bluuebunny/crossref_metadata_2025_split huggingface dataset:
DFT study of the mechanism of hydroamination of ethylene with ammonia catalyzed by diplatinum(II) complexes: Inner‐ or outer‐sphere?
Authors: Kefalidis Christos E. , Tsipis Constantinos A. 
Published: April 2012

AbstractA detailed analysis of the reaction profiles of the hydroamination reaction between ethylene and ammonia catalyzed by the diplatinum(II) [{Pt(NH2)(μ‐H)(PPh3)}2] complex is presented herein using density functional theory computational techniques. The coordinatively unsaturated 14e T‐shaped [Pt(NH2)(PPh3)H] species resulted from the dissociation of the diplatinum [{Pt(NH2)(μ‐H)(PPh3)}2] precatalyst are identified as the active catalytic species. All possible reaction pathways that constitute the entire catalytic cycle have exhaustively been investigated. Overall, the rate‐determining step of all catalytic cycles constructed was found to be the oxidative addition of ammonia that leads to the regeneration of the catalyst. According to the energy span model, the outer‐sphere mechanism for the hydroamination of ethylene with ammonia catalyzed by the diplatinum complexes is favored over the inner‐sphere one, whereas TOF values are in favor of the inner‐sphere mechanism. © 2012 Wiley Periodicals, Inc.
Embryonic Development and Gene Expression of Porcine SCNTEmbryos Treated With Sodium Butyrate
Authors: LIU LIMEI , LIU YING , GAO FEI , SONG GUANGQI , WEN JIANG , GUAN JIYU , YIN YUPENG , MA XIN , TANG BO , LI ZIYI 
Published: April 2012

ABSTRACTIncomplete epigenetic modification is one of important reasons of inefficient reprogramming of the donor cell nuclei in ooplasm after somatic cell nuclear transfer (SCNT). It may also underlie the observed reduced viability of cloned embryos. Sodium butyrate (NaBu) is a natural histone deacetylase inhibitor that is produced in the intestine. In the current study, we evaluated the effects of NaBu on preimplantation development, histone acetylation, and gene expression in porcine SCNT embryos. Our results showed that the blastocyst rate (24.88 ± 2.09) of cloned embryos treated with 1.0 mM NaBu for 12 hr after activation was significantly higher (P < 0.05) than that of untreated cloned embryos (13.15 ± 3.07). In addition, treated embryos displayed a global acetylated histone H3 at lysine 14 profile similar to that of in vitro fertilized (IVF) embryos during preimplantation development. Lower levels of Oct4 and Bcl‐2, but higher levels of Hdac1, in SCNT embryos at the two‐cell and blastocyst stages were observed, compared with those in the IVF counterparts. The four‐cell embryos showed no differences in the levels of these genes among IVF embryos or SCNT embryos treated with or without NaBu; however, the levels of Dnmt3b were significantly different. NaBu‐treated SCNT embryos showed similar levels of Oct4, Bcl‐2, and Dnmt3b as in IVF blastocysts. These results indicated that NaBu treatment in SCNT embryos alters their histone acetylation pattern to provide beneficial effects on in vitro developmental competence and gene expression. J. Exp. Zool. (Mol. Dev. Evol.) 318:224–234, 2012. © 2012 Wiley Periodicals, Inc.
Development and evaluation of TWIST Dixon for dynamic contrast‐enhanced (DCE) MRI with improved acquisition efficiency and fat suppression
Authors: Le Yuan , Kroeker Randall , Kipfer Hal D. , Lin Chen 
Published: April 2012

