bluuebunny/crossref_metadata_2025_split huggingface dataset:
Possible Intervention of Prototropic and Silatropic Ene‐type Mechanisms in Asymmetric Catalytic Mukaiyama Aldol Reactions
Authors: Honda Kazuya , Mikami Koichi 
Published: December 2013

AbstractPrototropic and silatropic ene mechanisms were analyzed in the BINOL‐TiIV, bisoxazoline (box)‐CuII, and BINAP‐PdII complex‐catalyzed asymmetric Mukaiyama aldol reaction of methyl glyoxylate and acetone‐derived 2‐trimethylsiloxypropene. Our ab initio calculations indicate that the BINOL‐TiIV‐catalyzed Mukaiyama aldol reaction proceeds through the concerted prototropic or silatropic ene pathways and that box‐CuII‐ and BINAP‐PdII‐catalyzed reactions proceed through the stepwise prototropic ene pathways. The transition‐state conformations are thus syn‐clinal with hydrogen and silane as the migratory groups aligned to the formyl oxygen atom in close syn‐clinal proximity, respectively.
Quasi All‐Silica Zeolite Obtained by Isomorphous Degermanation of an As‐Made Germanium‐Containing Precursor
Authors: Burel Laurence , Kasian Nataliia , Tuel Alain 
Published: December 2013

AbstractGe‐containing ITQ‐22 zeolites have been almost completely degermanated under strong acidic conditions without modifications of the framework topology. Simultaneous to Ge extraction, the framework was partially dissolved; mesopores were formed but the structure was maintained through the re‐incorporation of some of silicon species at vacant sites. The presence of many defects in the degermanated framework enabled the incorporation of tetrahedral aluminum, opening the way to the preparation of new and stable acid catalysts with original topologies.
Janus Nanoparticles: Preparation, Characterization, and Applications
Authors: Song Yang , Chen Shaowei 
Published: December 2013

AbstractIn chemical functionalization of colloidal particles, the functional moieties are generally distributed rather homogeneously on the particle surface. Recently, a variety of synthetic protocols have been developed in which particle functionalization may be carried out in a spatially controlled fashion, leading to the production of structurally asymmetrical particles. Janus particles represent the first example in which the two hemispheres exhibit distinctly different chemical and physical properties, which is analogous to the dual‐faced Roman god, Janus. Whereas a variety of methods have been reported for the preparation of (sub)micron‐sized polymeric Janus particles, it has remained challenging for the synthesis and (unambiguous) structural characterization of much smaller nanometer‐sized Janus particles. Herein, several leading methods for the preparation of nanometer‐sized Janus particles are discussed and the important properties and applications of these Janus nanoparticles in electrochemistry, sensing, and catalysis are highlighted. Some perspectives on research into functional patchy nanoparticles are also given.
Thermochemical biorefineries with multiproduction using a platform chemical
Authors: Haro Pedro , Villanueva Perales Ángel Luis , Arjona Ricardo , Ollero Pedro 
Published: December 2013

AbstractMultiproduction is a promising option for thermochemical biorefineries in order to reduce the risk of investment. It promotes the diversification of revenue, allows a better material and energy integration, and enhances profitability, which could improve the future development of thermochemical biorefineries. However, the design of thermochemical biorefineries with multiproduction requires of new tools and new perspectives that differ from those that have been used in the design of biomass‐to‐liquid/gas (BTL/G) processes, which are single‐product orientated. The use of a platform chemical has revealed a new field of promising possibilities for multiproduction. Nonetheless, the consideration of several kinds of final products makes difficult the calculation of the energy efficiency and the assessment of both sustainability and profitability. In the case of sustainability, it is necessary to know how to allocate the greenhouse gas (GHG) emissions of each product (including electricity) and the potential impact of the production of chemicals, which are not combusted in their final use and bring a net retention of carbon. The incorporation of bioenergy with carbon capture and storage (BECCS) is assessed as a potential income for this kind of biorefinery, which could also achieve a larger saving of GHG emissions than that regulated by European administration. The design of thermochemical biorefineries with multiproduction, in the case of using a platform chemical, are able to co‐produce low‐value high‐volume products like fuels along with high‐value low‐volume products like solvents and chemicals, which have been demonstrated by conventional oil refineries to be highly profitable. © 2013 Society of Chemical Industry and John Wiley & Sons, Ltd
Molecular dynamics simulation study on the interaction of collagen‐like peptides with gelatinase‐A (MMP‐2)
Authors: Azhagiya Singam E. R. , Rajapandian V. , Subramanian V. 
Published: December 2013

