bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi‐scale assimilation of root zone soil water predictions
Authors: Lü Haishen , Yu Zhongbo , Horton Robert , Zhu Yonghua , Wang Zhenlong , Hao Zhenchun , Xiang Long
Published: February 2011

When hydrology model parameters are determined, a traditional data assimilation method (such as Kalman filter) and a hydrology model can estimate the root zone soil water with uncertain state variables (such as initial soil water content). The simulated result can be quite good. However, when a key soil hydraulic property, such as the saturated hydraulic conductivity, is overestimated or underestimated, the traditional soil water assimilation process will produce a persistent bias in its predictions. In this paper, we present and demonstrate a new multi‐scale assimilation method by combining the direct insertion assimilation method, particle swarm optimisation (PSO) algorithm and Richards equation. We study the possibility of estimating root zone soil water with a multi‐scale assimilation method by using observedin situdata from the Wudaogou experiment station, Huaihe River Basin, China. The results indicate there is a persistent bias between simulated and observed values when the direct insertion assimilation surface soil water content is used to estimate root zone soil water contents. Using a multi‐scale assimilation method (PSO algorithm and direct insertion assimilation) and an assumed bottom boundary condition, the results show some obvious improvement, but the root mean square error is still relatively large. When the bottom boundary condition is similar to the actual situation, the multi‐scale assimilation method can well represent the root zone soil water content. The results indicate that the method is useful in estimating root zone soil water when available soil water data are limited to the surface layer and the initial soil water content even when the soil hydraulic conductivities are uncertain. Copyright © 2011 John Wiley & Sons, Ltd.
Skeletal recovery after weaning does not require PTHrP
Authors: Kirby Beth J , Ardeshirpour Laleh , Woodrow Janine P , Wysolmerski John J , Sims Natalie A , Karaplis Andrew C , Kovacs Christopher S
Published: February 2011

Mice lose 20% to 25% of trabecular bone mineral content (BMC) during lactation and restore it after weaning through unknown mechanisms. We found that tibial Pthrp mRNA expression was upregulated fivefold by 7 days after weaning versus end of lactation in wild-type (WT) mice. To determine whether parathyroid hormone–related protein (PTHrP) stimulates bone formation after weaning, we studied a conditional knockout in which PTHrP is deleted from preosteoblasts and osteoblasts by collagen I promoter–driven Cre (CreColI). These mice are osteopenic as adults but have normal serum calcium, calcitriol, and parathyroid hormone (PTH). Pairs of Pthrpflox/flox;CreColI (null) and WT;CreColI (WT) females were mated and studied through pregnancy, lactation, and 3 weeks of postweaning recovery. By end of lactation, both genotypes lost lumbar spine BMC: WT declined by 20.6% ± 3.3%, and null decreased by 22.5% ± 3.5% (p < .0001 versus baseline; p = NS between genotypes). During postweaning recovery, both restored BMC to baseline: WT to –3.6% ± 3.7% and null to 0.3% ± 3.7% (p = NS versus baseline or between genotypes). Similar loss and full recovery of BMC were seen at the whole body and hind limb. Histomorphometry confirmed that nulls had lower bone mass at baseline and that this was equal to the value achieved after weaning. Osteocalcin, propeptide of type 1 collagen (P1NP), and deoxypyridinoline increased equally during recovery in WT and null mice; PTH decreased and calcitriol increased equally; serum calcium was unchanged. Urine calcium increased during recovery but remained no different between genotypes. Although osteoblast-derived PTHrP is required to maintain adult bone mass and Pthrp mRNA upregulates in bone after weaning, it is not required for recovery of bone mass after lactation. The factors that stimulate postweaning bone formation remain unknown. © 2011 American Society for Bone and Mineral Research.
Safety and efficacy of the cathepsin K inhibitor ONO-5334 in postmenopausal osteoporosis: The OCEAN study
Authors: Eastell Richard , Nagase Shinichi , Ohyama Michiyo , Small Maria , Sawyer James , Boonen Steven , Spector Tim , Kuwayama Tomohiro , Deacon Steve
Published: February 2011

