bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin‐like mediator
Authors: Ramírez Cintia Soledad , Tolmie Carmien , Opperman Diederik Johannes , González Pablo Javier , Rivas María Gabriela , Brondino Carlos Dante , Ferroni Felix Martín 
Published: September 2021

AbstractWe report the crystal structure of the copper‐containing nitrite reductase (NirK) from the Gram‐negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non‐cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 Å, showed a striking resemblance with the overall structure of the well‐known Class I NirKs composed of two Greek key β‐barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.
Target highlights in CASP14: Analysis of models by structure providers
Authors: Alexander Leila T. , Lepore Rosalba , Kryshtafovych Andriy , Adamopoulos Athanassios , Alahuhta Markus , Arvin Ann M. , Bomble Yannick J. , Böttcher Bettina , Breyton Cécile , Chiarini Valerio , Chinnam Naga babu , Chiu Wah , Fidelis Krzysztof , Grinter Rhys , Gupta Gagan D. , Hartmann Marcus D. , Hayes Christopher S. , Heidebrecht Tatjana , Ilari Andrea , Joachimiak Andrzej , Kim Youngchang , Linares Romain , Lovering Andrew L. , Lunin Vladimir V. , Lupas Andrei N. , Makbul Cihan , Michalska Karolina , Moult John , Mukherjee Prasun K. , Nutt William (Sam) , Oliver Stefan L. , Perrakis Anastassis , Stols Lucy , Tainer John A. , Topf Maya , Tsutakawa Susan E. , Valdivia‐Delgado Mauricio , Schwede Torsten 
Published: September 2021

AbstractThe biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three‐dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically‐relevant properties of proteins.
Genome‐wide transcriptional response of the causal soybean sudden death syndrome pathogen Fusarium virguliforme to a succinate dehydrogenase inhibitor fluopyram
Authors: Sang Hyunkyu , Chang Hao‐Xun , Choi Sungyu , Son Doeun , Lee Gahee , Chilvers Martin I 
Published: September 2021

AbstractBACKGROUNDSuccinate dehydrogenase inhibitors (SDHIs) have been widely used to manage plant diseases caused by phytopathogenic fungi. Although attention to and use of SDHI fungicides has recently increased, molecular responses of fungal pathogens to SDHIs have often not been investigated. A SDHI fungicide, fluopyram, has been used as a soybean seed treatment and has displayed effective control of Fusarium virguliforme, one of the causal agents of soybean sudden death syndrome. To examine genome‐wide gene expression of F. virguliforme to fluopyram, RNA‐seq analysis was conducted on two field strains of F. virguliforme with differing SDHI fungicide sensitivity in the absence and presence of fluopyram.RESULTSThe analysis indicated that several xenobiotic detoxification‐related genes, such as those of deoxygenase, transferases and transporters, were highly induced by fluopyram. Among the genes, four ATP‐binding cassette (ABC) transporters were characterized by the yeast expression system. The results revealed that expression of three ABCG transporters was associated with reduced sensitivity to multiple fungicides including fluopyram. In addition, heterologous expression of a major facilitator superfamily (MFS) transporter that was highly expressed in the fluopyram‐insensitive F. virguliforme strain in the yeast system conferred decreased sensitivity to fluopyram.CONCLUSIONThis study demonstrated that xenobiotic detoxification‐related genes were highly upregulated in response to fluopyram, and expression of ABC or MFS transporter genes was associated with reduced sensitivity to the SDHI fungicide. This is the first transcriptomic analysis of the fungal species response to fluopyram and the finding will help elucidate the molecular mechanisms of SDHI resistance. © 2021 Society of Chemical Industry.
A multistate transition model for statin‐induced myopathy and statin discontinuation
Authors: Zhu Yuxi , Chiang Chien‐Wei , Wang Lei , Brock Guy , Milks M. Wesley , Cao Weidan , Zhang Pengyue , Zeng Donglin , Donneyong Macarius , Li Lang 
Published: September 2021