AbstractPurpose:To develop a new pulse sequence called time‐resolved angiography with stochastic trajectories (TWIST) Dixon for dynamic contrast enhanced magnetic resonance imaging (DCE‐MRI).Materials and Methods:The method combines dual‐echo Dixon to generate separated water and fat images with a k‐space view‐sharing scheme developed for 3D TWIST. The performance of TWIST Dixon was compared with a volume interpolated breathhold examination (VIBE) sequence paired with spectrally selective adiabatic inversion Recovery (SPAIR) and quick fat‐sat (QFS) fat‐suppression techniques at 3.0T using quantitative measurements of fat‐suppression accuracy and signal‐to‐noise ratio (SNR) efficiency, as well as qualitative breast image evaluations.Results:The water fraction of a uniform phantom was calculated from the following images: 0.66 ± 0.03 for TWIST Dixon; 0.56 ± 0.23 for VIBE‐SPAIR, and 0.53 ± 0.14 for VIBE‐QFS, while the reference value is 0.70 measured by spectroscopy. For phantoms with contrast (Gd‐BOPTA) concentration ranging from 0–6 mM, TWIST Dixon also provides consistently higher SNR efficiency (3.2–18.9) compared with VIBE‐SPAIR (2.8–16.8) and VIBE‐QFS (2.4–12.5). Breast images acquired with TWIST Dixon at 3.0T show more robust and uniform fat suppression and superior overall image quality compared with VIBE‐SPAIR.Conclusion:The results from phantom and volunteer evaluation suggest that TWIST Dixon outperforms conventional methods in almost every aspect and it is a promising method for DCE‐MRI and contrast‐enhanced perfusion MRI, especially at higher field strength where fat suppression is challenging. J. Magn. Reson. Imaging 2012;36:483–491. © 2012 Wiley Periodicals, Inc.
Optimized inversion‐prepared gradient echo imaging
Authors: Kir Albert , McMillan Alan 
Published: April 2012

AbstractPurpose:To implement a method using an extended phase graph (EPG)‐based simulation to optimize inversion‐prepared gradient echo sequences with respect to signal and contrast within the shortest acquisition time.Materials and Methods:A critical issue in rapid gradient‐echo imaging is the effect of residual transverse magnetization between consecutive data acquisition windows. Various spoiling schemes have been proposed to mitigate this problem, and while spoiling is often considered to be perfect, imaging can be more truthfully described using the EPG. An EPG‐based simulation is used to analyze and predict the image signal and contrast to serve as a basis for sequence optimization.Results:Fourteen biological phantom experiments and five brain imaging experiments on each of five healthy volunteers was performed to validate and verify the accuracy of the EPG‐based simulation. In addition, two experiments on an in‐cranial cadaver brain were performed to show the ability of the proposed method for improving overall image quality.Conclusion:From the experiment results, it is demonstrated that optimization of 3D magnetization‐prepared rapid gradient‐echo imaging sequences can be performed with an EPG‐based simulation to manipulate the sequence parameters for generating images with highly specific signal and contrast characteristics for quantitative T1‐weighted human brain imaging. J. Magn. Reson. Imaging 2012;36:748–755. © 2012 Wiley Periodicals, Inc.
Least square support vector and multi‐linear regression for statistically downscaling general circulation model outputs to catchment streamflows
Authors: Sachindra D. A. , Huang F. , Barton A. , Perera B. J. C. 
Published: April 2012

AbstractThis study employed least square support vector machine regression (LS‐SVM‐R) and multi‐linear regression (MLR) for statistically downscaling monthly general circulation model (GCM) outputs directly to monthly catchment streamflows. The scope of the study was limited to calibration and validation of the downscaling models. The methodology was demonstrated by its application to a streamflow site in the Grampian water supply system in northwestern Victoria, Australia. Probable predictors for the study were selected from the National Center for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis data set based on the past literature and hydrology. Probable variables that displayed the best significant correlations, consistently with the streamflows over the entire period of the study (1950–2010) and under three 20‐year time slices (1950–1969, 1970–1989 and 1990–2010) were selected as potential predictors. To better capture seasonal variations of streamflows, downscaling models were developed for each calendar month. The standardized potential predictors were introduced to the LS‐SVM‐R and MLR models, starting from the best correlated three and then, others one by one, based on their correlations with the streamflows, until the model performance in validation was maximized. This stepwise model development enabled the identification of the optimum number of potential variables for each month. The model calibration was performed over the period 1950–1989 and validation was done for 1990–2010. LS‐SVM‐R model parameter optimization was achieved using simplex algorithm and leave‐one‐out cross‐validation. The MLR models were optimized by minimizing the sum of squared errors. In both modelling techniques, validation was performed as an independent simulation. In calibration, LS‐SVM‐R and MLR models displayed equally good performances with a trend of under‐predicting high flows. During validation, LS‐SVM‐R outperformed MLR, though both techniques over‐predicted most of the streamflows. It was concluded that LS‐SVM‐R is a better technique for statistically downscaling GCM outputs to streamflows than MLR, but still MLR is a potential technique for the same task. Copyright © 2012 Royal Meteorological Society
Observed air/soil temperature trends in open land and understory of a subtropical mountain forest, SW China
Authors: You Guangyong , Zhang Yiping , Schaefer Douglas , Sha Liqing , Liu Yuhong , Gong Hede , Tan Zhenghong , Lu Zhiyun , Wu Chuansheng , Xie Youneng 
Published: April 2012