Osteoporosis occurs when there is an imbalance between resorption and formation of bone, with resorption predominating. Inhibitors of cathepsin K may rebalance this condition. This is the first efficacy study of a new cathepsin K inhibitor, ONO-5334. The objective of the study was to investigate the efficacy and safety of ONO-5334 in postmenopausal osteoporosis. This was a 12-month, randomized, double-blind, placebo- and active-controlled parallel-group study conducted in 13 centers in 6 European countries. Subjects included 285 postmenopausal women aged 55 to 75 years with osteoporosis. Subjects were randomized into one of five treatment arms: placebo; 50 mg twice daily, 100 mg once daily, or 300 mg once daily of ONO-5334; or alendronate 70 mg once weekly. Lumbar spine, total hip, and femoral neck BMD values were obtained along with biochemical markers of bone turnover and standard safety assessments. All ONO-5334 doses and alendronate showed a significant increase in BMD for lumbar spine, total hip (except 100 mg once daily), and femoral neck BMD. There was little or no suppression of ONO-5334 on bone-formation markers compared with alendronate, although the suppressive effects on bone-resorption markers were similar. There were no clinically relevant safety concerns. With a significant increase in BMD, ONO-5334 also demonstrated a new mode of action as a potential agent for treating osteoporosis. Further clinical studies are warranted to investigate long-term efficacy as well as safety of ONO-5334. © 2011 American Society for Bone and Mineral Research.
Bone turnover markers and bone mineral density response with risedronate therapy: Relationship with fracture risk and patient adherence
Authors: Eastell Richard , Vrijens Bernard , Cahall David L , Ringe Johann D , Garnero Patrick , Watts Nelson B
Published: February 2011

Surrogate markers of fracture risk—bone turnover markers (BTMs) and bone mineral density (BMD)—can be used to monitor treatment response. We assessed whether changes in these markers greater than the least significant change (LSC) were associated with fracture risk reduction and greater adherence. This secondary analysis of the Improving Measurements of Persistence on ACtonel Treatment (IMPACT) study—a multinational prospective, open-label, cluster-randomized study of postmenopausal women on oral risedronate 5 mg/d for 52 weeks—assessed adherence by electronic monitors. Urinary N-terminal cross-linked telopeptide of type 1 collagen (uNTX) and serum C-terminal cross-linked telopeptide of type 1 collagen (sCTX) levels were assessed at baseline and weeks 10 and 22, and BMD at baseline and week 52. Fractures were recorded as adverse events. In 2302 women, responses beyond LSC in BTMs (uNTX and sCTX) and BMD (spine only) were associated with a reduced risk of nonvertebral fractures (NVFs) and all fractures. NVF incidence was about 50% lower in patients with 30% or more of uNTX reduction at week 22 (1.6%) than in those with less than 30% reduction (3.2%, p = .015). NVFs also were reduced in patients with more than 3% spine BMD increase at 52 weeks than those with 3% or less. Responses greater than LSC in BTMs and BMD were associated with greater adherence, but there was no association between adherence and fracture outcomes at 52 weeks. Changes greater than the LSC in BTMs and BMD reflect better treatment adherence, were associated with fracture risk reduction, and identify differences in individual responsiveness to risedronate. © 2011 American Society for Bone and Mineral Research.
CYR61 downregulation reduces osteosarcoma cell invasion, migration, and metastasis
Authors: Fromigue Olivia , Hamidouche Zahia , Vaudin Pascal , Lecanda Fernando , Patino Ana , Barbry Pascal , Mari Bernard , Marie Pierre J
Published: February 2011

Osteosarcoma is the most common primary tumor of bone. The rapid development of metastatic lesions and resistance to chemotherapy remain major mechanisms responsible for the failure of treatments and the poor survival rate for patients. We showed previously that the HMGCoA (3-hydroxy-3-methylglutaryl-coenzyme A) reductase inhibitor statin exhibits antitumoral effects on osteosarcoma cells. Here, using microarray analysis, we identify Cyr61 as a new target of statins. Transcriptome and molecular analyses revealed that statins downregulate Cyr61 expression in human and murine osteosarcoma cells. Cyr61 silencing in osteosarcoma cell lines enhanced cell death and reduced cell migration and cell invasion compared with parental cells, whereas Cyr61 overexpression had opposite effects. Cyr61 expression was evaluated in 231 tissue cores from osteosarcoma patients. Tissue microarray analysis revealed that Cyr61 protein expression was higher in human osteosarcoma than in normal bone tissue and was further increased in metastatic tissues. Finally, tumor behavior and metastasis occurrence were analyzed by intramuscular injection of modified osteosarcoma cells into BALB/c mice. Cyr61 overexpression enhanced lung metastasis development, whereas cyr61 silencing strongly reduced lung metastases in mice. The results reveal that cyr61 expression increases with tumor grade in human osteosarcoma and demonstrate that cyr61 silencing inhibits in vitro osteosarcoma cell invasion and migration as well as in vivo lung metastases in mice. These data provide a novel molecular target for therapeutic intervention in metastatic osteosarcoma. © 2011 American Society for Bone and Mineral Research.
Trabecular bone microstructure and local gene expression in iliac crest biopsies of men with idiopathic osteoporosis
Authors: Patsch Janina M , Kohler Thomas , Berzlanovich Andrea , Muschitz Christian , Bieglmayr Christian , Roschger Paul , Resch Heinrich , Pietschmann Peter
Published: February 2011

