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Lu, Lu

Publications and source records attributed to Lu, Lu.

At least 73 records · Page 4

Graphics to facilitate informative discussion and team decision making

Everyone knows the expression “A picture is worth a thousand words,” and this effectively summarizes the ability of graphical summaries to convey information and persuade. However, in many cases, the goal for the right visualization is to encourage and guide discussion while helping focus a team to make carefully considered, defensible, and data-driven decisions. The aims of graphics differ if we are trying to communicate the merits of a single choice versus outlining several contending alternatives for further comparison and discussion. These choices each have their own strengths and weaknesses depending on how we value different criteria. They also serve different purposes at various stages of decision making. Often the role of statisticians is not to provide a single answer but to provide rich information and summaries in a manageable and compact form to enable productive discussion among team members. Through a series of diverse examples, this work present principles and strategies for encouraging discussion and informed decision making and discuss how they can be integrated with versatile use of graphical tools for examining multiple objectives, framing trade-offs between alternatives, and examining the impact of subjective priorities and uncertainty on the final decision.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

AIM2 regulates vascular smooth muscle cell migration in atherosclerosis

Highlights: • Our study demonstrated that AIM2 is involved in the progression of atherosclerosis in ApoE−/− mice for the first time. • We first found AIM2 could affect VSMCs migration and MMP2 expression. • We first found that AIM2 could active the TGF-β/SMAD signaling in VSMCs. Atherosclerosis (AS) is a common pathological basis of various cardiovascular and cerebrovascular diseases. Plaque formation is initiated and triggered by vascular smooth musclecells (VSMCs) migration in vascular wall, which gradually aggravates atherosclerosis progression. Absent in melanoma 2 (AIM2), a member of HIN-200 family, plays an important role in activating inflammasome. However, the role of AIM2 in atherosclerotic plaque progression outside of the inflammasome has not yet been reported.

60 APPLIED LIFE SCIENCES↗

The interaction of soybean reticulon homology domain protein (GmRHP) with Soybean mosaic virus encoded P3 contributes to the viral infection

Highlights: • GmRHP interacted with SMV-P3 in a screening of soybean cDNAs using mYTHS. • The interaction between GmRHP and SMV-P3 was confirmed using BiFC. • GmRHP's expression promoted TuMV replication and spread in N. benthamiana. • The interaction between SMV-P3 and GmRHP may contribute to the potyvirus infection. Soybean mosaic virus (SMV), a member of the Potyvirus genus, is a prevalent and devastating viral pathogen in soybean-growing regions worldwide. Potyvirus replication occurs in the 6K2-induced viral replication complex at endoplasmic reticulum exit sites. Potyvirus-encoded P3 is also associated with the endoplasmic reticulum and is as an essential component of the viral replication complex, playing a key role in viral replication. This study provides evidence that the soybean (Glycine max) reticulon homology domain protein (designated as GmRHP) interacts with SMV-P3 by using a two-hybrid yeast system to screen a soybean cDNA library. A bimolecular fluorescence complementation assay further confirmed the interaction, which occurred on the cytomembrane, endoplasmic reticulum and cytoskeleton in Nicotiana benthamiana cells. The transient expression of GmRHP can promote the coupling of Turnip mosaic virus replication and cell-to-cell movement in N. benthamiana. The interaction between the membrane protein SMV-P3 and GmRHP may contribute to the potyvirus infection, and GmRHP may be an essential host factor for P3's involvement in potyvirus replication.

60 APPLIED LIFE SCIENCES↗

Impaired autophagic flux and p62-mediated EMT are involved in arsenite-induced transformation of L-02 cells

Autophagy is a catabolic process essential for preserving cellular homeostasis, and the epithelial-to-mesenchymal transition (EMT) is involved during tissue development and cancer progression. In arsenite-treated human hepatic epithelial (L-02) cells, arsenite reduced the autophagic flux, which caused accumulation of p62, an adaptor and receptor of autophagy. Further, in arsenite-transformed L-02 cells, the levels of E-cadherin were attenuated, but the levels of vimentin, which is expressed in mesenchymal cells, and Snail, a transcription regulator of the EMT, were up-regulated. Thus, after chronic exposure of L-02 cells to arsenite, the impaired autophagic flux induced the accumulation of p62, which up-regulated the expression of Snail, a protein involved in arsenite-induced EMT of these cells. Knockdown of p62 by siRNA reversed the arsenite-induced EMT and decreased the capacities of arsenite-transformed L-02 cells for colony formation and invasion and migration. Therefore, in arsenite-induced transformation of L-02 cells, the accumulation of p62, by impairing autophagic flux, mediates the EMT via Snail. These results provide a previously unknown mechanism underlying arsenic toxicity and carcinogenicity. - Highlights: • Impaired autophagic flux induces the accumulation of p62 in arsenite-treated L-02 cells. • The EMT is associated with arsenite-induced transformation in L-02 cells. • p62 mediates the EMT via Snail in arsenite-induced transformation of L-02 cells.

