bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Plasmonic Photocatalyst by Site‐selective Loading of Bimetallic Nanoparticles of Au and Ag on Titanium(IV) Oxide
Authors: Zheng Zhi , Murakami Naoya , Liu Jingjing , Teng Zhenyuan , Zhang Qitao , Cao Yu , Cheng Honghui , Ohno Teruhisa 
Published: April 2020

AbstractMorphology‐controlled rutile titanium(IV) oxide (TiO2) and anatase TiO2 were prepared by a hydrothermal method and their surfaces were selectively loaded with Au, Ag and AuAg bimetallic nanoparticles (NPs) by photo‐deposition in order to obtain visible‐light responsive photocatalysts. With the help of local surface plasmon resonance (LSPR) of noble metal NPs, the photocatalytic activity of noble metal‐loaded TiO2 under visible‐light irradiation was improved compared to that of bare TiO2. The enhancement of LSPR on the photocatalytic activity of rutile TiO2 was larger than that of anatase TiO2 with optimum amount of Au or AuAg. In addition, the reusability (stability) of AuAg‐loaded TiO2 was much better than that of Ag‐loaded TiO2. Double‐beam photoacoustic results confirmed different trap energy level distribution lead to different electron transfer ways, resulting in different oxidizing capabilities and they gave one of important strategies for designing visible‐light responsive TiO2.
How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study
Authors: Cui Haiyang , Stadtmüller Tom H. J. , Jiang Qianjia , Jaeger Karl‐Erich , Schwaneberg Ulrich , Davari Mehdi D. 
Published: April 2020

AbstractExpanding synthetic capabilities to routinely employ enzymes in organic solvents (OSs) is a dream for protein engineers and synthetic chemists. Despite significant advances in the field of protein engineering, general and transferable design principles to improve the OS resistance of enzymes are poorly understood. Herein, we report a combined computational and directed evolution study of Bacillus subtlis lipase A (BSLA) in three OSs (i. e., 1,4‐dioxane, dimethyl sulfoxide, 2,2,2‐trifluoroethanol) to devise a rational strategy to guide engineering OS resistant enzymes. Molecular dynamics simulations showed that OSs reduce BSLA activity and resistance in OSs by (i) stripping off essential water molecules from the BLSA surface mainly through H‐bonds binding; and (ii) penetrating the substrate binding cleft leading to inhibition and conformational change. Interestingly, integration of computational results with “BSLA‐SSM” variant library (3439 variants; all natural diversity with amino acid exchange) revealed two complementary rational design strategies: (i) surface charge engineering, and (ii) substrate binding cleft engineering. These strategies are most likely applicable to stabilize other lipases and enzymes and assist experimentalists to design organic solvent resistant enzymes with reduced time and screening effort in lab experiments.
Construction of 2D BiVO4−CdS−Ti3C2Tx Heterostructures for Enhanced Photo‐redox Activities
Authors: Wang Wuyou , Hood Zachary D. , Zhang Xuanyu , Ivanov Ilia N. , Bao Zhenghong , Su Tongming , Jin Mingzhou , Bai Lei , Wang Xuewen , Zhang Rongbin , Wu Zili 
Published: April 2020

AbstractPhotocatalytic evolution of hydrogen and oxygen from water splitting over semiconductors is an efficient method for solar energy conversion. In this study, the 2D/2D BiVO4−CdS heterostructures with Ti3C2Tx (Tx=O, OH, F) as a co‐catalyst were synthesized by two steps as the visible‐light‐driven photocatalysts. Compared with BiVO4 and CdS, the heterostructured catalysis exhibit greatly enhanced photocatalytic hydrogen and oxygen production performances and excellent photodegradation and photoreduction activities of methylene blue (MB) and potassium dichromate Cr(VI), respectively. The remarkable enhancement is attributed to the proposed Z‐scheme carrier transfer derived from the 2D/2D BiVO4−CdS heterostructures. Charge separation and transfer of photoexcited electrons and holes pairs are further enhanced after loading Ti3C2Tx in the BiVO4−CdS heterostructures. The potential Z‐scheme photocatalytic system and co‐catalyst endows the BiVO4−CdS−Ti3C2Tx heterostructures with strong photo‐redox capacity and excellent stability in solar energy conversion.
Unique Role of Heterole‐Fused Structures in Aromaticity and Physicochemical Properties of 7,8‐Dehydropurpurins
Authors: Higashino Tomohiro , Nishimura Issei , Imahori Hiroshi 
Published: April 2020

