bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO
Authors: Lo Feng‐Chun , Hsieh Chang‐Chih , Maestre‐Reyna Manuel , Chen Chin‐Yu , Ko Tzu‐Ping , Horng Yih‐Chern , Lai Yei‐Chen , Chiang Yun‐Wei , Chou Chih‐Mao , Chiang Cheng‐Hung , Huang Wei‐Ning , Lin Yi‐Hung , Bohle D. Scott , Liaw Wen‐Feng 
Published: June 2016

AbstractMolecular mechanisms underlying the repair of nitrosylated [Fe–S] clusters by the microbial protein YtfE remain poorly understood. The X‐ray crystal structure of YtfE, in combination with EPR, magnetic circular dichroism (MCD), UV, and 17O‐labeling electron spin echo envelope modulation measurements, show that each iron of the oxo‐bridged FeII–FeIII diiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates and two terminal histidines in addition to an oxo‐bridge. Structural analysis reveals that there are two solvent‐accessible tunnels, both of which converge to the diiron center and are critical for capturing substrates. The reactivity of the reduced‐form FeII–FeII YtfE toward nitric oxide demonstrates that the prerequisite for N2O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation of the two iron sites prior to their reductive coupling to produce N2O is cooperative. This result suggests that, in addition to any repair of iron centers (RIC) activity, YtfE acts as an NO‐trapping scavenger to promote the NO to N2O transformation under low NO flux, which precedes nitrosative stress.
Kinetics and Mechanism of the Reaction of a Ruthenium(VI) Nitrido Complex with HSO3− and SO32− in Aqueous Solution
Authors: Wang Qian , Zhao Hong Yan , Man Wai‐Lun , Lam William W. Y. , Lau Kai‐Chung , Lau Tai‐Chu 
Published: June 2016

AbstractThe kinetics and mechanism of the reaction of SIV (SO32−+HSO3−) with a ruthenium(VI) nitrido complex, [(L)RuVI(N)(OH2)]+ (RuVIN, L=N,N′‐bis(salicylidene)‐o‐cyclohexyldiamine dianion), in aqueous acidic solutions are reported. The kinetic results are consistent with parallel pathways involving oxidation of HSO3− and SO32− by RuVIN. A deuterium isotope effect of 4.7 is observed in the HSO3− pathway. Based on experimental results and DFT calculations the proposed mechanism involves concerted N−S bond formation (partial N‐atom transfer) between RuVIN and HSO3− and H+ transfer from HSO3− to a H2O molecule.
Two‐Dimensional Ketone‐Driven Metal–Organic Coordination on Cu(111)
Authors: Della Pia Ada , Riello Massimo , Lawrence James , Stassen Daphne , Jones Tim S. , Bonifazi Davide , De Vita Alessandro , Costantini Giovanni 
Published: June 2016

AbstractInvited for the cover of this issue is a collaboration between the groups of D. Bonifazi (University of Namur, Cardiff University), A. De Vita (King's College London), and G. Costantini (University of Warwick). The shape of a scanning tunneling microscopy image of filament structures formed when pyrene 4,5,9,10‐tetraone is co‐deposited with iron on a Cu(111) surface is where the inspiration for the cover image created by the artist Mary Courtney came from. Read the full text of the article at 10.1002/chem.201600368.
Deep‐Ultraviolet Nonlinear Optics in a Borate Framework with 21‐Ring Channels
Authors: Wei Qi , Wang Jia‐Jia , He Chao , Cheng Jian‐Wen , Yang Guo‐Yu 
Published: June 2016

AbstractA new borate LiBa3(OH)[B9O16][B(OH)4], which combines the uniform porosity of open‐frameworks with the extraordinary NLO properties of borates, has been obtained under hydrothermal conditions by using mixed lithium and barium ions as templates. The framework displays an acs‐type net with large 21‐ring channels. The second harmonic generation (SHG) measurement shows that it is a type I phase‐matchable material with a strong SHG signal intensity about 3.1 times that of KDP (KH2PO4). UV/Vis–NIR diffuse reflectance analysis indicates that the compound has a wide transparency range with the short‐wavelength absorption edge below 200 nm. These characteristics reveal that the compound is a promising deep‐UV nonlinear optical material.
Electronic Modulation of the SOMO–HOMO Energy Gap in Iron(III) Complexes towards Unimolecular Current Rectification
Authors: Wickramasinghe Lanka D. , Mazumder Shivnath , Kpogo Kenneth K. , Staples Richard J. , Schlegel H. Bernhard , Verani Cláudio N. 
Published: June 2016