ABSTRACTAlthough several models have been proposed for the interaction of collagen with gelatinase‐A (matrix metalloproteinases‐2 (MMP‐2)), the extensive role of each domain of gelatinase A in hydrolyzing the collagens with and without interruptions is still elusive. Molecular docking, molecular dynamics (MD) simulation, normal mode analysis (NMA) and framework rigidity optimized dynamics algorithm (FRODAN) based analysis were carried out to understand the function of various domains of MMP‐2 upon interaction with collagen like peptides. The results reveal that the collagen binding domain (CBD) binds to the C‐terminal of collagen like peptide with interruption. CBD helps in unwinding the loosely packed interrupted region of triple helical structure to a greater extent. It can be possible to speculate that the role of hemopexin (HPX) domain is to prevent further unwinding of collagen like peptide by binding to the other end of the collagen like peptide. The catalytic (CAT) domain then reorients itself to interact with the part of the unwound region of collagen like peptide for further hydrolysis. In conclusion the CBD of MMP‐2 recognizes the collagen and aids in unwinding the collagen like peptide with interruptions, and the HPX domain of MMP‐2 binds to the other end of the collagen allowing CAT domain to access the cleavage site. This study provides a comprehensive understanding of the structural basis of collagenolysis by MMP‐2. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 779–794, 2014.
Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii
Authors: Ledesma‐Amaro Rodrigo , Kerkhoven Eduard J. , Revuelta José Luis , Nielsen Jens 
Published: December 2013

ABSTRACTAshbya gossypii is a filamentous fungus that naturally overproduces riboflavin, or vitamin B2. Advances in genetic and metabolic engineering of A. gossypii have permitted the switch from industrial chemical synthesis to the current biotechnological production of this vitamin. Additionally, A. gossypii is a model organism with one of the smallest eukaryote genomes being phylogenetically close to Saccharomyces cerevisiae. It has therefore been used to study evolutionary aspects of bakers' yeast. We here reconstructed the first genome scale metabolic model of A. gossypii, iRL766. The model was validated by biomass growth, riboflavin production and substrate utilization predictions. Gene essentiality analysis of the A. gossypii model in comparison with the S. cerevisiae model demonstrated how the whole‐genome duplication event that separates the two species has led to an even spread of paralogs among all metabolic pathways. Additionally, iRL766 was used to integrate transcriptomics data from two different growth stages of A. gossypii, comparing exponential growth to riboflavin production stages. Both reporter metabolite analysis and in silico identification of transcriptionally regulated enzymes demonstrated the important involvement of beta‐oxidation and the glyoxylate cycle in riboflavin production. Biotechnol. Bioeng. 2014;111: 1191–1199. © 2013 Wiley Periodicals, Inc.
DNA‐Directed Assembly of Antibody–Fluorophore Conjugates for Quantitative Multiparametric Flow Cytometry
Authors: Flor Amy C. , Williams Jimmy H. , Blaine Kelly M. , Duggan Ryan C. , Sperling Anne I. , Schwartz David A. , Kron Stephen J. 
Published: December 2013

AbstractMultiparametric flow cytometry offers a powerful approach to single‐cell analysis with broad applications in research and diagnostics. Despite advances in instrumentation, progress in methodology has lagged. Currently there is no simple and efficient method for antibody labeling or quantifying the number of antibodies bound per cell. Herein, we describe a DNA‐directed assembly approach to fluorescent labeling that overcomes these barriers. Oligonucleotide‐tagged antibodies and microparticles can be annealed to complementary oligonucleotides bearing fluorophores to create assay‐specific labeling probes and controls, respectively. The ratio of the fluorescence intensity of labeled cells to the control particles allows direct conversion of qualitative data to quantitative units of antibody binding per cell. Importantly, a single antibody can be labeled with any fluorophore by using a simple mix‐and‐match labeling strategy. Thus, any antibody can provide a quantitative probe in any fluorescent channel, thus overcoming major barriers to the use of flow cytometry as a technique for systems biology and clinical diagnostics.
High Selectivity Higher Alcohols Synthesis from Syngas over Three‐Dimensionally Ordered Macroporous Cu‐Fe Catalysts
Authors: Lu Yongwu , Cao Baobao , Yu Fei , Liu Jian , Bao Zhenghong , Gao Jinsen 
Published: December 2013

