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Chen Ling - - 2012
Improving traditional crown ether to the water-soluble and high binding ability host molecule is critical to our efforts to model or mimic biological supramolecular systems. In this paper, we converted two traditional crown ethers 1,5-dinaphtho-32-crown-8 and 1,5-dinaphtho-38-crown-10 into the water-soluble tetrasulfonated 1,5-dinaphtho-32-crown-8 and tetrasulfonated 1,5-dinaphtho-38-crown-10, evaluated their complexation with three ...
Abdollah Firas - - 2012
OBJECTIVES: The 2004 National Comprehensive Cancer Network practice guidelines recommend pelvic lymph node dissection at radical prostatectomy. We sought to examine the adherence to the 2004 National Comprehensive Cancer Network guidelines and to test the their accuracy, as well as the accuracy of the most contemporary National Comprehensive Cancer Network, ...
Sharma Anshuman - - 2012
Aim:  Congenital lumbar hernia is an uncommon anomaly with only few cases reported in the English literature. This study was done to study the incidence, associated conditions, management and complications of congenital lumbar hernia repair in paediatric patients. Methods:  Retrospective study of all patients over a period of 20 years ...
Toffoli Daniele - - 2012
A general implementation of the lowest nonvanishing order perturbation theory for the calculation of molecular multiphoton ionization cross sections is proposed in the framework of density functional theory. Bound and scattering wave functions are expanded in a multicentric basis set and advantage is taken of the full molecular point group ...
Amano T - - 2012
In view of recent tremendous advance in astronomical observations in the submillimeter to THz region brought by the Herschel space craft, laboratory high-resolution spectroscopic investigations in that frequency region into unstable molecules, in particular, light hydride ions, are urgently needed. As a part of such endeavor, rotational transitions of H(2)F(+) ...
Ferrara C Gastón - - 2012
Due to the importance of the hydrophobic interaction in protein folding, we decided to study the effect of pressure and temperature on the phase transitions of non-polar solutes in water, and thereby their solubility, using molecular dynamics simulations. The main results are: (1) within a certain range, temperature induces the ...
Vynck Kevin - - 2012
Elaborating reliable and versatile strategies for efficient light coupling between free space and thin films is of crucial importance for new technologies in energy efficiency. Nanostructured materials have opened unprecedented opportunities for light management, notably in thin-film solar cells. Efficient coherent light trapping has been accomplished through the careful design ...
Bowman Gregory R - - 2012
Markov state models (MSMs)--or discrete-time master equation models--are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative connection with experiments (often tens of thousands of states even for small systems) are generally too complicated to ...
Yuan Wei - - 2012
Electrospinning provides a versatile method for generating fibrous materials from a large variety of substances, including polymers, composites, proteins and nano/micro colloids. In particular, the incorporation of nano/micro particles with polymeric materials is beneficial to many of electrospun fibers with multiple functionalities. This report evaluates the spinnability of a polymer ...
Mosbech Anna - - 2012
Ubiquitin-mediated processes orchestrate critical DNA-damage signaling and repair pathways. We identify human DVC1 (C1orf124; Spartan) as a cell cycle-regulated anaphase-promoting complex (APC) substrate that accumulates at stalled replication forks. DVC1 recruitment to sites of replication stress requires its ubiquitin-binding UBZ domain and PCNA-binding PIP box motif but is independent of ...
McLaughlin Richard N RN Jr Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, - - 2012
Statistical analysis of protein evolution suggests a design for natural proteins in which sparse networks of coevolving amino acids (termed sectors) comprise the essence of three-dimensional structure and function. However, proteins are also subject to pressures deriving from the dynamics of the evolutionary process itself--the ability to tolerate mutation and ...
Cerioni Alessandro - - 2012
We present an explicit solver of the three-dimensional screened and unscreened Poisson's equation, which combines accuracy, computational efficiency, and versatility. The solver, based on a mixed plane-wave/interpolating scaling function representation, can deal with any kind of periodicity (along one, two, or three spatial axes) as well as with fully isolated ...