AbstractAmphiphilic five‐coordinate iron(III) complexes with {N2O2Cl} and {N2O3} coordination spheres are studied to elucidate the roles of electronic structure on the mechanisms for current rectification. The presence of an apical chlorido or phenolato ligand plays a crucial role, and the [FeIII{N2O2Cl}] species supports an asymmetric mechanism while its [FeIII{N2O3}] counterpart seems to allow for unimolecular mechanism. The effects of electron‐donating and electron‐withdrawing substituents in the ligand frameworks are also considered.
Diffusion of Large Nitrogen Bubbles into Tap Water Studied by the Rotary Chamber Technique
Authors: Nüllig Marius , Peters Franz 
Published: June 2016

AbstractThe rotary chamber technique allows extended observation times of rising bubbles up into the 10‐mm range. After establishing the technique in combination with optical sizing in previous publications, this work completes the case of nitrogen bubbles in tap water. The rise velocity and the mass transfer are measured for five degrees of water saturation. A one‐parameter model equation involving the Archimedes number is offered for calculation. The limit of the analytical boundary layer model is depicted.
A Potent Inhibitor of Protein Sequestration by Expanded Triplet (CUG) Repeats that Shows Phenotypic Improvements in a Drosophila Model of Myotonic Dystrophy
Authors: Luu Long M. , Nguyen Lien , Peng Shaohong , Lee JuYeon , Lee Hyang Yeon , Wong Chun‐Ho , Hergenrother Paul J. , Chan H. Y. Edwin , Zimmerman Steven C. 
Published: June 2016

AbstractMyotonic dystrophy is the most common form of adult‐onset muscular dystrophy, originating in a CTG repeat expansion in the DMPK gene. The expanded CUG transcript sequesters MBNL1, a key regulator of alternative splicing, leading to the misregulation of numerous pre‐mRNAs. We report an RNA‐targeted agent as a possible lead compound for the treatment of myotonic dystrophy type 1 (DM1) that reveals both the promise and challenges for this type of small‐molecule approach. The agent is a potent inhibitor of the MBNL1–rCUG complex with an inhibition constant (Ki) of 25±8 nm, and is also relatively nontoxic to HeLa cells, able to dissolve nuclear foci, and correct the insulin receptor splicing defect in DM1 model cells. Moreover, treatment with this compound improves two separate disease phenotypes in a Drosophila model of DM1: adult external eye degeneration and larval crawling defect. However, the compound has a relatively low maximum tolerated dose in mice, and its cell uptake may be limited, providing insight into directions for future development.
Fluorescent Detection of Lipid Droplets and Associated Proteins
Authors: Listenberger Laura L. , Studer Andrea M. , Brown Deborah A. , Wolins Nathan E. 
Published: June 2016

AbstractExcess lipid is stored in intracellular organelles known as lipid droplets. This unit discusses techniques for the visualization of lipid droplets and associated proteins in cultured mammalian cells. Protocols for the detection of lipid droplets in fixed or live cells with BODIPY 493/503 are included. The best method for combining visualization of intracellular lipid droplets with indirect immunofluorescent detection of lipid droplet–associated proteins is described. Techniques for sample fixation and permeabilization must be chosen carefully to avoid alterations to lipid droplet morphology. Immunofluorescent detection of perilipin 2, a broadly expressed, lipid droplet–associated protein, widely used as a marker for lipid droplet accumulation, is presented as an example. Finally, a simple protocol for enhancing lipid droplet accumulation through supplementation with excess fatty acid is included. © 2016 by John Wiley & Sons, Inc.
Fluorescence Dynamics in the Endoplasmic Reticulum of a Live Cell: Time‐Resolved Confocal Microscopy
Authors: Ghosh Shirsendu , Nandi Somen , Ghosh Catherine , Bhattacharyya Kankan 
Published: June 2016