Male idiopathic osteoporosis (MIO) is a metabolic bone disease that is characterized by low bone mass, microstructural alterations, and increased fracture risk in otherwise healthy men. Although the detailed pathophysiology of MIO has yet to be clarified, evidence increasingly suggests an osteoblastic defect as the underlying cause. In this study we tested the hypothesis that the expression profile of certain osteoblastic or osteoblast-related genes (ie, WNT10B, RUNX2, Osterix, Osteocalcin, SOST, RANKL, and OPG) is different in iliac crest biopsies of MIO patients when compared with healthy controls. Furthermore, we investigated the relation of local gene expression characteristics with histomorphometric, microstructural, and clinical features. Following written informed consent and diligent clinical patient characterization, iliac crest biopsies were performed in nine men. While RNA extraction, reverse-transcription, and real-time polymerase chain reactions (PCRs) were performed on one biopsy, a second biopsy of each patient was submitted for histomorphometry and micro–computed tomography (µCT). Age-matched bone samples from forensic autopsies served as controls. MIO patients displayed significantly reduced WNT10B, RUNX2, RANKL, and SOST expression. Performing µCT for the first time in MIO biopsies, we found significant decreases in trabecular number and connectivity density. Trabecular separation was increased significantly, but trabecular thickness was similar in both groups. Histomorphometry revealed decreased BV/TV and osteoid volume and fewer osteoclasts in MIO. By providing evidence for reduced local WNT10B, RUNX2, and RANKL gene expression and histomorphometric low turnover, our data support the osteoblast dysfunction model discussed for MIO. Further, MIO seems to lead to a different microstructural pathology than age-related bone loss. © 2011 American Society for Bone and Mineral Research.
Sclerostin is a locally acting regulator of late-osteoblast/preosteocyte differentiation and regulates mineralization through a MEPE-ASARM-dependent mechanism
Authors: Atkins Gerald J , Rowe Peter S , Lim Hui P , Welldon Katie J , Ormsby Renee , Wijenayaka Asiri R , Zelenchuk Lesya , Evdokiou Andreas , Findlay David M
Published: February 2011

The identity of the cell type responsive to sclerostin, a negative regulator of bone mass, is unknown. Since sclerostin is expressed in vivo by mineral-embedded osteocytes, we tested the hypothesis that sclerostin would regulate the behavior of cells actively involved in mineralization in adult bone, the preosteocyte. Differentiating cultures of human primary osteoblasts exposed to recombinant human sclerostin (rhSCL) for 35 days displayed dose- and time-dependent inhibition of in vitro mineralization, with late cultures being most responsive in terms of mineralization and gene expression. Treatment of advanced (day 35) cultures with rhSCL markedly increased the expression of the preosteocyte marker E11 and decreased the expression of mature markers DMP1 and SOST. Concomitantly, matrix extracellular phosphoglycoprotein (MEPE) expression was increased by rhSCL at both the mRNA and protein levels, whereas PHEX was decreased, implying regulation through the MEPE-ASARM axis. We confirmed that mineralization by human osteoblasts is exquisitely sensitive to the triphosphorylated ASARM-PO4 peptide. Immunostaining revealed that rhSCL increased the endogenous levels of MEPE-ASARM. Importantly, antibody-mediated neutralization of endogenous MEPE-ASARM antagonized the effect of rhSCL on mineralization, as did the PHEX synthetic peptide SPR4. Finally, we found elevated Sost mRNA expression in the long bones of HYP mice, suggesting that sclerostin may drive the increased MEPE-ASARM levels and mineralization defect in this genotype. Our results suggest that sclerostin acts through regulation of the PHEX/MEPE axis at the preosteocyte stage and serves as a master regulator of physiologic bone mineralization, consistent with its localization in vivo and its established role in the inhibition of bone formation. © 2011 American Society for Bone and Mineral Research.
13 years of cultured limbal epithelial cell therapy: A review of the outcomes
Authors: Baylis Oliver , Figueiredo Francisco , Henein Christin , Lako Majlinda , Ahmad Sajjad
Published: February 2011