60 APPLIED LIFE SCIENCES↗

Microbial Photoelectrosynthesis for Self-Sustaining Hydrogen Generation

Current artificial photosynthesis (APS) systems are promising for the storage of solar energy via transportable and storable fuels, but the anodic half-reaction of water oxidation is an energy intensive process which in many cases poorly couples with the cathodic half-reaction. Here in this paper, we demonstrate a self-sustaining microbial photoelectrosynthesis (MPES) system that pairs microbial electrochemical oxidation with photoelectrochemical water reduction for energy efficient H 2 generation. MPES reduces the overall energy requirements thereby greatly expanding the range of semiconductors that can be utilized in APS. Due to the recovery of chemical energy from waste organics by the mild microbial process and utilization of cost-effective and stable catalyst/electrode materials, our MPES system produced a stable current of 0.4 mA/cm 2 for 24 h without any external bias and ~10 mA/cm 2 with a modest bias under one sun illumination. Finally, this system also showed other merits, such as creating benefits of wastewater treatment and facile preparation and scalability.

08 HYDROGEN↗

Prioritization of Stockpile Maintenance with Layered Pareto Fronts

Difficult choices are required for a decision-making process where resources and budgets are increasingly constrained. This study demonstrates a structured decision-making approach using layered Pareto fronts to identify priorities about how to allocate funds between munitions stockpiles based on their estimated reliability, the urgency of needing available units, and the consequences if adequate numbers of units are not available. This case study, while specific to the characteristics of a group of munitions stockpiles, illustrates the general process of structured decision-making based on first identifying appropriate metrics that summarize the important dimensions of the decision, and then objectively eliminating non-contenders from further consideration. Finally, the final subjective stage incorporates user priorities to select the four stockpiles to receive additional maintenance and surveillance funds based on understanding the trade-offs and robustness to various user priorities.

42 ENGINEERING↗

Uncertainty analysis of trade-offs between multiple responses using hypervolume

When multiple responses are considered in process optimization, the degree to which they can be simultaneously optimized depends on the optimization objectives and the amount of trade-offs between the responses. The normalized hypervolume of the Pareto front is a useful summary to quantify the amount of trade-offs required to balance performance across the multiple responses. In order to quantify the impact of uncertainty of the estimated response surfaces and add realism to what future data to expect, 2 versions of the scaled normalized hypervolume of the Pareto front are presented. To demonstrate the variation of the hypervolume distributions, we explore a case study for a chemical process involving 3 responses, each with a different type of optimization goal. Our results show that the global normalized hypervolume characterizes the proximity to the ideal results possible, while the instance-specific summary considers the richness of the front and the severity of trade-offs between alternatives. Furthermore, the 2 scaling schemes complement each other and highlight different features of the Pareto front and hence are useful to quantify what solutions are possible for simultaneous optimization of multiple responses.

97 MATHEMATICS AND COMPUTING↗

Mesoscopic Adaptive Resolution Scheme toward Understanding of Interactions between Sickle Cell Fibers

Understanding of intracellular polymerization of sickle hemoglobin (HbS) and subsequent interaction with the membrane of a red blood cell (RBC) is important to predict the altered morphologies and mechanical properties of sickle RBCs in sickle cell anemia. However, modeling the integrated processes of HbS nucleation, polymerization, HbS fiber interaction, and subsequent distortion of RBCs is challenging as they occur at multispatial scales, ranging from nanometers to micrometers. To make progress toward simulating the integrated processes, we propose a hybrid HbS fiber model, which couples fine-grained and coarse-grained HbS fiber models through a mesoscopic adaptive resolution scheme (MARS). To this end, we apply a microscopic model to capture the dynamic process of polymerization of HbS fibers, while maintaining the mechanical properties of polymerized HbS fibers by the mesoscopic model, thus providing a means of bridging the subcellular and cellular phenomena in sickle cell disease. At the subcellular level, this model can simulate HbS polymerization with preexisting HbS nuclei. At the cellular level, if combined with RBC models, the generated HbS fibers could be applied to study the morphologies and membrane stiffening of sickle RBCs. One important feature of the MARS is that it can be easily employed in other particle-based multiscale simulations where a dynamic coarse-graining and force-blending method is required. As demonstrations, we first apply the hybrid HbS fiber model to simulate the interactions of two growing fibers and find that their final configurations depend on the orientation and interaction distance between two fibers, in good agreement with experimental observations. We also model the formation of fiber bundles and domains so that we explore the mechanism that causes fiber branching.