AbstractThis study seeks a further understanding on climate trends in a subtropical mountain forest, SW China. Air (Ta) and soil temperature (Ts), both in open land (1983–2010) and under a forest canopy (1986–2010), were investigated. Short‐term radiation components were also measured simultaneously both in open land and understory to explore the relationships of microclimatic variables. Correlations of Ta and Ts with sunshine hours (St) and wind speed (Ws) were also analysed as driving factors of the temperature trends.The results showed that (1) Understory radiation components were greatly reduced by the forest canopy, showing a strong effect of forest canopy on microclimatic variables. Ts_0 in open land was significantly correlated with solar radiation. Wind speed had significant influences on differences between Ta and Ts_0, between open land Ts_0 and understory Ts_0. The long‐term data showed that Ts_0 under forest canopy were closely coupled with Ta in open land. (2) Ta had a larger increase than Ts_0 in open land, and temperature increases in winter were greater than in other seasons. Soil temperature at depths under forest canopy had nearly twice the increases of those on open land; we attributed this to the higher relative increase of Ws over St. (3) A slope change in 1998 was detected in the Ts_0 and Ta difference (Ts_0 − Ta) series, suggesting different response of Ts_0 and Ta since that year. Deceleration of St and stability of Ws may have been factors.This study improves our understanding of warming in a nature reserve where anthropogenic influences are absent. Further studies are needed for the biological and biochemical implications on subtropical mountain forest. Copyright © 2012 Royal Meteorological Society
Lamb weather types derived from reanalysis products
Authors: Jones P. D. , Harpham C. , Briffa K. R. 
Published: April 2012

AbstractWeather typing, based on surface pressure charts, has been one of the principal means of analysis in synoptic climatology. Here, we summarize the history of manual and automated schemes, in the northwest European context, illustrating how the approaches can take advantage of the extended reanalysis products that have recently become available. The British Isles and the associated Lamb weather types (LWTs) are the focus of this study, but the approach can be applied to any mid‐to‐high latitude region to provide series back to 1871. However, caution is advised in the use of the approach where the quality and quantity of input data into the extended reanalysis are known to be temporally and spatially variable and/or poor in early years. This study intercompares the use of automated schemes with operational analyses, reanalyses and earlier manually derived LWTs. Copyright © 2012 Royal Meteorological Society
A Facile Route to Boronic Acid Functional Polymeric Microspheres via Epoxide Ring Opening
Authors: Vogt Andrew P. , Trouillet Vanessa , Greiner Alexandra M. , Kaupp Michael , Geckle Udo , Barner Leonie , Hofe Thorsten , Barner‐Kowollik Christopher 
Published: April 2012

AbstractBoronic acid‐functionalized microspheres are prepared for the first time via mild epoxide ring opening based on porous cross‐linked polymeric microspheres (diameter ≈ 10 μm, porosity ≈ 1000 Å). Quantitative chemical analysis by XPS and EA evidences that there is a greater functionalization with boronic acid when employing a sequential synthetic method [1.7 atom% boron (XPS); 1.12 wt% nitrogen (EA)] versus a one‐pot synthetic method [0.2 atom% boron (XPS); 0.60 wt% nitrogen (EA)] yielding grafting densities ranging from approximately 2.5 molecules of boronic acid per nm2 to 1 molecule of boronic acid per nm2, respectively. Furthermore, the boronic acid‐functionalized microspheres are conjugated with a novel fluorescent glucose molecule demonstrating a homogeneous spatial distribution of boronic acid.
A preconditioned MinRes solver for time‐periodic parabolic optimal control problems
Authors: Kollmann Markus , Kolmbauer Michael 
Published: April 2012

SUMMARYThis work is devoted to the multiharmonic analysis of parabolic optimal control problems in a time‐periodic setting. In contrast to previous approaches, we include the cases of different control and observation domains, the observation in certain energy spaces, and the presence of control constraints. In all these cases, we propose a new preconditioned MinRes solver for the frequency domain equations and show that this solver is robust with respect to the space and time discretization parameters as well as the involved ‘bad’ model parameters of the state equation. Copyright © 2012 John Wiley & Sons, Ltd.
Immersed finite element methods for parabolic equations with moving interface
Authors: He Xiaoming , Lin Tao , Lin Yanping , Zhang Xu 
Published: April 2012

