bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porphyrin Nanorods Modified Glassy Carbon Electrode for the Electrocatalysis of Dioxygen, Methanol and Hydrazine
Authors: C.George Reama , Mugadza Tawanda , Khene Samson , Egharevba Gabriel O. , Nyokong Tebello 
Published: May 2011

AbstractPorphyrin nanorods (PNR) were prepared by ionic self‐assembly of two oppositely charged porphyrin molecules consisting of free base meso‐tetraphenylsulfonate porphyrin (H4TPPS42−) and meso‐tetra(N‐methyl‐4‐pyridyl) porphyrin (MTMePyP4+M=Sn, Mn, In, Co). These consist of H4TPPS42−SnTMePyP4+, H4TPPS42−CoTMePyP4+, H4TPPS42−InTMePyP4+ and H4TPPS42−MnTMePyP4+ porphyrin nanorods. The absorption spectra and transmission electron microscopic (TEM) images of these structures were obtained. These porphyrin nanostructures were used to modify a glassy carbon electrode for the electrocatalytic reduction of oxygen, and the oxidation of hydrazine and methanol at low pH. The cyclic voltammogram of PNR‐modified GCE in pH 2 buffer solution has five irreversible processes, two distinct reduction processes and three oxidation processes. The porphyrin nanorods modified GCE produce good responses especially towards oxygen reduction at −0.50 V vs. Ag|AgCl (3 M KCl). The process of electrocatalytic oxidation of methanol using PNR‐modified GCE begins at 0.71 V vs. Ag|AgCl (3 M KCl). The electrochemical oxidation of hydrazine began at around 0.36 V on H4TPPS42−SnTMePyP4+ modified GCE. The GCE modified with H4TPPS42−CoTMePyP4+ H4TPPS42−InTMePyP4+ and H4TPPS42−MnTMePyP4+ porphyrin nanorods began oxidizing hydrazine at 0.54 V, 0.59 V and 0.56 V, respectively.
Maximum likelihood estimation of the dynamic coregionalization model with heterotopic data
Authors: Fassò Alessandro , Finazzi Francesco 
Published: May 2011

AbstractThe information content of multivariable spatio‐temporal data depends on the underlying spatial sampling scheme. The most informative case is represented by the isotopic configuration where all variables are measured at all sites. The opposite case is the completely heterotopic case where different variables are observed only at different locations. A well known approach to multivariate spatio‐temporal modelling is based on the linear coregionalization model (LCM).In this paper, the maximum likelihood estimation of the heterotopic spatio‐temporal model with spatial LCM components and temporal dynamics is developed. In particular, the computation of the estimates is based on the EM algorithm and two solutions are proposed: one is based on the more cumbersome exact maximization of the a posteriori expected log likelihood and the other is an approximate closed‐form solution. Their properties are assessed in terms of bias and efficiency through an example of air quality dinamic mapping using satellite data and a Monte Carlo simulation campaign based on a large data set. Copyright © 2011 John Wiley & Sons, Ltd.
A computational finite‐element program for hybrid simulation
Authors: Saouma Victor , Kang Dae‐Hung , Haussmann Gary 
Published: May 2011

SUMMARYThe essence of real time hybrid simulation (RTHS) is the reliance on a physical test (virtual finite element) in support of a numerical simulation, which is unable to properly simulate it numerically. Hence, the computational support for a hybrid simulation is of paramount importance, and one with anything less than a state of the art computational support may defeat the purpose of such an endeavor. A critical, yet often ignored, component of RTHS is precisely the computational engine, which unfortunately has been a bottleneck for realistic studies. Most researches have focused on either the control or on the communication (mostly in distributed, non‐real time hybrid simulation) leaving the third leg of RTHS (computation) ignored and limited to the simulation of simple models (small number of degrees of freedom and limited nonlinearities). This paper details the development of a specialized software written explicitly to perform, single site, hybrid simulation ranging from pseudo‐dynamic to hard real time ones. Solution strategy, implementation details, and actual applications are reported. Copyright © 2011 John Wiley & Sons, Ltd.
Evaluation of alginate dialdehyde cross‐linked gelatin hydrogel as a biodegradable sealant for polyester vascular graft
Authors: Manju Saraswathy , Muraleedharan Chirathodi Vayalappil , Rajeev Adathala , Jayakrishnan Attipettah , Joseph Roy 
Published: May 2011

