bluuebunny/crossref_metadata_2025_split huggingface dataset:
IRAK‐4 kinase activity‐dependent and ‐independent regulation of lipopolysaccharide‐inducible genes
Authors: Koziczak‐Holbro Magdalena , Glück Anton , Tschopp Claude , Mathison John C. , Gram Hermann 
Published: February 2008

AbstractIRAK‐4 kinase inactive (IRAK‐4 KD) knock‐in mice display defects in TLR‐ and IL‐1 receptor signaling and are resistant to LPS‐induced shock. In the present study we examined the LPS‐induced response in IRAK‐4 KD mice in more detail. We show that IRAK‐4 kinase activity is required for certain aspects of TLR‐mediated signaling but not for others. We found that IRAK‐4 KD cells displayed reduced JNK and p38 signaling, while NF‐κB was activated to a normal level but with delayed kinetics compared to wild‐type cells. TLR4‐mediated IRF3 activation was intact in these cells. Comprehensive analysis of expression of LPS‐inducible genes by microarray demonstrated that IRAK‐4 KD cells were severely impaired in the expression of many pro‐inflammatory genes, suggesting their dependence on IRAK‐4 kinase activity. In contrast, the expression of a subset of LPS‐induced genes of anti‐viral response was not affected by IRAK‐4 kinase deficiency. Additionally, we demonstrate that LPS‐activated early expression and production of some cytokines, e.g., TNF‐α, is partially induced in the absence of IRAK‐4 kinase activity. This suggests that the partially unaffected TLR4‐mediated signaling could still drive expression of these genes in early phases and that IRAK‐4 kinase activity is important for a more sustained anti‐bacterial response.See accompanying commentary http://dx.doi.org/10.1002/eji.200838161
Hydrothermal Synthesis and Structural Characterization of the High‐Valent Ruthenium‐Containing Polyoxoanion [{PW11O39}2{(HO)RuIV–O–RuIV(OH)}]10–
Authors: Chen Su‐Wen , Villanneau Richard , Li Yanling , Chamoreau Lise‐Marie , Boubekeur Kamal , Thouvenot René , Gouzerh Pierre , Proust Anna 
Published: February 2008

AbstractThe high‐valent ruthenium‐containing [{PW11O39}2{(HO)RuIV–O–RuIV(OH)}]10– anion (1) has been synthesized by hydrothermal reaction and characterized by X‐ray diffraction, IR, multinuclear (31P and 183W) NMR spectroscopy andelectrochemistry. Single‐crystal analysis was carried outon Rb10[{PW11O39}2{(HO)RuIV–O–RuIV(OH)}]·21H2O, which crystallizes in the monoclinic system, space group P21/n, with a = 11.1912(14), b = 21.9257(12), c = 38.7310(96) Å, β = 94.682(19)°, V = 9472(3) Å3, Z = 4. Polyanion 1 consists of two lacunary [α‐PW11O39]7– anions connected by a linear {(HO)Ru–O–Ru(OH)}4+ unit. Each ruthenium ion achieves six‐coordination through interaction with two terminal oxo ligands from the lacuna of each [PW11O39]7– anion.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Oxazoline‐Substituted Prolinamide‐Based Organocatalysts for the Direct Intermolecular Aldol Reaction between Cyclohexanone and Aromatic Aldehydes
Authors: Doherty Simon , Knight Julian G. , McRae Amy , Harrington Ross W. , Clegg William 
Published: February 2008

AbstractOxazoline‐substituted prolinamides catalyse the direct asymmetric aldol reaction between cyclohexanone and a range of aldehydes to give excellent conversions and enantioselectivities up to 84 % under optimum conditions. Reactions were highly substrate‐specific with electron‐deficient aldehydes giving the highest yields and ee values. The absolute configuration of the 4‐chlorobenzaldehyde‐derived product was unequivocally established as (2S,1′R) by single‐crystal X‐ray analysis, and the stereochemistry of the product was shown to be determined principally by the stereochemistry of the proline fragment.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Stable‐Ion NMR and GIAO‐DFT Study of the Carbocations from Benzofluorenes and Dibenzofluorenes; Synthesis of Nitro Derivatives; Mutagenicity Assay and X‐ray Analysis
Authors: Laali Kenneth K. , Okazaki Takao , Sultana Fatima , Bunge Scott D. , Banik Bimal K. , Swartz Carol 
Published: February 2008