Beltran-Villegas Daniel J - - 2012
The crystallization dynamics of a colloidal cluster is modeled using a low-dimensional Smoluchowski equation. Diffusion mapping shows that two order parameters are required to describe the dynamics. Using order parameters as metrics for condensation and crystallinity, free energy, and diffusivity landscapes are extracted from Brownian dynamics simulations using Bayesian inference. ...
Metzger Louis E LE - - 2012
Enzymes in lipid metabolism acquire and deliver hydrophobic substrates and products from within lipid bilayers. The structure at 2.55 Å of one isozyme of a constitutive enzyme in lipid A biosynthesis, LpxI from Caulobacter crescentus, has a novel fold. Two domains close around a completely sequestered substrate, UDP-2,3-diacylglucosamine, and open ...
Jakubec Pavol - - 2012
Total syntheses of three structurally complex marine natural products manzamine A, ircinol A, ircinal A are reported. The route pivoted on the construction of a late stage protecting group-free pentacyclic enol triflate coupling partner, from which all three family members were divergently accessed via palladium catalyzed reactions. The rapid synthesis ...
Baniecki Mary Lynn ML Biology Department, Brookhaven National Laboratory, Upton, New York 11973, - - 2013
The adenovirus proteinase (AVP), the first member of a new class of cysteine proteinases, is essential for the production of infectious virus, and here we report its structure at 0.98 Å resolution. AVP, initially synthesized as an inactive enzyme, requires two cofactors for maximal activity: pVIc, an 11-amino acid peptide, ...
Deguchi Kazuhiko - - 2012
Quasicrystals are metallic alloys that possess long-range, aperiodic structures with diffraction symmetries forbidden to conventional crystals. Since the discovery of quasicrystals by Schechtman et al. in 1984, there has been considerable progress in resolving their geometric structure. For example, it is well known that the golden ratio of mathematics and art ...
Galbán Craig J CJ Department of Radiology, University of Michigan, Ann Arbor, MI, - - 2012
Chronic obstructive pulmonary disease (COPD) is increasingly being recognized as a highly heterogeneous disorder, composed of varying pathobiology. Accurate detection of COPD subtypes by image biomarkers is urgently needed to enable individualized treatment, thus improving patient outcome. We adapted the parametric response map (PRM), a voxel-wise image analysis technique, for ...
Wang Hsun-Mo - - 2012
Abstract Conclusion: The percentage of the unilateral weakness of the caloric response also reflects the clinical progress of Meniere's disease (MD), including clinical hearing loss. Objective: To evaluate the relationship between hearing status and vestibular function in patients with MD. Methods: Seventy-nine patients with unilateral definite MD underwent bithermal air ...
Dethoff Elizabeth A - - 2012
The visualization of RNA conformational changes has provided fundamental insights into how regulatory RNAs carry out their biological functions. The RNA structural transitions that have been characterized so far involve long-lived species that can be captured by structure characterization techniques. Here we report the nuclear magnetic resonance visualization of RNA ...
Yasuda Satoshi - - 2012
A protein folds into its native structure with the α-helix and∕or β-sheet in aqueous solution under the physiological condition. The relative content of these secondary structures largely varies from protein to protein. However, such structural variability is not exhibited in nonaqueous environment. For example, there is a strong trend that ...
Graziano Vito V Biology Department, Brookhaven National Laboratory, Upton, New York 11973, - - 2013
The precursor to adenovirus protein VI, pVI, is a multifunctional protein with different roles early and late in virus infection. Here, we focus on two roles late in infection, binding of pVI to DNA and to the major capsid protein hexon. pVI bound to DNA as a monomer independent of ...
Moon Tae Seok TS Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, - - 2012
Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the implementation of process control in ...
Xu Qianqian - - 2012
Wall-coated open-tubular (WCOT) columns provide higher column efficiency and lower solute interfacial adsorption effect than packed columns. However, previous efforts used to measure infinite dilution activity coefficient (γ∞) via a chromatographic technique have used packed columns, because the low carrier gas flow rate (U) and the small stationary phase amount ...