AbstractThis article presents three Crank‐Nicolson‐type immersed finite element (IFE) methods for solving parabolic equations whose diffusion coefficient is discontinuous across a time dependent interface. These methods can use a fixed mesh because IFEs can handle interface jump conditions without requiring the mesh to be aligned with the interface. These methods will be compared analytically in the sense of accuracy and computational cost. Numerical examples are provided to demonstrate features of these three IFE methods. © 2012 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2013
Allogeneic hematopoietic stem cell transplantation in children with sickle cell disease
Authors: Locatelli Franco , Pagliara Daria 
Published: April 2012

AbstractAllogeneic hematopoietic stem cell transplantation (allo‐HSCT) represents the only curative treatment for sickle cell disease (SCD), being successful in around 85–90% of patients. Mortality and long‐term morbidity (including infertility, gonadal failure, and chronic graft‐vs.‐host disease) associated with conventional approaches curtail the number of patients who undergo allo‐HSCT. Recently, it has been demonstrated that cord blood is as effective as and possibly safer than bone marrow in pediatric patients with SCD. Likewise, transplant strategies based on the use of reduced‐intensity regimens and the induction of mixed chimerism have been explored to decrease allo‐HSCT short‐ and long‐term complications. Pediatr Blood Cancer 2012;59:372–376. © 2012 Wiley Periodicals, Inc.
Protein hydrogen exchange: Testing current models
Authors: Skinner John J. , Lim Woon K. , Bédard Sabrina , Black Ben E. , Englander S. Walter 
Published: April 2012

AbstractTo investigate the determinants of protein hydrogen exchange (HX), HX rates of most of the backbone amide hydrogens of Staphylococcal nuclease were measured by NMR methods. A modified analysis was used to improve accuracy for the faster hydrogens. HX rates of both near surface and well buried hydrogens are spread over more than 7 orders of magnitude. These results were compared with previous hypotheses for HX rate determination. Contrary to a common assumption, proximity to the surface of the native protein does not usually produce fast exchange. The slow HX rates for unprotected surface hydrogens are not well explained by local electrostatic field. The ability of buried hydrogens to exchange is not explained by a solvent penetration mechanism. The exchange rates of structurally protected hydrogens are not well predicted by algorithms that depend only on local interactions or only on transient unfolding reactions. These observations identify some of the present difficulties of HX rate prediction and suggest the need for returning to a detailed hydrogen by hydrogen analysis to examine the bases of structure‐rate relationships, as described in the companion paper (Skinner et al., Protein Sci 2012;21:996–1005).
X‐interface is not the explanation for the slow disassembly of N‐cadherin dimers in the apo state
Authors: Vunnam Nagamani , Pedigo Susan 
Published: April 2012

AbstractIn spite of structural similarities Epithelial‐ (E‐) and Neural‐ (N‐) cadherins are expressed at two types of synapses and differ significantly in dimer disassembly kinetics. Recent studies suggested that the formation of an X‐dimer intermediate in E‐cadherin is the key requirement for rapid disassembly of the adhesive dimer (Harrison et al., Nat Struct Mol Biol 2010;17:348–357 and Hong et al., J Cell Biol 2011;192:1073–1083). The X‐interface in E‐cadherin involves three noncovalent interactions, none of which is conserved in N‐cadherin. Dimer disassembly is slow at low calcium concentration in N‐cadherin, which may be due to the differences in the X‐interface residues. To investigate the origin of the slow disassembly kinetics we introduced three point mutations into N‐cadherin to provide the opportunity for the formation of X‐interface interactions. Spectroscopic studies showed that the triple mutation did not affect the stability or the calcium‐binding affinity of the X‐enabled N‐cadherin mutant. Analytical size exclusion chromatography was used to assay for the effect of the mutation on the rate of dimer disassembly. Contrary to our expectation, the disassembly of dimers of the X‐enabled N‐cadherin mutant was as slow as seen for wild‐type N‐cadherin in the apo‐state. Thus, the differences in the X‐interface residues are not the origin of slow disassembly kinetics of N‐cadherin in the apo‐state.
Mycobacterium thermoresistibile as a source of thermostable orthologs of Mycobacterium tuberculosis proteins
Authors: Edwards Thomas E. , Liao Reiling , Phan Isabelle , Myler Peter J. , Grundner Christoph 
Published: April 2012