Biophysics↗

Flexible Quasi-Two-Dimensional CoFe 2 O 4 Epitaxial Thin Films for Continuous Strain Tuning of Magnetic Properties

Epitaxial thin films of CoFe 2 O 4 (CFO) have successfully been transferred from a SrTiO 3 substrate onto a flexible polyimide substrate. By bending the flexible polyimide, different levels of uniaxial strain are continuously introduced into the CFO epitaxial thin films. Unlike traditional epitaxial strain induced by substrates, the strain from bending will not suffer from critical thickness limitation, crystalline quality variation, and substrate clamping, and more importantly, it provides a more intrinsic and reliable way to study strain-controlled behaviors in functional oxide systems. It is found that both the saturation magnetization and coercivity of the transferred films can be changed over the bending status and show a high accord with the movement of the curvature bending radius of the polyimide substrate. Lastly, this reveals that the mechanical strain plays a critical role in tuning the magnetic properties of CFO thin films parallel and perpendicular to the film plane direction.

36 MATERIALS SCIENCE↗

Photoactivation mechanism of a carotenoid-based photoreceptor

Photoprotection is essential for efficient photosynthesis. Cyanobacteria have evolved a unique photoprotective mechanism mediated by a water-soluble carotenoid-based photoreceptor known as orange carotenoid protein (OCP). OCP undergoes large conformational changes in response to intense blue light, and the photoactivated OCP facilitates dissipation of excess energy via direct interaction with allophycocyanins at the phycobilisome core. However, the structural events leading up to the OCP photoactivation remain elusive at the molecular level. Here we present direct observations of light-induced structural changes in OCP captured by dynamic crystallography. Difference electron densities between the dark and illuminated states reveal widespread and concerted atomic motions that lead to altered protein–pigment interactions, displacement of secondary structures, and domain separation. Based on these crystallographic observations together with site-directed mutagenesis, we propose a molecular mechanism for OCP light perception, in which the photochemical property of a conjugated carbonyl group is exploited. We hypothesize that the OCP photoactivation starts with keto–enol tautomerization of the essential 4-keto group in the carotenoid, which disrupts the strong hydrogen bonds between the bent chromophore and the protein moiety. Subsequent structural changes trapped in the crystal lattice offer a high-resolution glimpse of the initial molecular events as OCP begins to transition from the orange-absorbing state to the active red-absorbing state.

59 BASIC BIOLOGICAL SCIENCES↗

OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment—simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by multiple millions of mesoscopic particles—using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse three-dimensional space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of the key spatial searching data structure in our code, i.e., a lattice-free cell list, with a time and space cost linearly proportional to the number of particles in the system. The position and the shape of the cells also adapt automatically to the local density and curvature. The code implements OpenMP parallelization and scales to hundreds of hardware threads. It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and >40 times in problem size, thus providing, to our knowledge, a new platform for probing the biomechanics of red blood cells.

Biophysics↗

Choosing a reliability inspection plan for interval censored data

Reliability test plans are important for producing precise and accurate assessment of reliability characteristics. This paper explores different strategies for choosing between possible inspection plans for interval censored data given a fixed testing timeframe and budget. A new general cost structure is proposed for guiding precise quantification of total cost in inspection test plan. Multiple summaries of reliability are considered and compared as the criteria for choosing the best plans using an easily adapted method. Different cost structures and representative true underlying reliability curves demonstrate how to assess different strategies given the logistical constraints and nature of the problem. Results show several general patterns exist across a wide variety of scenarios. Given the fixed total cost, plans that inspect more units with less frequency based on equally spaced time points are favored due to the ease of implementation and consistent good performance across a large number of case study scenarios. Plans with inspection times chosen based on equally spaced probabilities offer improved reliability estimates for the shape of the distribution, mean lifetime, and failure time for a small fraction of population only for applications with high infant mortality rates. The paper uses a Monte Carlo simulation based approach in addition to the common evaluation based on the asymptotic variance and offers comparison and recommendation for different applications with different objectives. Additionally, the paper outlines a variety of different reliability metrics to use as criteria for optimization, presents a general method for evaluating different alternatives, as well as provides case study results for different common scenarios.