AbstractThe overarching goal of this study was to simultaneously model the dynamic relationships among statin exposure, statin discontinuation, and potentially statin‐related myopathic outcomes. We extracted data from the Indiana Network of Patient Care for 134,815 patients who received statin therapy between January 4, 2004, and December 31, 2008. All individuals began statin treatment, some discontinued statin use, and some experienced myopathy and/or rhabdomyolysis while taking the drug or after discontinuation. We developed a militate model to characterize 12 transition probabilities among six different states defined by use or discontinuation of statin and its associated myopathy or rhabdomyolysis. We found that discontinuation of statin therapy was common and frequently early, with 44.4% of patients discontinuing therapy after 1 month, and discontinuation is a strong indicator for statin‐induced myopathy (risk ratio, 10.8; p < 0.05). Women more likely than men (p < 0.05) and patients aged 65 years and older had a higher risk than those aged younger than 65 years to discontinue statin use or experience myopathy. In conclusion, we introduce an innovative multistate model that allows clear depiction of the relationship between statin discontinuation and statin‐induced myopathy. For the first time, we have successfully demonstrated and quantified the relative risk of myopathy between patients who continued and discontinued statin therapy. Age and sex were two strong risk factors for both statin discontinuation and incident myopathy.
A framework to guide dose & regimen strategy for clinical drug development
Authors: Sander Oliver , Magnusson Baldur , Ludwig Inga , Jullion Astrid , Meille Christophe , Lorand Daniel , Bornkamp Björn , Hinder Markus , Kovacs Steven J. , Looby Michael 
Published: September 2021

AbstractOptimizing new drug therapies remains a challenge for clinical development, despite the use of ever more sophisticated quantitative methodologies. Although conceptually simple, the idea of finding the right treatment at the right dose for the right patient to ensure an appropriate balance of risks and benefits is challenging and requires a multidisciplinary approach. In this paper, we present a framework developed as a tool for organizing knowledge and facilitating collaboration in development teams.
Metaheuristics for pharmacometrics
Authors: Kim Seongho , Hooker Andrew C. , Shi Yu , Kim Grace Hyun J. , Wong Weng Kee 
Published: September 2021

AbstractMetaheuristics is a powerful optimization tool that is increasingly used across disciplines to tackle general purpose optimization problems. Nature‐inspired metaheuristic algorithms is a subclass of metaheuristic algorithms and have been shown to be particularly flexible and useful in solving complicated optimization problems in computer science and engineering. A common practice with metaheuristics is to hybridize it with another suitably chosen algorithm for enhanced performance. This paper reviews metaheuristic algorithms and demonstrates some of its utility in tackling pharmacometric problems. Specifically, we provide three applications using one of its most celebrated members, particle swarm optimization (PSO), and show that PSO can effectively estimate parameters in complicated nonlinear mixed‐effects models and to gain insights into statistical identifiability issues in a complex compartment model. In the third application, we demonstrate how to hybridize PSO with sparse grid, which is an often‐used technique to evaluate high dimensional integrals, to search for‐efficient designs for estimating parameters in nonlinear mixed‐effects models with a count outcome. We also show the proposed hybrid algorithm outperforms its competitors when sparse grid is replaced by its competitor, adaptive gaussian quadrature to approximate the integral, or when PSO is replaced by three notable nature‐inspired metaheuristic algorithms.
Quantum Illumination with Multiple Entangled Photons
Authors: Gallego Torromé Ricardo 
Published: September 2021

AbstractIn this work, a theoretical generalization of Lloyd's quantum illumination model for signal beams described by two entangled photon states is developed. It is shown that the new protocol is more sensitive than Lloyd's model with respect to signal‐to‐noise ratio (SNR) and reduces the required time‐bandwidth product to have the same enhancement in the SNR. The protocol is resilient against noise, potentially resilient against losses, and offers a method to find the range of the target. However, the generation of the required three photon states for the protocol remains a technical problem for its practical implementation.
A novel domain of attraction based synthesis of inverse optimal control
Authors: Prasanna Parvathy , Jacob Jeevamma , Nandakumar Mattida P. 
Published: September 2021