The cornea is the clear tissue at the front of the eye which enables the transmission of light to the retina for normal vision. The surface of the cornea is composed of an epithelium which is renewed by stem cells located at the periphery of the cornea, a region known as the limbus. These limbal stem cells can become deficient as a result of various diseases of the eye's surface, resulting in the blinding disease of limbal stem cell deficiency. The treatment of this disease is often difficult and complex. In 1997, it was proposed that a small amount of limbal tissue containing limbal stem cells could be culture expanded and then transplanted. Since then various case reports and case series have been reported showing promising results. Here, we review the outcomes of this procedure over the past 13 years with the aim of highlighting the best culture and surgical techniques to date. J. Cell. Biochem. 112: 993–1002, 2011. © 2011 Wiley‐Liss, Inc.
Role of C/EBP‐β, p38 MAPK, and MKK6 in IL‐1β‐mediated C3 gene regulation in astrocytes
Authors: Maranto Jeffrey , Rappaport Jay , Datta Prasun K.
Published: February 2011

Complement component C3, the central player in the complement cascade and the pro‐inflammatory cytokine IL‐1β is expressed by activated glial cells and may contribute to neurodegeneration. This study examines the regulation of the expression of C3 by IL‐1β in astroglial cells focusing on the role of the upstream kinase MKK6, p38‐α MAPK, and C/EBP‐β isoforms (LAP1, LAP2, or LIP) in astroglial cells. Activation of human astroglial cell line, U373 with IL‐1β, led to the induction of C3 mRNA and protein expression as determined by real‐time RT‐PCR and Western blot analysis, respectively. This induction was suppressed by the pharmacological inhibitor of p38 MAPK (i.e., SB202190‐HCl), suggesting the involvement of p38 MAPK in C3 gene expression. IL‐1β also induced C3 promoter activity in U373 cells in a MAP kinase‐ and C/EBP‐β‐dependent manner. Cotransfection of C3 luciferase reporter construct with constitutively active form of the upstream kinase in the MAP kinase cascade, that is, MKK6 (the immediate upstream activator of p38 kinase) resulted in marked stimulation of the promoter activity, whereas overexpression of a dominant negative forms of MKK6 and p38α MAPK inhibited C3 promoter activity. Furthermore, a mutant form of C/EBP‐β, LAPT235A showed reduction in IL‐1β‐mediated C3 promoter activation. These results suggest that the p38α, MAPK, and MKK6 play prominent roles in IL‐1β and C/EBP‐β‐mediated C3 gene expression in astrocytes. J. Cell. Biochem. 112: 1168–1175, 2011. © 2011 Wiley‐Liss, Inc.
Web servers and services for electrostatics calculations with APBS and PDB2PQR
Authors: Unni Samir , Huang Yong , Hanson Robert M. , Tobias Malcolm , Krishnan Sriram , Li Wilfred W. , Nielsen Jens E. , Baker Nathan A.
Published: February 2011

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal‐enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Consideration of data load time on modern processors for the Verlet table and linked‐cell algorithms
Authors: Fomin Eduard S.
Published: February 2011

Neighbor search algorithms are widely used in molecular dynamics for the direct computation of short‐range pairwise interatomic potentials. These algorithms are based on the Verlet table (VT) and linked‐cell (LC) methods. It is widely believed that the VT is more efficient than the LC. The analysis of these methods shows that in case when the average number of interactions per particle is relatively large, or more specifically, the particle density ρ and skin radius rskin meet the condition (4π/6) ρr/27 ≫ 1, which may be true for most simulations of liquids, the number of memory data load operations in the LC is much less than that in the VT. Because memory access on modern processors is a bottleneck, this advantage of the LC should be and was in fact used, and a code outperforming the VT by a factor of almost 2 was obtained. Some modifications of the VT were proposed to reduce its disadvantage concerning memory data loading. The key modifications included automated skin radius tuning during simulations and compression of the VT to minimize duplications of atom identifiers in its nearby rows. Although these modifications had improved the performance, the VT failed to regain the superiority over the LC. The methods were tested in the MOLKERN simulation software by using SIMD and multithreading. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Bringing about matrix sparsity in linear‐scaling electronic structure calculations
Authors: Rubensson Emanuel H. , Rudberg Elias
Published: February 2011