97 MATHEMATICS AND COMPUTING↗

Design and construction of diverse structures of coordination polymers: Photocatalytic properties

The reaction of Cu(NO{sub 3}){sub 2}·3H{sub 2}O/Ni(NO{sub 3}){sub 2}·6H{sub 2}O with 4′-(4-(3,5-dicarboxylphenoxy)phenyl)-4,2′:6′,4′′-terpyridine (H{sub 2}dbp) gave [Cu{sub 0.5}(Hdbp)]{sub n} (1) and [Ni(dbp)(H{sub 2}O)]{sub n} (2), while the reactions of Co(NO{sub 3}){sub 2}·6H{sub 2}O with H{sub 2}dbp in the presence of 4,4′-bipy and 2,2′-bpy generated [Co(dbp)(4,4′-bipy)]{sub n} (3) and ([Co(dbp)(2,2′-bipy)]{sub n}·H{sub 2}O) (4), respectively (4,4′-bipy=4.4′-pyridine and 2,2′-bipy=2,2′-bipyridine). X-Ray single-crystal analyses reveal that 1 contains a 1D double chain. 2 possesses a 3D architecture with (4.6{sup 2}0.8{sup 3}){sub 2} topology that is interpenetrated with each other to form a 2-fold network. In 3, the 2D [Co(dbp)]n sheets are pillared by 4,4′-bpy to form a 3D framework with 1D open channel. Compound 4 consists of a 1D ladder-like chain. The results showed that the structural diversity of the coordination polymers resulted from the different geometries of metal ions and effect of assistant ligands. Furthermore, the photocatalytic properties of 1–4 for degradation of the methyl violet (MV) have been examined. - Graphical abstract: The photocatalytic activity and selectivity of complexes 1–4 prove that they may be good and stable photocatalysts for degradation of organic dyes.

36 MATERIALS SCIENCE↗

TopN-Pareto Front Search

The JMP Add-In TopN-PFS provides an automated tool for finding layered Pareto front to identify the top N solutions from an enumerated list of candidates subject to optimizing multiple criteria. The approach constructs the N layers of Pareto fronts, and then provides a suite of graphical tools to explore the alternatives based on different prioritizations of the criteria. The tool is designed to provide a set of alternatives from which the decision-maker can select the best option for their study goals.

Anderson-Cook, ChristineM.↗

TopN-Pareto Front Search

The JMP Add-In TopN-PFS provides an automated tool for finding layered Pareto front to identify the top N solutions from an enumerated list of candidates subject to optimizing multiple criteria. The approach constructs the N layers of Pareto fronts, and then provides a suite of graphical tools to explore the alternatives based on different prioritizations of the criteria. The tool is designed to provide a set of alternatives from which the decision-maker can select the best option for their study goals.

Anderson-Cook, Christine M.↗

Best Bang for the Buck: Part 2 – Choosing Between Different Sized Designs

Last month, we considered four potential designs of varying sizes and a variety of their attributes for an engineering problem involving a screening design with seven factors. The engineer’s original request was to find a design with 14 runs that could estimate all of the main effects, as well as have some potential for finding important two-factor interactions and possibly curvature in the underlying surface. This assessment was that the proposed size of design was potentially a bit too ambitious for the experiment’s goals, so we explored three other competing designs that had slightly larger sizes but were able to improve several aspects of the design.

97 MATHEMATICS AND COMPUTING↗

Multiple objective optimization in reliability demonstration test

Reliability demonstration tests are usually performed in product design or validation processes to demonstrate whether a product meets specified requirements on reliability. For binomial demonstration tests, the zero-failure test has been most commonly used due to its simplicity and use of minimum sample size to achieve an acceptable consumer’s risk level. However, this test can often result in unacceptably high risk for producers as well as a low probability of passing the test even when the product has good reliability. This paper explicitly explores the interrelationship between multiple objectives that are commonly of interest when planning a demonstration test and proposes structured decision-making procedures using a Pareto front approach for selecting an optimal test plan based on simultaneously balancing multiple criteria. Different strategies are suggested for scenarios with different user priorities and graphical tools are developed to help quantify the trade-offs between choices and to facilitate informed decision making. As a result, potential impacts of some subjective user inputs on the final decision are studied to offer insights and useful guidance for general applications.

97 MATHEMATICS AND COMPUTING↗