AbstractFirst examples of stable carbocations are reported from 7H‐benzo[c]fluorene (2), 11H‐benzo[b]fluorene (3), 11H‐benzo[a]fluorene (4), 2‐methoxy‐ (5), 7‐methoxy‐ (6), and 9‐methoxy‐11H‐benzo[a]fluorene (7), 7H‐dibenzo[c,g]fluorene (8), 13H‐dibenzo[a,g]fluorene (9), 2‐methoxy‐13H‐dibenzo[a,g]fluorene (10) and 5,6‐dihydro‐13H‐dibenzo[a,g]fluorene (11). Charge‐delocalization modes in the resulting carbocations were derived based on experimental and/or computed (GIAO‐DFT) Δδ13C values and through the NPA‐derived changes in charges (Δq). Whereas protonation regioselectivity in the parent systems (2, 3, 4, 8, and 9) corresponds to the energetically most favored carbocations computed by DFT, selectivity in the OMe‐substituted derivatives (5, 6, 7, 10, and 11) is strongly controlled by the methoxy group. Benzofluorenes 3, 5, 6, and 7 and dibenzofluorenes 8, and 10 were nitrated under very mild conditions. Nitration selectivity in the parent systems 3 and 8 parallels those in stable‐ion protonation, whereas regioselectivity in the MeO derivatives (6, 7, and 10) corresponds more closely to relative arenium ion energies in the parent unsubstituted systems. Comparative mutagenicity assays (Ames tests) were performed on 3NO2, 5NO2, 7NO2, 8NO2, and 10NO2 relative to their precursors. Compounds 10NO2, 7NO2, and 8NO2 were found to be potent direct‐acting mutagens (with 10NO2, 8NO2 also capable of acting as potent indirect mutagens). The X‐ray structures of 5NO2 and 8NO2 were determined. The angle between the plane of the nitro group and the aromatic ring bearing the NO2 group is 89.4° in 5NO2 and 32.4° in 8NO2. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Asymmetric Synthesis of cis‐4‐ and trans‐3‐Hydroxypipecolic Acids
Authors: Alegret Carlos , Ginesta Xavier , Riera Antoni 
Published: February 2008

AbstractEnantioselective syntheses of cis‐4‐ and trans‐3‐hydroxypipecolic acids from 2,3‐epoxy‐5‐hexen‐1‐ol (7) are described. Regioselective C‐3 or C‐2 ring opening of the epoxide by the appropriate nitrogen nucleophile is the key step in each route. As enantiomerically enriched epoxy alcohols are readily available in any configuration by Sharpless epoxidation, both enantiomers are equally accessible. This approach was also employed to synthesize the natural product baikiain and the important synthetic intermediate trans‐3‐hydroxy‐2‐hydroxymethylpiperidine. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
A Modular Methodology for the Synthesis of 4‐ and 3‐Substituted Benzene and Aniline C‐Ribonucleosides
Authors: Štefko Martin , Pohl Radek , Klepetářová Blanka , Hocek Michal 
Published: February 2008

AbstractA modular, efficient, and practical methodology for the preparation of 4‐ and 3‐substituted benzene and aniline C‐ribonucleosides was developed. Addition of 4‐ or 3‐bromophenyllithium (2 or 12) to TBDMS‐protected ribonolactone 3 gave hemiacetal adducts 4 or 13 as pure β‐anomers. Their reduction with Et3SiH and BF3·Et2O afforded the desired protected 4‐ or 3‐bromophenyl‐C‐ribonucleosides 6 or 15 in 66 and 75 %, respectively, over two steps from 3. Bromophenyl intermediates 6 and 15 were subjected to a series of palladium‐catalyzed cross‐coupling, alkoxylation, and amination reactions to give a series of protected 1β‐(3‐ and 4‐substituted phenyl)ribonuleosides 9 and 18. Deprotection of silylated nucleosides 9 or 18 by Et3N·3HF afforded a series of free C‐ribonucleosides 10 or 19 (20 examples). (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Heritability of body size and muscle strength in young adulthood: a study of one million Swedish men
Authors: Silventoinen Karri , Magnusson Patrik K. E. , Tynelius Per , Kaprio Jaakko , Rasmussen Finn 
Published: February 2008