AbstractPorphyrins with a fused five‐membered ring, such as 7,8‐dehydropurpurins, have appeared as an emerging class of unique porphyrinoids. Their altered absorption spectra, relatively short lifetimes of excited states, and small HOMO–LUMO gaps arise from the harmony of the antiaromatic 20π‐circuit and the aromatic 18π‐circuit. In this regard, the electronic properties of 7,8‐dehydropurpurins are expected to be controlled by modulating the contribution of the antiaromatic π‐circuit to the whole aromaticity. Here the comparison of pyrrole‐ and phosphole‐fused 7,8‐dehydropurpurins is reported in terms of their aromaticity and physicochemical properties. The spectroscopic investigation revealed the larger contribution of the antiaromatic 24π‐circuit in pyrrole‐fused 7,8‐dehyrdopurpurins than in phosphole‐fused 7,8‐dehydropurpurins. The DFT calculations also supported the feasibility of tuning the aromaticity of 7,8‐dehydropurpurins by heterole‐fused structures. Thus, the introduction of heterole‐fused structures into porphyrinoids is a universal strategy to get new insight into aromaticity and their intrinsic properties in cyclic π‐conjugated molecules.
Spectrum of PALB2 germline mutations and characteristics of PALB2‐related breast cancer: Screening of 16,501 unselected patients with breast cancer and 5890 controls by next‐generation sequencing
Authors: Zhou Jiaojiao , Wang Honglian , Fu Fangmeng , Li Zhanwen , Feng Qingjian , Wu Weizhu , Liu Yun , Wang Chuan , Chen Yiding 
Published: April 2020

BackgroundPartner and localizer BRCA2 (PALB2) is a breast cancer predisposition gene, but the clinical relevance of PALB2 germline mutations in Chinese patients with breast cancer remains unknown. This study attempted to investigate the full prevalence and spectrum of PALB2 germline mutations in China and the associations between PALB2 germline mutations and breast cancer risk.MethodsA total of 21,216 unselected patients with breast cancer were enrolled from 10 provinces in China, and 5890 Chinese women without cancer were enrolled as healthy controls. PALB2 screening was based on next‐generation sequencing.ResultsA total of 16,501 BRCA1/2‐negative patients with breast cancer were analyzed. Deleterious PALB2 mutation carriers accounted for 0.97% (n = 160) in the breast cancer cohort and for 0.19% (n = 11) in the healthy control cohort. Forty‐one novel PALB2 germline mutations were identified. A high frequency of PALB2 c.751C>T was detected, and it accounted for 10.63% of the PALB2 germline mutations detected (17 of 160). PALB2 mutations were significantly associated with increased breast cancer risk (odds ratio [OR], 5.23; 95% confidence interval [CI], 2.84‐9.65; P < .0001), especially among women 30 years old or younger (OR, 10.09; 95% CI, 3.95‐25.79; P < .0001). Clinical characteristics, including a family history, bigger tumor size, triple‐negative breast cancer, positive lymph nodes, and bilateral breast cancer, were closely related to PALB2 mutations.ConclusionsThis study revealed a comprehensive spectrum of PALB2 germline mutations and characteristics of PALB2‐related breast cancer in China. PALB2 germline mutations confer a moderately increased risk for breast cancer but profoundly increase breast cancer risk for those 30 years old or younger in the Chinese population.
Parallel performance of molecular dynamics trajectory analysis
Authors: Khoshlessan Mahzad , Paraskevakos Ioannis , Fox Geoffrey C. , Jha Shantenu , Beckstein Oliver 
Published: April 2020