AbstractVascular grafts are devices intended to replace compromised arteries in the body and grafts made of polyethylene terephthalate (PET) fabric have been used mainly for synthetic grafting procedures involving medium to large diameter vascular grafts. Though porosity of the graft permits tissue in‐growth, it would lead to bleeding through the graft walls immediately after implantation. So it is essential to seal the pores either by preclotting with patient's own blood or by other sealing materials prior to implantation in order to prevent blood leakage through the graft wall. Biodegradable hydrogel materials are ideal candidates for this purpose. Apart from sealing the pores, they offer biocompatible and low‐thrombogenic surfaces when coated on vascular graft. In the present study, a biodegradable hydrogel, derived from oxidized alginate and gelatin, has been deposited on PET grafts by dip coating and were characterized for its efficacy on sealing the pores of the graft. Water permeability in the static and pulsatile conditions, burst strength, in vitro cell culture cytotoxicity, hemocompatibility, and endothelial cell adhesion and proliferation of the coated grafts were investigated. Results showed that the alginate dialdehyde cross‐linked gelatin hydrogel was nontoxic, hemocompatible, and was efficient in sealing the pores of the graft. Blood perfusion study showed that when hydrogel‐coated grafts were exposed to blood for 30 min, they showed little affinity toward platelets or leukocytes. Hemolytic potential of PET was significantly reduced when it was coated with hydrogel. Improved adhesion and proliferation of endothelial cells were observed when PET grafts were coated with hydrogel. Results also showed that coating with hydrogel did not affect the burst strength of the PET graft. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
Cooperative DNA and histone binding by Uhrf2 links the two major repressive epigenetic pathways
Authors: Pichler Garwin , Wolf Patricia , Schmidt Christine S. , Meilinger Daniela , Schneider Katrin , Frauer Carina , Fellinger Karin , Rottach Andrea , Leonhardt Heinrich 
Published: May 2011

AbstractGene expression is regulated by DNA as well as histone modifications but the crosstalk and mechanistic link between these epigenetic signals are still poorly understood. Here we investigate the multi‐domain protein Uhrf2 that is similar to Uhrf1, an essential cofactor of maintenance DNA methylation. Binding assays demonstrate a cooperative interplay of Uhrf2 domains that induces preference for hemimethylated DNA, the substrate of maintenance methylation, and enhances binding to H3K9me3 heterochromatin marks. FRAP analyses revealed that localization and binding dynamics of Uhrf2 in vivo require an intact tandem Tudor domain and depend on H3K9 trimethylation but not on DNA methylation. Besides the cooperative DNA and histone binding that is characteristic for Uhrf2, we also found an opposite expression pattern of uhrf1 and uhrf2 during differentiation. While uhrf1 is mainly expressed in pluripotent stem cells, uhrf2 is upregulated during differentiation and highly expressed in differentiated mouse tissues. Ectopic expression of Uhrf2 in uhrf1−/− embryonic stem cells did not restore DNA methylation at major satellites indicating functional differences. We propose that the cooperative interplay of Uhrf2 domains may contribute to a tighter epigenetic control of gene expression in differentiated cells. J. Cell. Biochem. 112: 2585–2593, 2011. © 2011 Wiley‐Liss, Inc.
Apolipoprotein A‐I mimetic peptide L‐4F prevents myocardial and coronary dysfunction in diabetic mice
Authors: Vecoli C. , Cao J. , Neglia D. , Inoue K. , Sodhi K. , Vanella L. , Gabrielson K.K. , Bedja D. , Paolocci N. , L'Abbate A. , Abraham N.G. 
Published: May 2011