AbstractWe show that higher alcohols can be produced with high selectivity from syngas over three‐dimensionally ordered macroporous Cu–Fe catalyst. The catalyst was developed by using a glyoxylate route colloidal crystal template method. The high intrinsic activity was ascribed to three factors. First, the unique ordered structure has a large pore size and interconnected macroporous tunnels of the catalyst with a large accessible surface area improves the catalytic activity. Second, a high density of uniformly distributed defective Cu0 and χ‐Fe5C2 nanoparticles derived from the glyoxylate route helps to provide abundant, active, stable dual sites. Third, atomic steps on the Cu surface, induced by planar defects and lattice strain, serve as high‐activity oxygenation sites; and active χ‐Fe5C2 chain‐growth sites surrounds the defective and strained form of Cu surface intimately, which results in a synergetic effect between the active and stable Cu–FexCy dual sites for higher alcohols synthesis.
Activation of a Carbon Support Through a Two‐Step Wet Oxidation and Highly Active Ruthenium–Activated Carbon Catalysts for the Hydrogenation of Benzene
Authors: Li Ying , Lan Guojun , Feng Guoquan , Jiang Wei , Han Wenfeng , Tang Haodong , Liu Huazhang 
Published: December 2013

AbstractA two‐step liquid oxidation approach was developed for the activation of carbon materials. Following nitric acid treatment and subsequent liquid oxidation by a mild oxidant such as H2O2, the number of surface acidic functional groups was increased without destroying the physical structures of the carbon materials. Ruthenium catalysts supported on activated carbon prepared by this two‐step liquid oxidation method show significantly improved Ru dispersion and excellent catalytic performance in the hydrogenation of benzene. The dispersion of ruthenium and the catalytic performance of Ru/activated carbon increases monotonically with the amount of surface functional groups.
The Effect of Various Zinc Binding Groups on Inhibition of Histone Deacetylases 1–11
Authors: Madsen Andreas S. , Kristensen Helle M. E. , Lanz Gyrithe , Olsen Christian A. 
Published: December 2013

AbstractHistone deacetylases (HDACs) have the ability to cleave the acetyl groups of ε‐N‐acetylated lysine residues in a variety of proteins. Given that human cells contain thousands of different acetylated lysine residues, HDACS may regulate a wide variety of processes including some implicated in conditions such as cancer and neurodegenerative disorders. Herein we report the synthesis and in vitro biochemical profiling of a series of compounds, including known inhibitors as well as novel chemotypes, that incorporate putative new zinc binding domains. By evaluating the compound collection against all 11 recombinant human HDACs, we found that the trifluoromethyl ketone functionality provides potent inhibition of all four subclasses of the Zn2+‐dependent HDACs. Potent inhibition was observed with two different scaffolds, demonstrating the efficiency of the trifluoromethyl ketone moiety as a zinc binding motif. Interestingly, we also identified silanediol as a zinc binding group with potential for future development of non‐hydroxamate class I and class IIb HDAC inhibitors.
N‐Cinnamoylation of Antimalarial Classics: Quinacrine Analogues with Decreased Toxicity and Dual‐Stage Activity
Authors: Gomes Ana , Pérez Bianca , Albuquerque Inês , Machado Marta , Prudêncio Miguel , Nogueira Fátima , Teixeira Cátia , Gomes Paula 
Published: December 2013