SummaryThe performance of biomolecular molecular dynamics simulations has steadily increased on modern high‐performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations is becoming a bottleneck. To close this gap, we studied the performance of trajectory analysis with message passing interface (MPI) parallelization and the PythonMDAnalysislibrary on three different Extreme Science and Engineering Discovery Environment (XSEDE) supercomputers where trajectories were read from a Lustre parallel file system. Strong scaling performance was impeded by stragglers, MPI processes that were slower than the typical process. Stragglers were less prevalent for compute‐bound workloads, thus pointing to file reading as a bottleneck for scaling. However, a more complicated picture emerged in which both the computation and the data ingestion exhibited close to ideal strong scaling behavior whereas stragglers were primarily caused by either large MPI communication costs or long times to open the single shared trajectory file. We improved overall strong scaling performance by either subfiling (splitting the trajectory into separate files) or MPI‐IO with parallel HDF5 trajectory files. The parallel HDF5 approach resulted in near ideal strong scaling on up to 384 cores (16 nodes), thus reducing trajectory analysis times by two orders of magnitude compared with the serial approach.
LSR‐forest: An locality sensitive hashing‐based approximate k‐nearest neighbor query algorithm on high‐dimensional uncertain data
Authors: Wang Jiagang , Qian Tu , Yang Anbang , Wang Hui , Qian Jiangbo 
Published: April 2020

SummaryUncertain data is widely used in many practical applications, such as data cleaning, location‐based services, privacy protection, and so on. With the development of technology, data has a tendency to high‐dimensionality. The most common indexes for nearest neighbor search on uncertain data are the R‐Tree and the KD‐Tree. These indexes will inevitably bring about “curse of dimension.” Focus on this problem, article proposes a new hash algorithm, called the LSR‐forest, which based on locality sensitive hashing and R‐Tree, to solve the high‐dimensional uncertain data approximate neighbor search problem. The LSR‐forest can hash similar high‐dimensional uncertain data into a same bucket with a high probability, and then constructs multiple R‐Tree‐based indexes for hashed buckets. When querying, it is possible to judge neighbors by checking the data in the hypercube which the query point is in. One can also adjust the query range automatically by different parameter of k. Many experiments on different datasets are presented in this article. The results show that LSR‐forest has better effectiveness and efficiency than R‐Tree on high‐dimensional datasets.
Kinetic Isotope Effect as a Tool To Investigate the Oxygen Reduction Reaction on Pt‐based Electrocatalysts – Part II: Effect of Platinum Dispersion
Authors: Rezaei Talarposhti Morteza , Asset Tristan , Garcia Samuel T. , Chen Yechuan , Herrera Sergio , Dai Sheng , Peterson Eric J. , Artyushkova Kateryna , Zenyuk Iryna , Atanassov Plamen 
Published: April 2020

AbstractWe investigated the oxygen reduction reaction (ORR) mechanism on Pt nanoparticles (NPs) dispersed on several carbon blacks with various physicochemical properties (i. e. specific surface ranging from 80 to 900 m2 g−1, different graphitization degree, etc.). Using the kinetic isotope effect (KIE) along with various electrochemical characterizations, we determined that the rate determining step (RDS) of the ORR is a proton‐independent step when the density of Pt NPs on the surface of the carbon support is high. Upon decrease of the density of Pt NPs on the surface, the RDS of the ORR starts involving a proton, as denoted by an increase of the KIE >1. This underlined the critical role played by the carbon support in the oxygen reduction reaction electrocatalysis by Pt supported on high surface area carbon.
Clathrate III (Bromine Hydrate): Structural Relationship with Clathrate I
Authors: Pomeransky Anatoly A. 
Published: April 2020

AbstractTetragonal structure of clathrate III (TS−I) is found in bromine hydrate, ionic hydrates, in particular, in hydrates of tetraalkylammonium salts, as well as in clathrate compounds of the group IV elements (‘Zintl clathrates’). In this paper new description of this clathrate structure is suggested. Main structural unit in this description is ‘4‐column’, the set of four nearest columns of 14‐hedral T‐cages together with its internal filling by the pillar of mutually orthogonal pairs of T‐cages. Comparison based on this new description of clathrate III and clathrate I (CS−I) shows that 4‐column is maximal common structural element of these two structures. On this ground it is argued that clathrate III can be considered as a modification of the clathrate I, formed as a result of multiple interruption of clathrate I crystal growth. At the same time, it is shown that due to crucial differences between these two structures there does not exist structural or reconstructive phase transition between them. Integral character of 4‐columns as the structural units of clathrate III is confirmed by the analysis of the most studied case of ionic hydrates of tetraalkylammonium salts in which guest molecules occupy simultaneously T‐cages in outer columns and inner T‐cages. This analysis allows also to state important hypothesis that in general case for formation of clathrate III crystals presence of special guest molecules occupying several cages (or special ions in the host lattice) is necessary.
Determination of Electronic Recombination Free Energy in Zeolites: Effects of the Charge Balancing Cation and Confinement
Authors: Hureau Matthieu , Moissette Alain , Gaillard Jérémy 
Published: April 2020