AbstractThis article proposes a novel and systematic methodology for the inverse optimal control (IOC) of a class of input affine nonlinear systems. First, the system is represented in the pseudo‐linear state‐dependent coefficient (SDC) form so as to facilitate the use of matrix algebraic concepts in the design, while preserving the nonlinear system dynamics. Second, the IOC problem which seeks the solution to the Hamilton–Jacobi–Bellman equation is translated to a diagonal stability (D‐stability) problem. Therefore, the general notion of D‐stability, which deals with the characterization of a matrix for the existence of a diagonal matrix such that , is redefined with respect to SDC factored matrices in this work. Consequently, the criteria for the existence (necessary condition) and determination of a diagonal solution (sufficient condition) are formulated in terms of the SDC matrices. It is shown in this work that these criteria can be readily met by the closed‐loop system matrix , for any arbitrary domain in state‐space, by manipulating only the diagonal elements using the diagonal matrix constituted by the IOC feedback. In short, the IOC feedback is designed such that the criteria for D‐stability by the closed‐loop system matrix is fulfilled. Hence this novel design methodology is meaningfully named as “Inverse optimal control via diagonal stabilization” (IOC‐D). The main advantages of IOC‐D include: (i) guaranteed estimate of the domain of attraction (DOA), (ii) Immense flexibility of design, and (iii) guaranteed closed form solution which makes the design procedure analytic and computationally efficient. Numerical simulations validate the theoretical developments and the overall efficiency of the proposed approach.
control of stochastic networked control systems with time‐varying delays: The event‐triggered sampling case
Authors: Zhu Quanxin , Huang Tingwen 
Published: September 2021

AbstractIn this article, we aim to study the robust stabilization problem for a class of stochastic networked control delay systems with time‐varying delays and unknown parameters. By developing an event‐triggered strategy, the robustly exponential stability in mean‐square of the suggested system with an performance is obtained. Furthermore, the robustly exponential stabilization problem in mean‐square is also solved by designing an controller. Compared with many published results in the literature for discrete‐time stochastic systems, our work mainly focuses on the case of continuous‐time stochastic systems. In particular, time‐varying delays and unknown parameters are also considered. Finally, the applications of the theoretical results are illustrated by two numerical examples.
Hierarchical 3D Cuprous Sulfide Nanoporous Cluster Arrays Self‐Assembled on Copper Foam as a Binder‐Free Cathode for Hybrid Magnesium‐Based Batteries
Authors: Zhu Guilei , Xia Guanglin , Yu Xuebin 
Published: September 2021

AbstractOn account of easy accessibility, high theoretical volumetric capacity and dendrite‐free magnesium (Mg) anode, Mg battery has a great promise to be next generation rechargeable batteries, yet still remains a challenging task in acquiring fast Mg2+ kinetics and effective cathode materials. Herein, hierarchical 3D cuprous sulfide porous nanosheet decorated nanowire cluster arrays with robust adhesion on copper foam (Cu2S HP/CF), which is employed as a binder‐free conversion cathode material for magnesium/lithium hybrid battery, delivering impressively initial and reversible specific capacity of 383 and 311 mAh g−1 at 100 mA g−1, respectively, which are obviously outperformed corresponding powder cathode in a traditional method by using polymer binder, is reported. Intriguingly, benefiting from the hierarchical nanoporous array architecture and self‐assembly feature, Cu2S HP/CF cathode shows a remarkable cycling stability with a high capacity of 129 mAh g−1 at 300 mA g−1 over 500 cycles. This work not only highlights a guide for designing hierarchical nanoporous materials derived from metal–organic frameworks, but also provides a novel strategy of in situ formation to fabricate binder‐free cathodes.
Phase‐Transfer Exchange Lead Chalcogenide Colloidal Quantum Dots: Ink Preparation, Film Assembly, and Solar Cell Construction
Authors: Yuan Mohan , Wang Xia , Chen Xiao , He Jungang , Li Kanghua , Song Boxiang , Hu Huicheng , Gao Liang , Lan Xinzheng , Chen Chao , Tang Jiang 
Published: September 2021