AbstractPlasmodium falciparum, the causative agent of the most lethal form of malaria, is becoming increasingly resistant to most available drugs. A convenient approach to combat parasite resistance is the development of analogues of classical antimalarial agents, appropriately modified in order to restore their relevance in antimalarial chemotherapy. Following this line of thought, the design, synthesis and in vitro evaluation of N‐cinnamoylated quinacrine surrogates, 9‐(N‐cinnamoylaminobutyl)‐amino‐6‐chloro‐2‐methoxyacridines, is reported. The compounds were found to be highly potent against both blood‐stage P. falciparum, chloroquine‐sensitive 3D7 (IC50=17.0–39.0 nM) and chloroquine‐resistant W2 and Dd2 strains (IC50=3.2–41.2 and 27.1–131.0 nM, respectively), and liver‐stage P. berghei (IC50=1.6–4.9 μM) parasites. These findings bring new hope for the possible future “rise of a fallen angel” in antimalarial chemotherapy, with a potential resurgence of quinacrine‐related compounds as dual‐stage antimalarial leads.
Studying the influence of hydrogel injections into the infarcted left ventricle using the element‐free Galerkin method
Authors: Legner D. , Skatulla S. , MBewu J. , Rama R. R. , Reddy B. D. , Sansour C. , Davies N. H. , Franz T. 
Published: December 2013

SUMMARYMyocardial infarction is an increasing health problem worldwide. Because of an under‐supply of blood, the cardiomyocytes in the affected region permanently lose their ability to contract. This in turn gradually weakens the overall heart function. A new therapeutic approach based on the injection of a gel into the infarcted area aims to support the healing and to inhibit adverse remodelling that can lead to heart failure. A computational model is the basis for obtaining a better understanding of the heart mechanics, in particular, how myocardial infarction and gel injections affect its pumping performance. A strain invariant‐based stored energy function is proposed to account for the passive mechanical behaviour of the model, which also makes provision for active contraction. To incorporate injections an additive homogenization approach is introduced. The numerical framework is developed using an in‐house code based on the element‐free Galerkin method. The main focus of this contribution is to investigate the influence of gel injections on the mechanics of the left ventricle during the diastolic filling and systolic isovolumetric (isochoric) contraction phases. It is found that gel injections are able to reduce the elevated fibre stresses caused by an infarct. Copyright © 2013 John Wiley & Sons, Ltd.
Design and performance characterization of electronic structure calculations on massively parallel supercomputers: a case study of GPAW on the Blue Gene/P architecture
Authors: Romero N.A. , Glinsvad C. , Larsen A.H. , Enkovaara J. , Shende S. , Morozov V.A. , Mortensen J.J. 
Published: December 2013

SUMMARYDensity function theory (DFT) is the most widely employed electronic structure method because of its favorable scaling with system size and accuracy for a broad range of molecular and condensed‐phase systems. The advent of massively parallel supercomputers has enhanced the scientific community's ability to study larger system sizes. Ground‐state DFT calculations on ∼ 103 valence electrons using traditional algorithms can be routinely performed on present‐day supercomputers. The performance characteristics of these massively parallel DFT codes on > 104 computer cores are not well understood. The GPAW code was ported an optimized for the Blue Gene/P architecture. We present our algorithmic parallelization strategy and interpret the results for a number of benchmark test cases.Copyright © 2013 John Wiley & Sons, Ltd.
Tunable Surface‐Enhanced Raman Scattering from High‐Density Gold Semishell Arrays with Controllable Dimensions
Authors: Lang Xianzhong , Li Jiaqi , Luo Xiaoguang , Zhang Yan , Yin Yin , Qiu Teng 
Published: December 2013

AbstractA convenient reproducible technique is reported for the fabrication of large‐area gold semishell arrays by mechanically pressing porous anodic alumina (PAA) stamps into gold/polymer bilayer structures that serve as robust and cost‐efficient surface‐enhanced Raman‐scattering (SERS) substrates. The surface structure can be tuned further to optimize the enhancement factor according to optional PAA fabrication parameters and imprinting pressures. Finite‐difference time‐domain calculations indicate that the structure may possess excellent SERS characteristics due to the high density and abundance of hot spots.
The Non‐Ergodic Nature of Internal Conversion
Authors: Sølling Theis I. , Kuhlman Thomas S. , Stephansen Anne B. , Klein Liv B. , Møller Klaus B. 
Published: December 2013