AbstractDiabetes is a major health problem associated with adverse cardiovascular outcomes. The apolipoprotein A‐I mimetic peptide L‐4F is a putative anti‐diabetic drug, has antioxidant and anti‐inflammatory proprieties and improves endothelial function. In obese mice L‐4F increases adiponectin levels, improving insulin sensitivity, and reducing visceral adiposity. We hypothesized that the pleiotropic actions of L‐4F can prevent heart and coronary dysfunction in a mouse model of genetically induced Type II diabetes. We treated db/db mice with either L‐4F or vehicle for 8 weeks. Trans‐thoracic echocardiography was performed; thereafter, isolated hearts were subjected to ischemia/reperfusion (IR). Glucose, insulin, adiponectin, and pro‐inflammatory cytokines (IL‐1β, TNF‐α, MCP‐1) were measured in plasma and HO‐1, pAMPK, peNOS, iNOS, adiponectin, and superoxide in cardiac tissue. In db/db mice L‐4F decreased accumulation of subcutaneous and total fat, and increased insulin sensitivity and adiponectin levels while lowering inflammatory cytokines (P < 0.05). L‐4F normalized in vivo left ventricular (LV) function of db/db mice, increasing (P < 0.05) fractional shortening and decreasing (P < 0.05) LV dimensions. In I/R experiments, L‐4F prevented coronary microvascular resistance from increasing and LV function from deteriorating in the db/db mice. These changes were associated with increased cardiac expression of HO‐1, pAMPK, peNOS, and adiponectin and decreased levels of superoxide and iNOS (P < 0.01). In the present study we showed that L‐4F prevented myocardial and coronary functional abnormalities in db/db mice. These effects were associated with stimulation of HO‐1 resulting in increased levels of anti‐inflammatory, anti‐oxidative, and vasodilatatory action through a mechanism involving increased levels of adiponectin, pAMPK, and peNOS. J. Cell. Biochem. 112: 2616–2626, 2011. © 2011 Wiley‐Liss, Inc.
Retraction: Genistein protects genioglossus myocyte against hypoxia‐induced injury through PI3K‐Akt and ERK MAPK pathways
Authors: Ding Wanghui , Liu Yuehua 
Published: May 2011

AbstractRetraction:The following article from Journal of Cellular Biochemistry, Genistein protects genioglossus myocyte against hypoxia‐induced injury through PI3K‐Akt and ERK MAPK pathways by Wanghui Ding and Yuehua Liu, posted online on May 19, 2011 in Wiley Online Library (onlinelibrary.wiley.com), has been retracted by agreement between the authors, the journal Editor in Chief, Dr. Gary S. Stein and Wiley‐Liss, Inc. The retraction has been made as authorization to publish was not granted by one of the funding bodies. J. Cell. Biochem. 113: 1809–1809, 2012. © 2012 Wiley Periodicals, Inc.
Harmonic vibrational frequencies: Scale factors for pure, hybrid, hybrid meta, and double‐hybrid functionals in conjunction with correlation consistent basis sets
Authors: Laury Marie L. , Boesch Scott E. , Haken Ian , Sinha Pankaj , Wheeler Ralph A. , Wilson Angela K. 
Published: May 2011

AbstractScale factors for (a) low (<1000 cm−1) and high harmonic vibrational frequencies, (b) thermal contributions to enthalpy and entropy, and (c) zero‐point vibrational energies have been determined for five hybrid functionals (B3P86, B3PW91, PBE1PBE, BH&HLYP, MPW1K), five pure functionals (BLYP, BPW91, PBEPBE, HCTH93, and BP86), four hybrid meta functionals (M05, M05‐2X, M06, and M06‐2X) and one double‐hybrid functional (B2GP‐PLYP) in combination with the correlation consistent basis sets [cc‐pVnZ and aug‐cc‐pVnZ, n = D(2),T(3),Q(4)]. Calculations for vibrational frequencies were carried out on 41 organic molecules and an additional set of 22 small molecules was used for the zero‐point vibrational energy scale factors. Before scaling, approximately 25% of the calculated frequencies were within 3% of experimental frequencies. Upon application of the derived scale factors, nearly 90% of the calculated frequencies deviated less than 3% from the experimental frequencies for all of the functionals when the augmented correlation consistent basis sets were used. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
On the applicability of cluster models to study the chemical reactivity of carbon nanotubes
Authors: Denis Pablo A. , Iribarne Federico 
Published: May 2011

AbstractWe have performed a comparative study on the reactivity of metallic and semiconducting nanotubes using infinite and finite models. Infinite models were created using periodic boundary conditions while finite ones were constructed by means of hydrogen terminated nanotubes sections. Cluster models systematically underestimate the reactivity of metallic single wall carbon nanotube (SWCNT)s. We have confirmed that metallic nanotubes are more reactive than semiconducting species, in disagreement with previous works. The differences can be attributed to the presence of an instability in the singlet ground state of the wavefunction corresponding to semiconducting nanotubes clusters. When lower electronic states of the pristine cluster are considered, semiconducting nanotubes become less reactive as compared with metallic SWCNTs. Particularly, if an antiferromagnetic solution is considered for the semiconducting (10,0) SWCNT cluster, it becomes less reactive than the (5,5) SWCNT, as observed for infinite models. Because semiconducting nanotubes are less reactive than metallic counterparts, their reaction energies converge faster to the values observed for graphene. For a 1.6‐nm diameter semiconducting nanotube, the addition energy is comparable with graphene. Thus, semiconducting nanotubes with diameters larger than 1.6 nm are going to be as reactive as graphene and the effects of curvature will be unimportant. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
He molecular ion in a strong time‐dependent magnetic field: A current‐density functional study
Authors: Vikas  
Published: May 2011