AbstractModerate heritability for skeletal muscle strength has been reported in twin studies, but genetic co‐variation between muscle strength at different parts of body and body size is not well known. Further, representativeness of twin cohorts needs to be critically evaluated. Height, weight, elbow flexion, hand grip and knee extension strength were measured in young adulthood in 1,139,963 Swedish men born between 1951 and 1976. We identified 154,970 full‐brother pairs and 1582 monozygotic (MZ) and 1864 same‐sex dizygotic (DZ) complete twin pairs. The data were analyzed using quantitative genetic modeling for twin and family data. Twins compared to singletons and MZ twins compared to DZ twins were shorter, lighter and had lower muscle strength. In singletons, there was more variation in weight and the strength measures compared to twins with known zygosity but not when compared to twins with unknown zygosity. Full‐sib correlations for these traits were lower than DZ correlations. Additive genetic factors explained 81% of variation in height, 59% in body mass index and 50–60% in the strength measures. Additive genetic correlations varied from 0.13 between height and elbow flexion strength to 0.78 between elbow flexion and hand grip strength. Our results suggest that extra variation may exist in general populations not found in twin samples, probably because of selection due to non‐participation. This may have inflated heritability estimates in previous twin studies. Nonetheless, we showed that genetic factors affect muscle strength and part of these genes are common to different strength indicators and body size. Genet. Epidemiol. © 2008 Wiley‐Liss, Inc.
Hepatitis C infection and risk of malignant lymphoma
Authors: Schöllkopf Claudia , Smedby Karin Ekström , Hjalgrim Henrik , Rostgaard Klaus , Panum Inge , Vinner Lasse , Chang Ellen T. , Glimelius Bengt , Porwit Anna , Sundström Christer , Hansen Mads , Adami Hans‐Olov , Melbye Mads 
Published: February 2008

AbstractThe association between hepatitis C virus (HCV) infection and risk of malignant lymphoma remains controversial, perhaps due to small‐sized studies and low prevalence of HCV in the general population. On the basis of a large Danish‐Swedish population‐based case‐control study, 2,819 lymphoma patients and 1,856 controls of second‐generation Danish‐Swedish origin were screened for HCV infection using an enzyme‐linked immunosorbent assay and a confirming recombinant immunoblot assay (RIBA) test. Positive samples were tested with real‐time PCR for the presence of HCV RNA. The association between HCV infection and risk of malignant lymphoma was assessed by logistic regression. When intermediate RIBA test results were interpreted as positive, anti‐HCV antibody positivity was associated with a nonsignificant increased risk of non‐Hodgkin lymphoma (NHL) overall (odds ratio (OR) = 2.2; 95% confidence interval (CI) 0.9–5.3; n = 20 cases), of B‐cell lymphomas combined (OR = 2.4 [1.0–5.8]; n = 20) and of lymphoplasmacytic lymphoma (OR = 5.2 [1.0–26.4]; n = 2). No patients with T‐cell or Hodgkin lymphoma were HCV‐positive. A more conservative definition of HCV positivity (disregarding intermediate RIBA results) resulted in an OR = 1.6 (0.3–8.5; n = 5) for NHL overall. When the definition was further restricted to require HCV RNA positivity, OR was 1.7 (0.2–16.2; n = 3) for NHL overall. Our findings from a population with a low prevalence of HCV suggest a positive association between HCV and risk of NHL, in particular of B‐cell origin. © 2008 Wiley‐Liss, Inc.
First‐principles and molecular‐dynamics study of structure and bonding in perovskite‐type oxynitrides ABO2N (A = Ca, Sr, Ba; B = Ta, Nb)
Authors: Wolff Holger , Dronskowski Richard 
Published: February 2008

AbstractA series of perovskite‐type phases of alkaline‐earth‐based tantalum and niobium oxynitrides has been studied using both first‐principles electronic‐structure calculations and molecular‐dynamics simulations, in particular by investigating different structural arrangements and anion distributions in terms of total‐energy calculations. The structural properties are explained on the basis of COHP chemical bonding analyses and semiempirical molecular orbital calculations. We provide theoretical proof for the surprising result that the local site symmetries of these phases are lower than cubic because density‐functional calculations clearly show that all crystallographic unit cells are better described as being orthorhombic with space group Pmc21 to optimize metal–nitrogen bonding; nonetheless, there is no contradiction with a macroscopic cubic description of the structures of BaTaO2N and BaNbO2N adopting space group Pmm. Additionally, we find that the anionic sublattice is ordered in all compounds studied over a wide temperature range. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
DFT study of the cryptand and benzocryptand and their complexes with alkali metal cations: Li+, Na+, K+
Authors: Wang Xueye , Wang Hengliang , Tan Yuanqiang 
Published: February 2008