Rana Malay Kumar - - 2012
Molecular dynamics simulations have been performed to investigate the solvation characteristics of neutral fullerene (C(60)) and charged fulleride anion (C(60) (5-)) in liquid ammonia. Potassium ions are present as counterions in the system containing fulleride ion. In addition to solvation characteristics, dynamical properties of solvation shells are also found out ...
Putsche Bernhard - - 2012
The interaction of potassium with mica(001) and its influence on the subsequent film growth of para-hexaphenyl (6P) was studied by Auger electron spectroscopy, thermal desorption spectroscopy, and atomic force microscopy (AFM). Freshly cleaved mica is covered with 0.5 monolayer (ML) of potassium. By intentional potassium deposition in ultra-high vacuum a ...
Bissett Mark Alexander - - 2012
We investigate the effect of mechanical strain on graphene synthesized by chemical vapor deposition (CVD) transferred onto flexible polymer substrates by observing the change in the Raman spectrum and then compare this to the behavior of exfoliated graphene. Previous studies into the effect of strain on graphene have focused on ...
Litcofsky Kevin D - - 2012
We present a methodology for the design, construction and modification of synthetic gene networks. This method emphasizes post-assembly modification of constructs based on network behavior, thus facilitating iterative design strategies and rapid tuning and repurposing of gene networks. The ease of post-construction modification afforded by this approach and the ever-increasing ...
Hou Guangjin - - 2012
(13)C and (15)N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely ...
Hirota Tomomitsu - - 2012
Atopic dermatitis is a common inflammatory skin disease caused by interaction of genetic and environmental factors. On the basis of data from a genome-wide association study (GWAS) and a validation study comprising a total of 3,328 subjects with atopic dermatitis and 14,992 controls in the Japanese population, we report here ...
Tao Peng - - 2012
An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program ...
Siednienko Jakub - - 2012
Toll-like receptors (TLRs) sense pathogen-associated molecules and respond by inducing cytokines and type I interferon. Here we show that genetic ablation of the E3 ubiquitin ligase Pellino3 augmented the expression of type I interferon but not of proinflammatory cytokines in response to TLR3 activation. Pellino3-deficient mice had greater resistance against ...
Hio Sachiko - - 2012
Abstract Conclusions: This study showed that patients with acoustic tumor (AT) with hearing loss in the contralateral side had severe mood disturbances. It is important for physicians to provide patients who have better hearing in the tumor side with adequate information regarding the possibility of profound bilateral hearing loss and ...
Greives Nicholas - - 2012
A method developed by Northrup et al. [J. Chem. Phys. 80, 1517 (1984)] for calculating protein-ligand binding rate constants (k(a)) from brownian dynamics (BD) simulations has been widely used for rigid molecules. Application to flexible molecules is limited by the formidable computational cost to treat conformational fluctuations during the long ...
Kim Hyung J HJ Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, UT 84132, - - 2012
Succinate dehydrogenase (SDH) requires a covalent addition of FAD for catalytic function. Mutational analyses of Sdh1 implicate C-terminal region Arg residues involvement in covalent flavinylation and SDH assembly. SDH assembly is dependent on FAD binding to Sdh1 but not covalent binding. These results document the basis for the SDH deficiency ...
Li Lenong - - 2012
E3-19K binds to and retains MHC class I molecules in the endoplasmic reticulum, suppressing anti-adenovirus activities of T cells. We determined the structure of the adenovirus serotype 2 (Ad2, species C) E3-19K-HLA-A2 complex to 1.95-Å resolution. Ad2 E3-19K binds to the N terminus of the HLA-A2 groove, contacting the α1, ...
Freyer Christoph C Max Planck Institute for Biology of Ageing, Cologne, - - 2012
A genetic bottleneck explains the marked changes in mitochondrial DNA (mtDNA) heteroplasmy that are observed during the transmission of pathogenic mutations, but the precise timing of these changes remains controversial, and it is not clear whether selection has a role. These issues are important for the genetic counseling of prospective ...
Chwee T S - - 2012
The adsorption energies and changes in surface work functions for benzene on unreconstructed Cu(111), Ag (111), and Au (111) at low coverages have been studied within the framework of dispersion corrected Kohn-Sham density functional theory. Corrections to account for long range dispersive effects between the adsorbate and metal substrate were ...