AbstractSolution‐processed colloidal quantum dots (CQDs) are promising candidates for the third‐generation photovoltaics due to their low cost and spectral tunability. The development of CQD solar cells mainly relies on high‐quality CQD ink, smooth and dense film, and charge‐extraction‐favored device architectures. In particular, advances in the processing of CQDs are essential for high‐quality QD solids. The phase transfer exchange (PTE), in contrast with traditional solid‐state ligand exchange, has demonstrated to be the most promising approach for high‐quality QD solids in terms of charge transport and defect passivation. As a result, the efficiencies of Pb chalcogenide CQD solar cells have been rapidly improved to 14.0%. In this review, the development of the PTE method is briefly reviewed for lead chalcogenide CQD ink preparation, film assembly, and device construction. Particularly, the key roles of lead halides and additional additives are emphasized for defect passivation and charge transport improvement. In the end, several potential directions for future research are proposed.
Highly Controllable Hierarchically Porous Ag/Ag2S Heterostructure by Cation Exchange for Efficient Hydrogen Evolution
Authors: Xu Huajie , Niu Xiaoxiao , Liu Zhuangzhuang , Sun Mingzi , Liu Zhaodi , Tian Zhimei , Wu Xiaoxia , Huang Bolong , Tang Yu , Yan Chun‐Hua 
Published: September 2021

AbstractEstablishing the hierarchical porous architectures has been considered to be the most efficient approach to realize the efficient mass diffusion and large exposed active sites of designed micro/nanomaterial catalysts for hydrogen evolution reactions (HER). In this work, the nonequivalent cation exchange strategy is developed to fabricate the hierarchically porous Ag/Ag2S heterostructure based on the rapid cation exchange by the metal‐organic framework (MOF)‐derived CoS. The as‐prepared Ag/Ag2S inherits the original 3D hollow morphology of CoS with porous nature, possessing abundant S‐vacancies and lattice strain simultaneously due to the coordination loss and in‐situ epitaxial growth of metallic Ag on the surface. Owing to the optimizations of lattice and electronic structures, the unique hierarchically porous Ag/Ag2S heterostructure exhibits superior catalytic performance than previously reported catalysts derived from MOF. Theoretical calculations have confirmed that the co‐existence of Ag cluster and sulfur vacancies activates the electroactivity of the interfacial defective region to boost the HER process. The binding strength of the proton and energetic trend of HER has been optimized with the formation of Ag/Ag2S heterostructure, which guarantees the efficient generation of H2. This study opens a new strategy for the utilization of the nonequivalent cation exchange strategy to efficiently synthesize advanced electrocatalysts with high performances.
All‐in‐One Nanomedicine: Multifunctional Single‐Component Nanoparticles for Cancer Theranostics
Authors: Cai Yu , Chen Xiaoyi , Si Jingxing , Mou Xiaozhou , Dong Xiaochen 
Published: September 2021

AbstractThe development of cancer diagnostic imaging and treatment is a major concern worldwide. By integrating imaging and therapy into one theranostic nanoplatform for simultaneously detecting tumors, evaluating the targeting ability and timely monitoring therapeutic responses provide more opportunities for precision medicine. Among various theranostic nanosystems, a series of single‐component nanoparticles (NPs) have been developed for “all‐in‐one” theranostics, which presents the unique properties of facile preparation, simple composition, defined structure, high reproducibility, and excellent biocompatibility. Specifically, utilizing single‐component NPs for both diagnostics and therapeutics can reduce the possible numerous untoward side effects and risks to the living body. In this review, the recent progress of multifunctional single‐component NPs in the applications of cancer theranostics is systematically summarized. Notably, the structure design, categories of NPs, targeted strategies, biomedical applications, potential barriers, challenges, and prospects for the future clinical practice of this rapidly growing field are discussed.
A Metallic Ion‐Induced Self‐Assembly Enabling Nanowire‐Based Aerogels
Authors: Shang Qi‐Guo , Wang Kang , Li Lin‐Ge , He Zhen , Jiang Hui‐Jun , Zhu Jian‐Hua , Liu Jian‐Wei 
Published: September 2021