AbstractIn the present work, a theoretical study of the cryptand 4, 7, 13, 16, 21, 24‐hexaoxa‐1, 10‐ diazabicyclo [8,8,8] hexacosan (the named [222]) and the cryptand 5, 6‐benzo‐4, 7, 13, 16, 21, 24‐hexaoxa‐1, 10‐diazabicyclo [8, 8, 8] hexacosan (the nemed [222B]) had been done using density functional theory (DFT) with B3LYP/6‐31G* method in order to obtain the electronic and geometrical structure of the cryptands and their complexes with alkali metal ions: Li+, Na+, and K+. The nucleophilicity of cryptands had been investigated by the Fukui function. For complexes, the match between cation and cavity size, the status of interaction between alkali metal ions and donor atoms in the cryptands and the rigidity of the cryptands had been analyzed through the other calculated parameters. In addition, the enthalpies of complexation reaction and cation exchange reaction had been studied by the calculated thermodynamic data. The calculated results are in a good agreement with the experimental data for the complexes. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
The calculation of static polarizabilities of 1‐3D periodic compounds. the implementation in the crystal code
Authors: Ferrero Mauro , Rérat Michel , Orlando Roberto , Dovesi Roberto 
Published: February 2008

AbstractThe Coupled Perturbed Hartree–Fock (CPHF) scheme has been implemented in the CRYSTAL06 program, that uses a gaussian type basis set, for systems periodic in 1D (polymers), 2D (slabs), 3D (crystals) and, as a limiting case, 0D (molecules), which enables comparison with molecular codes. CPHF is applied to the calculation of the polarizability α of LiF in different aggregation states: finite and infinite chains, slabs, and cubic crystal. Correctness of the computational scheme for the various dimensionalities and its numerical efficiency are confirmed by the correct trend of α: α for a finite linear chain containing N LiF units with large N tends to the value for the infinite chain, N parallel chains give the slab value when N is sufficiently large, and N superimposed slabs tend to the bulk value. CPHF results compare well with those obtained with a saw‐tooth potential approach, previously implemented in CRYSTAL. High numerical accuracy can easily be achieved at relatively low cost, with the same kind of dependence on the computational parameters as for the SCF cycle. Overall, the cost of one component of the dielectric tensor is roughly the same as for the SCF cycle, and it is dominated by the calculation of two‐electron four‐center integrals. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Collective motions of rigid fragments in protein structures from smoothed electron density distributions
Authors: Leherte Laurence , Vercauteren Daniel P. 
Published: February 2008

AbstractIn this work, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM) approaches are applied to describe the dynamics of protein structure graphs built from calculated promolecular electron density (ED) distribution functions. A first set of analyses is carried out on results obtained from ED maxima calculated at various smoothing levels. A second set is achieved for ED networks whose edges are weighted by ED overlap integral values. Results are compared with those obtained through the classical GNM and ANM approaches applied to networks of Cα atoms. It is shown how the network model and the consideration of crystal packing as well as of the side chains may lead to various improvements dependent upon the structure under study. The selected protein structures are Crambin and Pancreatic Trypsin Inhibitor because of their small size and numerous dynamical data obtained by other authors. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
A versatile AMBER‐Gaussian QM/MM interface through PUPIL
Authors: Torras Juan , Seabra Gustavo de M. , Deumens Erik , Trickey S. B. , Roitberg Adrian E. 
Published: February 2008

AbstractThe PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface different programs for multiscale calculations in materials sciences (Torras et al., J Comput Aided Mater Des 2006, 13, 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we present an extension of PUPIL to computational chemistry by interfacing two widely used computational chemistry programs: AMBER (molecular dynamics) and Gaussian (quantum chemistry). The benefit is to allow the application of the advanced MD techniques available in AMBER to a hybrid QM/MM system in which the forces and energy on the QM part can be computed by any of the methods available in Gaussian. To illustrate, we present two example applications: A MD calculation of alanine dipeptide in explicit water, and a use of the steered MD capabilities in AMBER to calculate the free energy of reaction for the dissociation of Angeli's salt. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Reaction mechanisms of dissociative chemisorption of HI, I2, and CH3I on a magic cluster Al
Authors: Kim Jong Chan , Kim Kyoung Hoon , Jung Jaehoon , Han Young‐Kyu 
Published: February 2008