AbstractThe absorption of light by molecules can induce ultrafast dynamics and coupling of electronic and nuclear vibrational motion. The ultrafast nature in many cases rests on the importance of several potential energy surfaces in guiding the nuclear motion—a concept of central importance in many aspects of chemical reaction dynamics. This Minireview focuses on the non‐ergodic nature of internal conversion, that is, on the concept that the nuclear dynamics only sample a reduced phase space, potentially resulting in localization of the dynamics in real space. A series of results that highlight the nonstatistical nature of the excited‐state deactivation process is presented. The examples are categorized into four groups. 1) Localization of the energy in one degree of freedom in S2→S1 transitions, in which the transition is either determined by the time spent in the S2→S1 coupling region or by the time it takes to reach it. 2) Localization of energy into a single reactive mode, which is dictated by the internal conversion process. 3) Initiation of the internal conversion by activation of a single complex motion, which then specifically couples to a reactive mode. 4) Nonstatistical internal conversion as a tool to accomplish biomolecular stability. Herein, the discussion on nonstatistical internal conversion in DNA as a mechanism to eliminate electronic excitation energy is extended to include molecules with an SS bond as a model of the disulfide bridge in peptides. All of these examples are summed up in Kasha’s rule. For systems with multiple degrees of freedom it will be possible to locate an appropriate motion somewhere in phase space that will take the wavepacket to the coupling region and facilitate an ultrafast transition to S1. Once at S1, the momentum of the wavepacket is lost and the only options left are the statistical processes of reaction or light emission.
Performance analysis of multi‐input multi‐output systems with maximum likelihood detection over shadowed fading channels
Authors: Leib Harry , Lin Wenjing 
Published: December 2013

SummaryMultiple‐input multiple‐output (MIMO) transmission techniques constitute an important technology in modern wireless communication. Hence, performance analysis methods for such systems are of considerable interest. This paper considers first the average pairwise error probability for uncoded MIMO systems employing maximum likelihood detection over a composite Rayleigh‐Lognormal fading channel with spatial correlation. It provides general results, applicable also to a wider class of shadowing models, concerning asymptotical diversity gains and shows that they are not changed by such shadowing. Then, analytical evaluation techniques for bit‐error‐rate (BER) over composite Rayleigh‐Lognormal fading channels, based on the truncated union bound and the transfer function, are considered. Furthermore, these techniques are modified for applications over spatially correlated channels. This paper shows that such performance evaluation techniques provide good approximations to BER of spatially uncorrelated MIMO systems and also in the presence of moderate spatial correlation, over Rayleigh‐Lognormal fading channels. Copyright © 2013 John Wiley & Sons, Ltd.
Quinic Acid Derivative KZ‐41 Exhibits Radiomitigating Activity in Preclinical Models of Radiation Injury
Authors: Thompson Karin E. , Zeng Kui , Wilson Christy M. , Gaber Mostafa W. , Miller Duane D. , Yates Charles R. 
Published: December 2013

Abstract

Preclinical Research

Acute radiation syndrome is induced when a significant portion of the body receives high‐dose, as well as high‐dose rate, radiation. We have previously identified a quinic acid‐based derivative, KZ‐41, that protects from radiation injury. Further preclinical efficacy studies were conducted to determine the radiomitigating activity of KZ‐41. C57BL/6 mice received total body irradiation (TBI—LD80/30, 137Cs; ∼2 min) followed by either normal saline or KZ‐41 (100 mg/kg sc ∼26 h post‐TBI). KZ‐41 increased 30‐day survival by approximately 45% compared with vehicle controls (P < 0.05). To further investigate the potential radiomodulating mechanisms of KZ‐41, we developed a combined radiation and vascular injury model. C57BL/6 mice surgically fixed with dorsal windows for dermal vasculature imaging received either sham or TBI (137Cs; 6 Gray). Postcapillary venule injury was induced (24, 48, 72, and 96 h post‐TBI) followed by imaging at 5 min and 24 h to assess clot formation and blood flow. Impairment in flow (P < 0.05) and clot formation (P < 0.05) were observed as early as 48 and 72 h, respectively. Thus, vascular injury 72 h post‐TBI was used to evaluate intervention (KZ‐41; 100 mg/kg i.p. at 12, 36, and 60 h post‐TBI) on radiation‐induced changes in both flow and clot formation. KZ‐41, although not improving flow, increased clot formation (P < 0.05). Platelet counts were lower in both irradiated groups compared with sham controls (P < 0.05). In summary, KZ‐41 exerts radiomitigating activity in lethally irradiated mice. Imaging results suggest KZ‐41 exerts radiomitigating activity through mechanisms involving promotion of initial clot formation and vascular flow restoration. The imaging model described herein is useful for further examination of radiation‐induced vascular injury repair mechanisms.