AbstractThe controlled assembly of nanowires is one of the key challenges in the development of a range of functional 3D aerogels with unique physicochemical properties for practical applications. However, the deep understanding of the dynamic assemble process for fabricating nanowire aerogels remains elusive. Herein, a facile strategy is presented for the metallic ion‐induced assembly of nanowires into macroscopic aerogels via a solution‐based process. This method enables the interconnecting between polymer‐decorated nanowires via metallic coordination, resulting in plenty of nanowire bundles with the same orientation. Besides, the coordinated binding strength of nanowires with different metallic ions is also discussed. The assembly mechanism that the metallic ions induced dynamic behavior of nanowires is revealed via molecular dynamics theoretical evaluation. These findings benefit for constructing nanowire‐based aerogels with unique structural features and multi‐function, which pave new opportunities for other material systems.
Optimizing checkpoint‐based fault‐tolerance in distributed stream processing systems: Theory to practice
Authors: Jayasekara Sachini , Karunasekera Shanika , Harwood Aaron 
Published: September 2021

AbstractFault‐tolerance is an essential part of a stream processing system that guarantees data analysis could continue even after failures. State‐of‐the‐art distributed stream processing systems use checkpointing to support fault‐tolerance for stateful computations where the state of the computations is periodically persisted. However, the frequency of performing checkpoints impacts the performance (utilization, latency, and throughput) of the system as the checkpointing process consumes resources and time that can be used for actual computations. In practice, systems are often configured to perform checkpoints based on crude values ignoring factors such as checkpoint and restart costs, leading to suboptimal performance. In our previous work, we proposed a theoretical optimal checkpoint interval that maximizes the system utilization for stream processing systems to minimize the impact of checkpointing on system performance. In this article, we investigate the practical benefits of our proposed theoretical optimal by conducting experiments in a real‐world cloud setting using different streaming applications; we use Apache Flink, a well‐known stream processing system for our experiments. The experiment results demonstrate that an optimal interval can achieve better utilization, confirming the practicality of the theoretical model when applied to real‐world applications. We observed utilization improvements from 10% to 200% for a range of failure rates from 0.3 failures per hour to 0.075 failures per minute. Moreover, we explore how performance measures: latency and throughput are affected by the optimal interval. Our observations demonstrate that significant improvements can be achieved using the optimal interval for both latency and throughput.
Chiral Triarylborane‐Based Small Organic Molecules for Circularly Polarized Luminescence
Authors: Wang Min , Zhao Cui‐Hua 
Published: September 2021

AbstractCircularly polarized luminescence (CPL) has shown promising application potentials in 3D display, optical data storage, smart sensors/probers, CPL lasers, and light source for asymmetric photosynthesis. In the last decade, the CPL‐active small organic molecules (CPL‐SOMs) have attracted rapidly increasing research interest owing to the great advantages of SOMs, such as high luminescence efficiency, facile modification of chemical structure, fine emission wavelength tuning, precise relationships between structure and properties, and as well as easy fabrication. Promoted by the unique effects of boryl group, such as strong electron‐accepting ability, great steric effect, and Lewis acidity to bind with Lewis bases, we herein summarized our recent research results about the creation of CPL‐SOMs by modification of chiral scaffolds, such as [2.2]paracyclophane, [5]/[7]helicene, and binaphthyl, with boryl group. The preliminary results have well demonstrated that the chiral triarylborane‐based SOMs exhibit promising CPL properties, such as intense CPL in combination of high luminescence dissymmetry factor (|glum|) with high fluorescence efficiency, solvent‐induced sign inversion, facile emission wavelength tuning, high fluorescence efficiency in the solid, and substituent‐induced sign inversion.