AbstractWe have investigated the transition‐state structures and reaction mechanisms for the dissociative chemisorption reactions of HI, I2, and CH3I on the magic cluster Al. The HI, I2, and CH3I molecules approach Al with an end‐on orientation rather than a side‐on orientation because of the more effective orbital overlap in the end‐on orientation. The reactions of Al with HI and I2 would produce Al13HI– and Al13I2−, respectively, because of large exothermic energy changes and relatively small activation energies. The reaction of Al with CH3I is unlikely to take place because of the low mobility of CH3 on Al and the high activation barrier for the SN2‐type reaction. The dissociative chemisorption reactions are preferred thermodynamically to the abstractive chemisorption reactions. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Targeted combinatorial therapy of non‐small cell lung carcinoma using a GST‐fusion protein of full‐length or truncated MDA‐7/IL‐24 with Tarceva
Authors: Gupta Pankaj , Emdad Luni , Lebedeva Irina V. , Sarkar Devanand , Dent Paul , Curiel David T. , Settleman Jeffrey , Fisher Paul B. 
Published: February 2008

AbstractMelanoma differentiation associated gene‐7/interleukin‐24 (mda‐7/IL‐24), a cytokine belonging to the IL‐10 family, displays cancer‐specific apoptosis‐inducing properties when delivered by a replication‐incompetent adenovirus (Ad.mda‐7) or as a GST‐tagged recombinant protein (GST‐MDA‐7). Previous studies demonstrated that an adenovirus expressing M4, a truncated version of MDA‐7/IL‐24 containing amino acid residues 104–206, also induced similar cancer‐specific apoptosis. We generated recombinant GST‐M4 proteins and examined the potency of GST‐MDA‐7 and GST‐M4 on a panel of epidermal growth factor receptor (EGFR) wild type and mutant non‐small cell lung carcinoma (NSCLC) cells either as a single agent or in combination with a reversible EGFR inhibitor, Tarceva. The combination of either GST‐MDA‐7 or GST‐M4 (∼0.1 µM) and Tarceva (10 µM), at sub‐optimal apoptosis‐inducing concentrations synergistically enhanced growth inhibition and apoptosis induction over that observed with either agent alone. The combination treatment also augmented inhibition of EGFR signaling, analyzed by phosphorylation of EGFR and its downstream effectors AKT and ERK1/2, over that with single‐agent therapy. Tarceva enhanced GST‐MDA‐7 and GST‐M4 toxicity in cells expressing mutated EGFR proteins that are resistant to the inhibitory effects of Tarceva. In total, these data suggest that combined treatment of NSCLC cells with an EGFR inhibitor can augment the efficacy of GST‐MDA‐7 and GST‐M4 and that the EGFR inhibitor Tarceva may mediate this combinatorial effect by inhibiting multiple tyrosine kinases in addition to the EGFR. This approach highlights a potential new combinatorial strategy, which may prove beneficial for NSCLC patients with acquired resistance to EGFR inhibitors. J. Cell. Physiol. 215: 827–836, 2008. © 2008 Wiley‐Liss, Inc.
Compressive moduli of the human medial meniscus in the axial and radial directions at equilibrium and at a physiological strain rate
Authors: Chia Helena N. , Hull M. L. 
Published: February 2008

AbstractThe axial and radial compressive moduli of the human meniscus are important material properties in tibiofemoral joint models, but they have not been determined previously for fresh‐frozen tissue. Our goals were to measure the moduli at equilibrium and at a physiological strain rate, to determine whether the axial and radial compressive moduli are equal for each type of loading, and to determine whether they depend on the region (i.e., anterior, middle, posterior) of the meniscus. Samples from each region from 10 fresh‐frozen human medial menisci were tested in unconfined compression at four strain levels (3%, 6%, 9%, and 12%) at 32%/s, a strain rate determined to be physiologically relevant to walking, and then allowed to reach equilibrium in stress relaxation. At equilibrium, the axial and radial compressive moduli at 12% strain were 83.4 kPa and 76.1 kPa, respectively (p = 0.58), whereas at the physiological strain rate, the axial and radial compressive moduli at 12% strain were 718 kPa and 605 kPa, respectively (p = 0.61). At the physiological strain rate, the modulus increased with increasing strain (79.2 kPa at 3% strain vs. 662 kPa at 12% strain) and the modulus in the anterior region (1,048 kPa at 12% strain) was significantly greater than that in the posterior region (329 kPa at 12% strain) (p = 0.04). Our study supports a plane of isotropy for the material properties of meniscal tissue. However, the material behavior is strongly nonlinear because the compressive modulus is several orders of magnitude smaller than previously reported values for tensile modulus. Further, the compressive modulus depends on the activity of interest (i.e., static such as standing or dynamic such as walking) due to viscoelastic effects, the strain level, and the region of the tissue. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:951–956, 2008