AbstractThe He molecular ion exposed to a strong ultrashort time‐dependent (TD) magnetic field of the order of 109 G is investigated through a quantum fluid dynamics (QFD) and current‐density functional theory (CDFT) based approach using vector exchange‐correlation (XC) potential and energy density functional that depend not only on the electronic charge‐density but also on the current density. The TD‐QFD‐CDFT computations are performed in a parallel internuclear‐axis and magnetic field‐axis configuration at the field‐free equilibrium internuclear separation R = 1.3 au with the field‐strength varying between 0 and 1011 G. The TD behavior of the exchange‐ and correlation energy of the He is analyzed and compared with that obtained using a [B‐TD‐QFD‐density functional theory (DFT)] approach based on the conventional TD‐DFT under similar computational constraints but using only scalar XC potential and energy density functional dependent on the electronic charge‐density alone. The CDFT based approach yields TD exchange‐ and correlation energy and TD electronic charge‐density significantly different from that obtained using the conventional TD‐DFT based approach, particularly, at typical magnetic field strengths and during a typical time period of the TD field. This peculiar behavior of the CDFT‐based approach is traced to the TD current‐density dependent vector XC potential, which can induce nonadiabatic effects causing retardation of the oscillating electronic charge density. Such dissipative electron dynamics of the He molecular ion is elucidated by treating electronic charge density as an electron‐“fluid” in the terminology of QFD. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Theoretical study of valance photoelectron spectra of hypoxanthine, xanthine, and caffeine using direct symmetry‐adapted cluster/configuration interaction methodology
Authors: Farrokhpour Hossein , Fathi Fariman 
Published: May 2011

AbstractUV photoelectron spectra of hypoxanthine, xanthine, and caffeine, up to 20 eV, were calculated and compared with the experimental spectra reported in literature. The calculations were performed using a novel version of the quantum mechanical symmetry‐adapted cluster/configuration interaction (SAC‐CI) method termed, direct SAC‐CI. The Duning/Huzinaga valance double‐zeta D95+(d,p) Gaussian basis set was also employed with this method. The ionization energies and intensities were calculated, and the corresponding spectral bands were assigned. Natural bonding orbital (NBO) calculations were employed for better spectral band assignment. The calculated ionization energies and intensities reasonably produced the experimental photoelectron spectra. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Theoretical study on the ring‐opening isomerization reaction mechanism of the ring isomers of N8H8
Authors: Wu Han‐Ying , Cai Wan‐Fei , Li Lai‐Cai , Tian An‐Min , Wong Ning‐Bew 
Published: May 2011

AbstractRing‐opening isomerization from ring‐shaped isomers to chain‐shaped isomers of N8H8 has been studied by a density function B3LYP method at 6‐311++G** level. 20 ring‐shaped isomers have been found to be able to transform into chain‐shaped isomers, with 20 possible transition states got by ring‐opening structure optimization. Furthermore, the ring‐openings have been found in the longer NN single bond by analyzing the length change of NN bond of ring‐shaped isomers in ring‐opening processes. In addition, with the activation energies in ring‐opening processes, the differences of the activation energies in isomerization between the isomers have been found according to the classification of rings. The activation energies in ring‐opening isomerization of six‐membered ring‐shaped isomers are higher than that of the four‐membered ring‐shaped isomers. It indicates that six‐membered ring‐shaped isomers difficult in ring‐opening in the isomerization are the steadiest ring‐shaped isomers of N8H8 while four‐membered ring‐shaped isomers easy in ring‐opening are the most unstable. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Accurate assessment of the strain energy in a protein‐bound drug using QM/MM X‐ray refinement and converged quantum chemistry
Authors: Fu Zheng , Li Xue , Merz Kenneth M. 
Published: May 2011

