-based liver regeneration strategy. We hypothesize the primary concepts necessary for constructing tissue-engineered liver organs based on either an intact (from a naïve liver) or a partial (from a pretreated liver) structure via simulating the natural development and regenerative processes

eX-ViT: A Novel eXplainable Vision Transformer for Weakly Supervised Semantic Segmentation

Recently vision transformer models have become prominent models for a range of vision tasks. These models, however, are usually opaque with weak feature interpretability. Moreover, there is no method currently built for an intrinsically interpretable transformer, which is able to explain its reasoning process and provide a faithful explanation. To close these crucial gaps, we propose a novel vision transformer dubbed the eXplainable Vision Transformer (eX-ViT), an intrinsically interpretable transformer model that is able to jointly discover robust interpretable features and perform the prediction. Specifically, eX-ViT is composed of the Explainable Multi-Head Attention (E-MHA) module, the Attribute-guided Explainer (AttE) module and the self-supervised attribute-guided loss. The E-MHA tailors explainable attention weights that are able to learn semantically interpretable representations from local patches in terms of model decisions with noise robustness. Meanwhile, AttE is proposed to encode discriminative attribute features for the target object through diverse attribute discovery, which constitutes faithful evidence for the model's predictions. In addition, a self-supervised attribute-guided loss is developed for our eX-ViT, which aims at learning enhanced representations through the attribute discriminability mechanism and attribute diversity mechanism, to localize diverse and discriminative attributes and generate more robust explanations. As a result, we can uncover faithful and robust interpretations with diverse attributes through the proposed eX-ViT

Conforming an Extracorporeal Lithotripter System for Video Urodynamic Studies

Objectives: This study aimed to evaluate the efficiency using existing fluoroscopic unit and lithotripter table of an extracorporeal lithotripter system for video urodynamic studies (VUDS) to determine anatomical abnormalities in patients with neurogenic lower urinary tract dysfunction (NLUTD). Methods: The extracorporeal lithotripsy system was adapted to obtain optimum fluoroscopic view according to body shape and observed organs of patients. We reviewed the VUDS data of 25 patients with NLUTD. Results: “Christmas tree bladder” (CTB) was found in 5 (20%) patients. Vesicoureteral reflux (VUR) and external detrusor sphincter dyssynergia (DESD) were detected in 3 (12%) and 4 (16%) patients, respectively. Four (16%) patients with normal coordination between detrusor contraction and external sphincter relaxation were proven by VUDS. CTB, VUR, or DESD was not observed in 10 (40%) patients with flaccid bladder. Hematuria, urinary tract infection, or autonomic dysreflexia did not occur in any of the patients. Conclusions: VUDS can discern anatomical abnormalities of the urinary tract, and patients in undeveloped areas of the world who have NLUTD can have easier access to VUDS because of the decreasing capital cost of VUDS

Resveratrol Ameliorates Cardiac Remodeling in a Murine Model of Heart Failure With Preserved Ejection Fraction

Objective: Accumulating evidence suggested that resveratrol (RES) could protect against adverse cardiac remodeling induced by several cardiovascular diseases. However, the role of RES in the setting of heart failure with preserved ejection fraction (HFpEF) and the underlying mechanisms of its action remain understood. This study was to determine whether RES could ameliorate HFpEF-induced cardiac remodeling and its mechanisms.Methods:In vivo, C57BL/6 mice served as either the sham or the HFpEF model. The HFpEF mice model was induced by uninephrectomy surgery and d-aldosterone infusion. RES (10 mg/kg/day, ig) or saline was administered to the mice for four weeks. In vitro, transforming growth factor β1 (TGF-β1) was used to stimulate neonatal rat cardiac fibroblasts (CFs) and Ex-527 was used to inhibit sirtuin 1 (Sirt1) in CFs. Echocardiography, hemodynamics, western blotting, quantitative real-time PCR, histological analysis, immunofluorescence, and ELISA kits were used to evaluate cardiac remodeling induced by HFpEF. Sirt1 and Smad3 expressions were measured to explore the underlying mechanisms of RES.Results: HFpEF mice developed left ventricular hypertrophy, preserved ejection fraction, diastolic dysfunction, and pulmonary congestion. Moreover, HFpEF mice showed increased infiltration of neutrophils and macrophages into the heart, including increased interleukin (IL)-1β, IL-6, and TNF-α. We also observed elevated M1 macrophages and decreased M2 macrophages, which were exhibited by increased mRNA expression of M1 markers (iNOS, CD86, and CD80) and decreased mRNA expression of M2 markers (Arg1, CD163, and CD206) in HFpEF hearts. Moreover, HFpEF hearts showed increased levels of intracellular reactive oxygen species (ROS). Importantly, HFpEF mice depicted increased collagen-I and -III and TGF-β mRNA expressions and decreased protein expression of phosphorylated endothelial nitric-oxide synthase (p-eNOS). Results of western blot revealed that the activated TGF-β/Smad3 signaling pathway mediated HFpEF-induced cardiac remodeling. As expected, this HFpEF-induced cardiac remodeling was reversed when treated with RES. RES significantly decreased Smad3 acetylation and inhibited Smad3 transcriptional activity induced by HFpEF via activating Sirt1. Inhibited Sirt1 with Ex-527 increased Smad3 acetylation, enhanced Smad3 transcriptional activity, and offset the protective effect of RES on TGF-β–induced cardiac fibroblast–myofibroblast transformation in CFs.Conclusion: Our results suggested that RES exerts a protective action against HFpEF-induced adverse cardiac remodeling by decreasing Smad3 acetylation and transcriptional activity via activating Sirt1. RES is expected to be a novel therapy option for HFpEF patients

Comment on "Carnot efficiency at divergent power output" (and additional discussion)

In a recent Letter [EPL, 118 (2017) 40003], Polettini and Esposito claimed that it is theoretically possible for a thermodynamic machine to achieve Carnot efficiency at divergent power output through the use of infinitely-fast processes. It appears however that this assertion is misleading as it is not supported by their derivations as demonstrated below. In this Comment, we first show that there is a confusion regarding the notion of optimal efficiency. We then analyze the quantum dot engine described in Ref. [EPL, 118 (2017) 40003] and demonstrate that Carnot efficiency is recovered only for vanishing output power. Moreover, a discussion on the use of infinite thermodynamical forces to reach Carnot efficiency is also presented in the appendix.Comment: Modified version compared to the manuscript submitted to EP