AbstractThe genus Mycobacterium comprises major human pathogens such as the causative agent of tuberculosis, Mycobacterium tuberculosis (Mtb), and many environmental species. Tuberculosis claims ∼1.5 million lives every year, and drug resistant strains of Mtb are rapidly emerging. To aid the development of new tuberculosis drugs, major efforts are currently under way to determine crystal structures of Mtb drug targets and proteins involved in pathogenicity. However, a major obstacle to obtaining crystal structures is the generation of well‐diffracting crystals. Proteins from thermophiles can have better crystallization and diffraction properties than proteins from mesophiles, but their sequences and structures are often divergent. Here, we establish a thermophilic mycobacterial model organism, Mycobacterium thermoresistibile (Mth), for the study of Mtb proteins. Mth tolerates higher temperatures than Mtb or other environmental mycobacteria such as M. smegmatis. Mth proteins are on average more soluble than Mtb proteins, and comparison of the crystal structures of two pairs of orthologous proteins reveals nearly identical folds, indicating that Mth structures provide good surrogates for Mtb structures. This study introduces a thermophile as a source of protein for the study of a closely related human pathogen and marks a new approach to solving challenging mycobacterial protein structures.
Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata
Authors: Sampathkumar Parthasarathy , Kim Seung Joong , Manglicmot Danalyn , Bain Kevin T. , Gilmore Jeremiah , Gheyi Tarun , Phillips Jeremy , Pieper Ursula , Fernandez‐Martinez Javier , Franke Josef D. , Matsui Tsutomu , Tsuruta Hiro , Atwell Shane , Thompson Devon A. , Emtage J. Spencer , Wasserman Stephen R. , Rout Michael P. , Sali Andrej , Sauder J. Michael , Almo Steven C. , Burley Stephen K. 
Published: April 2012

AbstractThe nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of ∼456 polypeptide chains contributed by ∼30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N‐terminal “FG” repeats containing a Gle2p‐binding sequence motif and a NPC targeting domain at its C‐terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882–1034 [CgNup116(882–1034)], at 1.94 Å resolution. The X‐ray structure of CgNup116(882–1034) is consistent with the molecular envelope determined in solution by small‐angle X‐ray scattering. Structural similarities of CgNup116(882–1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Bondpseudorotation, Jahn‐Teller, and pseudo‐Jahn‐Teller effects in the cyclopentadienyl cation and its pentahalogeno derivatives
Authors: Zou Wenli , Filatov Michael , Cremer Dieter 
Published: April 2012

AbstractMultireference averaged quadratic coupled cluster (MRAQCC) (4,5)/cc‐pVTZ calculations predict that bond pseudorotation (BPR) in the first excited singlet state of the cyclopentadienyl cation (CPC) proceeds with a barrier of just 0.35 kcal/mol, where five dienylic forms present the minima and five allylic forms the transition states of the pseudorotation process. Vibrational and entropic corrections revert the order of stabilities and lead to a Δ G(298) of just 0.05 kcal/mol indicating that BPR is unhindered at room temperature. The description of the CPC ring in terms of curvilinear deformation coordinates (seven for C5, seven for X5, and three coupling coordinates) make it possible to explore both the six‐dimensional (6D) Jahn‐Teller and the 8D pseudo‐Jahn‐Teller space and assess the importance of Jahn–Teller and pseudo‐Jahn–Teller deformations of the CPC ring. The latter dominate the ring deformations along the BPR path. The only somewhat larger Jahn–Teller contribution results from a E‐symmetrical CCH bending motion. For the perhalogenated CPCs, the dominance of the pseudo‐Jahn–Teller effect increases, however, the total deformation of the D5h‐symmetrical ring decreases and thereby also the stabilization of the 1A1 forms along the BPR path. This leads to a reduction of the BPR barriers to just 0.14 kcal/mol for C5I. For all pentahalogeno CPCs, the dienylic form is more stable both at the energy and free energy level. The use of curvilinear deformation coordinates facilitates the understanding of the electronic features of cyclic (pseudo‐) Jahn–Teller systems. © 2012 Wiley Periodicals, Inc.