AbstractThe adsorption of DPH in M6.6ZSM‐5 (M=Na+, K+, Rb+, Cs+), RbFER and RbMOR channel zeolites takes place without chemical or structural modification. After photoexcitation of these systems, a radical cation–electron pair is observed and has a sufficiently long lifetime to be studied by diffuse reflectance UV‐visible spectroscopy. The study of the recombination of this radical cation‐electron pair was carried out at different temperatures and allowed the determination of the activation energy as a function of the nature of the charge‐balancing cation but also of the confinement effect. It appears that the activation energy decreases progressively from Na+ to Cs+ but also when the confinement decreases. To go further, the free enthalpies have been calculated from the Marcus theory demonstrating experimentally that these systems are located in the inverted Marcus region.
Functionalized Macrocycles in Supramolecular Organocatalysis
Authors: Kauerhof Dana , Niemeyer Jochen 
Published: April 2020

AbstractSupramolecular organocatalysis has emerged as a novel research field in the context of homogeneous catalysis. In particular, the use of functionalized macrocycles as supramolecular catalysts is highly promising, as these systems are oftentimes easily accessible and offer distinct advantages in catalysis. Macrocyclic catalysts can provide defined binding pockets, such as hydrophobic cavities, and can thus create a reaction microenvironment for catalysis. In addition, macrocycles can offer a preorganized arrangement of functional groups, such as binding sites or catalytically active groups, thus enabling a defined and possibly multivalent binding and activation of substrates. The aim of this Minireview is to provide an overview of recent advances in the area of supramolecular organocatalysis based on functionalized macrocycles (including cyclodextrins, calixarenes, and resorcinarenes), with a focus on those examples where certain catalytically active groups (such as hydrogen bond donors/acceptors, Brønsted acid or base groups, or nucleophilic units) are present in or have been installed on the macrocycles.
Two‐Step Preparation of Highly Pure, Soluble HIV Protease from Inclusion Bodies Recombinantly Expressed in Escherichia coli
Authors: Sherry Dean , Worth Roland , Sayed Yasien 
Published: April 2020

AbstractHeterologous expression of exogenous proteases in Escherichia coli often results in the formation of insoluble inclusion bodies. When sequestered into inclusion bodies, the functionality of the proteases is minimized. To be characterized structurally and functionally, however, proteases must be obtained in their native conformation. HIV protease is readily expressed as inclusion bodies, but must be recovered from the inclusion bodies. This protocol describes an efficient method for recovering HIV protease from inclusion bodies, as well as refolding and purifying the protein. HIV protease–containing inclusion bodies are treated with 8 M urea and purified via cation‐exchange chromatography. Subsequent refolding by buffer exchange via dialysis and further purification by anion‐exchange chromatography produces highly pure HIV protease that is functionally active. © 2020 by John Wiley & Sons, Inc.Basic Protocol: Recovery, refolding, and purification of HIV protease from inclusion bodiesSupport Protocol 1: Expression and extraction of inclusion bodies containing HIV protease expressed in Escherichia coliSupport Protocol 2: Determination of the active site concentration of HIV protease via isothermal titration calorimetry
Selective Electrocatalytic Oxidation of Biomass‐Derived 5‐Hydroxymethylfurfural to 2,5‐Diformylfuran: from Mechanistic Investigations to Catalyst Recovery
Authors: Kisszekelyi Peter , Hardian Rifan , Vovusha Hakkim , Chen Binglin , Zeng Xianhai , Schwingenschlögl Udo , Kupai Jozsef , Szekely Gyorgy 
Published: April 2020