AbstractAn ongoing question regarding the energetics of protein‐ligand binding has been; what is the strain energy that a ligand pays (if any) when binding to its protein target? The traditional method to estimate strain energy uses force fields to calculate the energy difference between the ligand bound conformation and its nearest local minimum/global minimum on the gas‐phase or aqueous phase potential energy surface. This makes the implicit assumption that the underlying force field as well as the reference crystal structure is accurate. Herein, we use ibuprofen as a test case and compare MMFF and ab initio QM methods to identify the local and global minimum conformations. Nine low energy conformations were identified with HF/6‐31G* geometry optimization in vacuo. We also obtained highly accurate relative energies for ibuprofen's conformational energy surface based on M06/aug‐cc‐pVXZ (X = D and T), MP2/aug‐cc‐pVXZ (X = D and T) and the MP2/CBS method (with and without solvent corrections). Moreover, we curate and re‐refine the ibuprofen‐protein complex (PDB 2BXG) using QM/MM X‐ray refinement approaches (HF/6‐31G* was the QM method and the MM model was the AMBER force field ff99sb), which were compared with the low energy conformers to calculate the strain energy. The result indicates that there was an 88% reduction in ibuprofen conformation strain using the QM/MM refined structure versus the original PDB ibuprofen conformations. Furthermore, our results indicate that, due to its inherent limitations in estimating electrostatic interactions, force fields are not suitable to gauge strain energy for charged drug molecules like ibuprofen. The present work offers a carefully validated conformational potential energy surface for a drug molecule as well as a reliable QM/MM re‐refined X‐ray structure that can be used to test current structure‐based drug design approaches. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Evaluating neurophylogenetic patterns in the larval nervous systems of brachiopods and their evolutionary significance to other bilaterian phyla
Authors: Santagata Scott 
Published: May 2011

AbstractRecent structural analyses of invertebrate nervous systems have supported hypotheses stating that specific developmental and cytological aspects of larval and adult brains are conserved among bilaterian animals. Opposing views argue that structural similarities in larval nervous systems may be the result of convergent evolution and that the developmental diversity of adult brains is more indicative of several independent origins. Here, I use various cytological probes, confocal microscopy, and reconstruction techniques to investigate the cellular diversity within the larval nervous systems of Glottidia pyramidata and Terebratalia transversa (Brachiopoda). Neuronal cell types are compared among the rhynchonelliform, linguliform, and craniiform brachiopods as well as the phoronids. Although the respective larval types of the previously mentioned systematic groups clearly diverge in the neuroarchitecture of their larval apical organs (and nervous systems in general), a ground plan is proposed based on shared, centrally‐located, peptidergic neuronal cell types that can be compared with similar cell types in other lophotrochozoan phyla (bryozoans and spiralians). Assessing hierarchal levels of homology within and among the nervous systems of morphologically disparate phyla is challenging in that many phyla share early developmental signals that induce the specification of the neural ectoderm, clouding our ability to discern divergent larval and juvenile brain structure. Solving these problems will require a combined effort involving both traditional and more recent cytological techniques with a diversity of molecular probes that will better map the neuronal complexity of diverse invertebrate nervous systems. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc.
Immunohistological classification of ionocytes in the external gills of larval Japanese black salamander, Hynobius nigrescens Stejneger
Authors: Uchiyama Minoru , Kumano Tomoko , Komiyama Makiko , Yoshizawa Hideki , Matsuda Kouhei 
Published: May 2011

AbstractIn this cytological and immunohistological study, we clarified the localization of the membrane transporters Na+, K+‐ATPase (NKA), vacuolar‐type H+‐ATPase (VHA), and epithelial sodium channel (ENaC) and distinguished ionocyte subtypes in the gill of the Japanese salamander (Hynobius nigrescens). In larvae (IY stages 43–65), NKA immunoreactivity was observed on the basolateral plasma membrane in more than 60% cells and less than 20% cells in the primary filaments and secondary lamellae of the external gills, respectively. VHA immunoreactivity was observed on the apical membrane of some epithelial cells in the secondary lamellae of the external gills. High ENaCα immunoreactivity was widely observed on the apical cell membrane of a population of squamous cells, presumably pavement cells (PVCs), and mitochondria‐rich cells (MRCs), in the primary filaments and secondary lamellae of the external gills. Using double immunofluorescence microscopy, epithelial cell types involved in ionic regulation were characterized and divided into three ionocyte types: NKA‐, NKA‐ and ENaC‐, and VHA‐positive cells. VHA‐immunoreactive cells as well as NKA‐positive cells were observed during IY stages 43–65 of the salamander larvae. During late stages of metamorphosis, NKA, VHA, and ENaCα immunoreactivities in the external gills decreased and finally disappeared during the completion of metamorphosis (IY stage 68). PVCs and MRCs in the external gills are probably involved in acid–base balance regulation and osmoregulation in urodele amphibian larvae. The results are discussed in relation to the ionocytes previously reported in fish gills and the frog skin epithelium. J. Morphol., 2011. © 2011Wiley‐Liss, Inc.