AbstractFluorescence dynamics in the endoplasmic reticulum (ER) of a live non‐cancer lung cell (WI38) and a lung cancer cell (A549) are studied by using time‐resolved confocal microscopy. To selectively study the organelle, ER, we have used an ER‐Tracker dye. From the emission maximum
of the ER‐Tracker dye, polarity (i.e. dielectric constant, ϵ) in the ER region of the cells (≈500 nm in WI38 and ≈510 nm in A549) is estimated to be similar to that of chloroform (
=506 nm, ϵ≈5). The red shift by 10 nm in
in the cancer cell (A549) suggests a slightly higher polarity compared to the non‐cancer cell (WI38). The fluorescence intensity of the ER‐Tracker dye exhibits prolonged intermittent oscillations on a timescale of 2–6 seconds for the cancer cell (A549). For the non‐cancer cell (WI38), such fluorescence oscillations are much less prominent. The marked fluorescence intensity oscillations in the cancer cell are attributed to enhanced calcium oscillations. The average solvent relaxation time (<τs>) of the ER region in the lung cancer cell (A549, 250±50 ps) is about four times faster than that in the non‐cancer cell (WI38, 1000±50 ps).
Amphiphilic Carbonaceous Microsphere‐Stabilized Oil‐in‐Water Pickering Emulsions and Their Applications in Enzyme Catalysis
Authors: Liu Li , Jiang Linlin , Xie Xiaomin , Yang Sen 
Published: June 2016

AbstractAn oil‐in‐water Pickering emulsion system stabilized by amphiphilic porous carbonaceous microspheres was prepared and successfully used in enzyme‐catalyzed hydrolysis. The control of the emulsion droplet size and size distribution were investigated by adjusting the particle content and the dispersed phase volume fraction. More than 99 % of the lipase was adsorbed at the interface of the emulsion droplets and showed excellent stability and activity. The size of the emulsion droplets exerted two opposite influences on the catalytic efficiency of the enzyme: increasing the rate of the process by providing a large interfacial area, thereby overcoming mass transfer limitations, and reducing the rate of the process by decreasing the interfacial enzyme concentration. A high hydrolysis yield (up to 100 %) was obtained after 2 h. This study shows the great potential and advantages of using an oil‐in‐water Pickering emulsion system for enzyme‐catalyzed reactions.
Mouse Models of Asthma
Authors: Debeuf Nincy , Haspeslagh Eline , van Helden Mary , Hammad Hamida , Lambrecht Bart N. 
Published: June 2016

AbstractAllergic asthma is a chronic inflammatory disease of the conducting airways characterized by the presence of allergen‐specific IgE, Th2 cytokine production, eosinophilic airway inflammation, bronchial hyperreactivity, mucus overproduction, and structural changes in the airways. Investigators have tried to mimic these features of human allergic asthma in murine models. Whereas the surrogate allergen ovalbumin has been extremely valuable for unravelling underlying mechanisms of the disease, murine asthma models depend nowadays on naturally occurring allergens, such as house dust mite (HDM), cockroach, and Alternaria alternata. Here we describe a physiologically relevant model of acute allergic asthma based on sensitization and challenge with HDM extracts, and compare it with the ovalbumin/alum‐induced asthma model. Moreover, we propose a detailed readout of the asthma phenotype, determining the degree of eosinophilia in bronchoalveolar lavage fluids by flow cytometry, visualizing goblet cell metaplasia, and measuring Th cytokine production by lung‐draining mediastinal lymph node cells restimulated with HDM. © 2016 by John Wiley & Sons, Inc.
Diffraction Techniques in Structural Biology
Authors: Egli Martin 
Published: June 2016

AbstractA detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic‐resolution structural data. Diffraction‐based techniques such as single‐crystal X‐ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern‐day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high‐speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single‐crystal X‐ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping‐stone to more in‐depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc.
Selection of Natural and Base‐Modified DNA Aptamers for a Camptothecin Derivative
Authors: Fujita Hiroto , Kuwahara Masayasu 
Published: June 2016