Manjarrez-Orduño Nataly N Center for Autoimmune and Musculoskeletal Disorders, The Feinstein Institute for Medical Research, North Shore-Long Island Jewish, Manhasset, New York, - - 2012
The c-Src tyrosine kinase, Csk, physically interacts with the intracellular phosphatase Lyp (encoded by PTPN22) and can modify the activation state of downstream Src kinases, such as Lyn, in lymphocytes. We identified an association of CSK with systemic lupus erythematosus (SLE) and refined its location to the intronic polymorphism rs34933034 ...
Ten-No Seiichiro - - 2012
We propose explicitly correlated Ansatz for four-component relativistic methods within the framework of the no-pair approximation. Kinetically balanced geminal basis is derived to satisfy the cusp conditions in the non-relativistic limit based on the Lévy-Leblend-like equation. Relativistic variants of strong-orthogonality projection operator (Ansätze 2α and 2β) suitable for practical calculations ...
Meng Qingyong - - 2012
Full dimensional multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) calculations of the dynamics of the three difluorobenzene cationic isomers in five lowest-lying doublet electronic states using the ab initio multistate multimode vibronic coupling Hamiltonian (MMVCH) model are carried out using the Heidelberg MCTDH package. The same dynamical problems, but treated with the ...
Mazzola Guglielmo - - 2012
The adiabatic approximation, typically assumed when performing standard Born-Oppenheimer (BO) molecular dynamics, can become unreliable at finite temperature, and specifically when the temperature is larger than the electronic energy gap between the ground state and the low-lying excited states. In this regime, relevant for many important chemical processes, the non-adiabatic ...
Do Hainam - - 2012
Identifying the energy minima of molecular clusters is a challenging problem. Traditionally, search algorithms such as simulated annealing, genetic algorithms, or basin hopping are usually used in conjunction with empirical force fields. We have implemented a basin hopping search algorithm combined with density functional theory to enable the optimization of ...
Kiran B - - 2012
Using global-minima search methods based on the density functional theory calculations of (AlH(3))(n) (n = 1-8) clusters, we show that the growth pattern of alanes for n ≥ 4 is dominated by structures containing hexa-coordinated Al atoms. This is in contrast to the earlier studies where either linear or ring ...
Seyednejad Hajar - - 2012
The aim of this study was to fabricate nanofibrous scaffolds based on blends of a hydroxyl functionalized polyester (poly(hydroxymethylglycolide-co-ε-caprolactone), pHMGCL) and poly(ε-caprolactone) (PCL), loaded with bovine serum albumin (BSA) as a protein stabilizer and vascular endothelial growth factor (VEGF) as a potent angiogenic factor by means of a coaxial electrospinning ...
Chatterjee Avik P - - 2012
The impact of particle clustering and correlation upon the percolation behavior of polydisperse cylinders with finite hard core diameter is examined within an analogy to a lattice percolation problem. Percolation thresholds and percolation and backbone probabilities are explored as functions of the degree of clustering and extent of correlation among ...
Hukkerikar Amol Shivajirao - - 2012
The aim of this work is to develop group-contribution+ (GC+) method (combined group-contribution (GC) method and atom connectivity index (CI) method) based property models to provide reliable estimations of environment-related properties of organic chemicals together with uncertainties of estimated property values. For this purpose, a systematic methodology for property modeling ...
Molenaar Jan J - - 2012
LIN28B regulates developmental processes by modulating microRNAs (miRNAs) of the let-7 family. A role for LIN28B in cancer has been proposed but has not been established in vivo. Here, we report that LIN28B showed genomic aberrations and extensive overexpression in high-risk neuroblastoma compared to several other tumor entities and normal ...
Namasivayam Vigneshwaran - - 2012
The selection of active compounds for chemical optimization efforts typically requires the consideration of multiple properties beyond potency. Herein we introduce a multi-objective particle swarm optimization approach to automatically extract compound subsets from large data sets that reveal structure-activity relationship (SAR) information and display physicochemical property distributions that are indicative ...
Zhang Qiong - - 2012
ABSTRACT: BACKGROUND: Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled ...
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