AbstractThe catalytic transformation of bio‐derived compounds, specifically 5‐hydroxymethylfurfural (HMF), into value‐added chemicals may provide sustainable alternatives to crude oil and natural gas‐based products. HMF can be obtained from fructose and successfully converted to 2,5‐diformylfuran (DFF) by an environmentally friendly organic electrosynthesis performed in an ElectraSyn reactor, using cost‐effective and sustainable graphite (anode) and stainless‐steel (cathode) electrodes in an undivided cell, eliminating the need for conventional precious metal electrodes. In this work, the electrocatalysis of HMF is performed by using green solvents such as acetonitrile, γ‐valerolactone, as well as PolarClean, which is used in electrocatalysis for the first time. The reaction parameters and the synergistic effects of the TEMPO catalyst and 2,6‐lutidine base are explored both experimentally and through computation modeling. The molecular design and synthesis of a size‐enlarged C3‐symmetric tris‐TEMPO catalyst are also performed to facilitate a sustainable reaction work‐up through nanofiltration. The obtained performance is then compared with those obtained by heterogeneous TEMPO alternatives recovered by using an external magnetic field and microfiltration. Results show that this new method of electrocatalytic oxidation of HMF to DFF can be achieved with excellent selectivity, good yield, and excellent catalyst recovery.
A high‐resolution all‐digital pulse‐width modulator architecture with a tunable delay element in CMOS
Authors: Morales Juan Ignacio , Chierchie Fernando , Mandolesi Pablo Sergio , Paolini Eduardo Emilio 
Published: April 2020

SummaryA design for an all‐digital high‐resolution pulse‐width modulator (HRPWM) architecture is presented in this work. The architecture is based on a novel digitally controlled delay element that combines two different approaches, achieving a variable time interval up to 54 ps, and adjustable against process, voltage, and temperature (PVT) variations. The proposed system uses several delay elements with a counter‐based digital pulse‐width modulator (DPWM) in a hybrid configuration, which allows to obtain duty cycles with 18‐bit resolution without using a high‐frequency internal clock and maintaining a low power dissipation.The HRPWM was implemented in a standard low‐cost 130‐nm CMOS technology, together with a memory used to store the duty cycles, and a serial communication module. Post layout simulation results show good linearity between the control word and the duty cycle in all the range. The chip can be fine tuned to improve its performance using the calibration capabilities of the architecture. The analysis includes a comparison with another state‐of‐art HRPWMs showing the advantages of the proposed approach.
Flow Cytometric Monitoring of Dynamic Cytosolic Calcium, Sodium, and Potassium Fluxes Following Platelet Activation
Authors: Aliotta Alessandro , Bertaggia Calderara Debora , Alberio Lorenzo 
Published: April 2020

AbstractThe interaction of platelet agonists with their respective membrane receptors triggers intracellular signaling, among which cytosolic ion fluxes play an important role in activation processes. While the key contribution of intercellular free calcium is accepted, sodium and potassium roles in platelet activation have been less investigated in recent studies. Here, we implemented a novel flow‐cytometric method to monitor over time cytosolic free calcium, sodium, and potassium ion fluxes upon platelet activation and we demonstrate the feasibility of real‐time visualization of ion kinetics, in particular with a focus on sodium and potassium. Platelets were loaded with selective ion indicators, Fluo‐3 (Ca2+), ION NaTRIUM Green‐2 (Na+), and ION Potassium Green‐2 (K+). Fluorescence was monitored by flow cytometry. After measurement of a stable baseline, platelets were activated and ion indicator fluorescence was acquired over time, up to 10 min. Platelets were activated with either thromboxane analogue U46619, ADP, thrombin, TRAP6 (PAR‐1 agonist), AYPGKF (PAR‐4 agonist), convulxin (collagen receptor GPVI agonist), or combinations thereof. We evaluated preanalytical parameters (in particular dye loading time and concentration) to implement an accurate method. Subsequently, we characterized cytosolic calcium, sodium, and potassium kinetics in response to platelet agonists. We observed different patterns of agonist synergism. In conclusion, the present work highlights the use of cytosolic ion monitoring by flow cytometry to investigate characteristic calcium, sodium, and potassium mobilization patterns following platelet activation. This easy technique opens a new way to analyze signaling in different platelet subpopulations and it should prove useful for investigating platelet pathophysiology. © 2020 International Society for Advancement of Cytometry