AbstractNucleic acid aptamers for small molecules are currently being developed and have a potential role in diverse applications including biosensing, diagnostics, and therapeutics involving low‐molecular‐weight biomarkers and drugs. To enhance and broaden their functions through chemical modification, systematic evolution of ligands by exponential enrichment (SELEX) selection has been attempted with modified DNA/RNA libraries. Recently, we demonstrated the superior efficacy of base modification for affinity enhancement and the usefulness of unnatural nucleic acid libraries for development of small‐molecule aptamers. In this unit, we describe construction of a modified DNA library that includes (E)‐5‐(2‐(N‐(2‐(N
6‐adeninyl)ethyl))carbamylvinyl)uracil bases and acquisition of high‐affinity camptothecin‐binding DNA aptamers, in addition to those of the corresponding natural DNA library and aptamers, using the SELEX method. © 2016 by John Wiley & Sons, Inc.
Gravitational outlier detection for wireless sensor networks
Authors: Bharti Sourabh , Pattanaik Kiran K. 
Published: June 2016

SummaryAccuracy of sensed data and reliable delivery are the key concerns in addition to several other network‐related issues in wireless sensor networks (WSNs). Early detection of outliers reduces subsequent unwanted transmissions, thus preserving network resources. Recent techniques on outlier detection in WSNs are computationally expensive and based on message exchange. Message exchange‐based techniques incur communication overhead and are less preferred in WSNs. On the other hand, machine learning‐based outlier detection techniques are computationally expensive for resource constraint sensor nodes. The novelty of this paper is that it proposes a simple, non message exchange based, in‐network, real‐time outlier detection algorithm based on Newton's law of gravity. The mechanism is evaluated for its accuracy in detecting outliers, computational cost, and its influence on the network traffic and delay. The outlier detection mechanism resulted in almost 100% detection accuracy. Because the mechanism involves no message exchanges, there is a significant reduction in network traffic, energy consumption and end‐to‐end delay. An extension of the proposed algorithm for transient data sets is proposed, and analytic evaluation justifies that the mechanism is reactive to time series data. Copyright © 2016 John Wiley & Sons, Ltd.
Affinity Biosensors for Detection Immunoglobulin E and Cellular Prions. Antibodies vs. DNA Aptamers
Authors: Hianik Tibor 
Published: June 2016

AbstractImmunosensors for detection of proteins are of high importance for medical diagnostics. There exists continuous effort in their development using new methods of antibody immobilizations at the various surfaces including novel nanomaterials, such as carbon nanotubes, graphene, dendrimers and combination of these materials with nanoparticles of various origin. At the same time as an alternative to antibodies DNA or RNA aptamers are considered as novel receptors during last 2 decades. In contrast with antibodies aptamers are more flexible and stable, allowing various chemical modification without lost of their sensitivity. This review compares the properties of existing immuno‐ and aptasensors for detection human immunoglobulin E (IgE) and cellular prions (PrPC). It has been shown, that both immuno‐ and aptasensors are of comparable sensitivity and selectivity that depends on the method of receptor immobilization and detection.
Quick Determination of Electroactive Surface Area of Some Oxide Electrode Materials
Authors: Watzele Sebastian , Bandarenka Aliaksandr S. 
Published: June 2016

AbstractQuick and accurate determination of the real electroactive surface area of oxide electrodes remains one of the most challenging but at the same time important unsolved methodological tasks in the field of electroanalysis. For instance, the widely used Brunauer−Emmett−Teller (BET) method unfortunately provides no direct connection to it. On the other hand, its assessment through the double layer capacitance is complicated and not accurate enough, as the bulk oxide films themselves contribute to the measured capacitance, not mentioning the double layer frequency dispersion and other poorly understood factors. In this work, we propose a relatively simple methodology for a quick assessment of the electroactive surface area of some electron conducting oxide and perovskite materials. The methodology involves several steps. Initially, “calibration” experiments are performed aiming to form the thinnest (practically below ∼100–200 nm) flat oxide films, which exhibit necessary functional properties (close to those expected for the bulk material) without significant side influence of the substrate. Then, AFM measurements are implemented to estimate the surface roughness of the resulting samples. Finally, electrochemical impedance measurements are done at a small overpotential related to the oxygen evolution reaction (OER) aiming to extract not the double layer but the capacitance of adsorption Ca of the OER intermediates. The Ca values can then be used to evaluate the electroactive surface area of “real‐world” high surface area oxide electrodes composed of the same material. Other words, similar to the hydrogen underpotential deposition or CO oxidation in the case of metals, we propose to use the oxygen evolution reaction as the probing reaction to evaluate the surface area of oxide electrocatalysts. However, instead of cyclic voltammetry, electrochemical impedance spectroscopy is used as the main probing technique. Due to relatively high reproducibility, clear physical meaning and exclusive connection to the electroactive area, the measurements of Ca can become a viable method in numerous electrochemical applications. An example using Ni‐oxide electrodes is given to illustrate the methodology.
Graphical methods of river profile analysis to unravel drainage area change, uplift and erodibility contrasts in the Central Range of Taiwan
Authors: Chen Chia‐Yu , Willett Sean D. 
Published: June 2016

AbstractTo reveal river channel steepness patterns and variance in settings with significant variation in rock uplift rate, rock erodibility and moving water divides, we present a series of graphical methods to interpret channel profiles. To complement Cartesian χ plots, longitudinal profiles and mapping methods, we introduce a new method based on a radial coordinate system. We map each basin onto polar coordinates in which the radial dimension is χ and the azimuthal coordinate, ϕ, is calculated with an increment (Δϕ) scaled to the distance to neighboring channel heads. The elevation is contoured on this mapping. Average channel steepness is estimated by fitting a conical surface to the elevation. The graph simplifies the comparison of χ and elevation between channels that share a divide, and helps identify spatial changes in drainage area and patterns of erodibility.We apply this approach to derive the uplift pattern in the eastern and southern Central Range of Taiwan, where the high tectonic convergence and uplift rates combined with sub‐tropical climate and frequent typhoons results in high exhumation rate, and well‐developed, detachment‐limited river networks. Additionally, the tectonic activity leads to drainage basin reorganization. We identify examples of divide migration, discrete river capture as well as anomalous steepness that we attribute to local variability in rock erodibility.Estimated basin‐average steepness values show the highest and a near constant value from Hsinwulu basin to Liwu basin in the center of the Island. To the north and south of this region, the values gradually decrease. These estimates show good correlation with the topography of the Central Range and erosion rates derived from in situ 10Be concentrations in river‐borne quartz. We conclude that the basin steepness reflects systematic differences in rock uplift rate and erosion rate. Copyright © 2016 John Wiley & Sons, Ltd.
Removal of cadmium from contaminated Lentinula edodes by optimized complexation and coagulation
Authors: Wang Yi , Wang Chen , Cheng Wei , Bian Yinbing , Guo Peng 
Published: June 2016

AbstractHeavy metal pollution is a serious problem for Lentinula edodes; however, the treatment of contaminated L. edodes has seldom been studied. This study investigated the removal of cadmium (Cd) from contaminated L. edodes and its lentinan by complexation and coagulation. Some influencing factors, such as pH, medical dosage, and preoxidation were examined. Cd complexation from contaminated L. edodes was shown to be more efficient under acidic conditions (pH 5.0), with a clearance rate of 80.47% in 25 mmol/L EDTA and 78.45% in 25 mmol/L sodium citrate. The Cd content in the lentinan of the contaminated L. edodes was markedly lower than that in the powdered mushroom (2.77 mg/kg vs. 19.49 mg/kg) and was easier to remove. The maximum Cd clearance rate (96.3%) for lentinan was obtained using an optimized process that involved preoxidation with 0.5 mg/L KMnO4, complexing with 25 mmol/L EDTA and 25 mmol/L sodium citrate, and coagulation with 50 mg/L activated carbon (AC) at pH 10.0.