The performance of linear‐scaling electronic structure calculations depends critically on matrix sparsity. This article gives an overview of different strategies for removal of small matrix elements, with emphasis on schemes that allow for rigorous control of errors. In particular, a novel scheme is proposed that has significantly smaller computational overhead compared with the Euclidean norm‐based truncation scheme of Rubensson et al. (J Comput Chem 2009, 30, 974) while still achieving the desired asymptotic behavior required for linear scaling. Small matrix elements are removed while ensuring that the Euclidean norm of the error matrix stays below a desired value, so that the resulting error in the occupied subspace can be controlled. The efficiency of the new scheme is investigated in benchmark calculations for water clusters including up to 6523 water molecules. Furthermore, the foundation of matrix sparsity is investigated. This includes a study of the decay of matrix element magnitude with distance between basis function centers for different molecular systems and different methods. The studied methods include Hartree–Fock and density functional theory using both pure and hybrid functionals. The relation between band gap and decay properties of the density matrix is also discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Sensitivity analysis and uncertainty calculation for dispersion corrected density functional theory
Authors: Hanke Felix
Published: February 2011

The precision of binding energies and distances computed with dispersion‐corrected density functional theory (DFT‐D) is investigated by propagation of uncertainties, yielding relative uncertainties of several percent. Sensitivity analysis is used to calculate the geometry‐dependent relative importance of each input parameter for the dispersion correction. While DFT‐Ds are exact at asymptotically large distances, their damping functions are shown to play a significant role in binding geometries. This is demonstrated in detail for the interlayer binding of graphite. The techniques presented allow practitioners to quickly compute error bars and to get an a posteriori estimate about the transferability of their results. They can also aid the development of future dispersion corrections. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions
Authors: Brice Allyn R. , Dominy Brian N.
Published: February 2011

The ability to predict and characterize free energy differences associated with conformational equilibria or the binding of biomolecules is vital to understanding the molecular basis of many important biological functions. As biological studies focus on larger molecular complexes and properties of the genome, proteome, and interactome, the development and characterization of efficient methods for calculating free energy becomes increasingly essential. The aim of this study is to examine the robustness of the end‐point free energy method termed the molecular mechanics Poisson‐Boltzmann solvent accessible surface area (MM/PBSA) method. Specifically, applications of MM/PBSA to the conformational equilibria of nucleic acid (NA) systems are explored. This is achieved by comparing A to B form DNA conformational free energy differences calculated using MM/PBSA with corresponding free energy differences determined with a more rigorous and time‐consuming umbrella sampling algorithm. In addition, the robustness of NA MM/PBSA calculations is also evaluated in terms of the sensitivity towards the choice of force field and the choice of solvent model used during conformational sampling. MM/PBSA calculations of the free energy difference between A‐form and B‐form DNA are shown to be in very close agreement with the PMF result determined using an umbrella sampling approach. Further, it is found that the MM/PBSA conformational free energy differences were also in agreement using either the CHARMM or AMBER force field. The influence of ionic strength on conformational stability was particularly insensitive to the choice of force field. Finally, it is also shown that the use of a generalized Born implicit solvent during conformational sampling results in free energy estimates that deviate slightly from those obtained using explicitly solvated MD simulations in these NA systems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Electron localization function and electron localizability indicator applied to study the bonding in the peroxynitrous acid HOONO
Authors: Berski Slawomir , Latajka Zdzislaw , Gordon Agnieszka J.
Published: February 2011

The ground‐state electronic structure of peroxynitrous acid (HOONO) and its singlet biradicaloid form (HO···ONO) have been studied using topological analysis of the electron localization function (ELF), together with the electron localizability indicator (ELI‐D), at the DFT (B3LYP, M05, M052X, and M06), CCSD, and CASSCF levels. Three isomers of HOONO (cis‐cis, cis‐perp, and trans‐perp) have been considered. The results show that from all functionals applied, only B3LYP yields the correct geometrical structure. The ELF and ELI‐D‐topology of the OO and central NO bonds strongly depends on the wave function used for analysis. Calculations carried out at CAS (14,12)/aug‐cc‐pVTZ//CCSD(T)/aug‐cc‐pVTZ level reveal two bonds of the charge‐shift type: a protocovalent NO bond with a basin population of 0.82–1.08e, and a more electron depleted OO bond with a population of 0.66–0.71e. The most favorable dissociation channel (HOONO → HO + ONO) corresponds to breaking of the most electron‐deficient bond (OO). In the case of cis‐ and trans‐HO···ONO, the ELF, ELI‐D, and electron density fields results demonstrate a closed‐shell O···O interaction. The α‐spin electrons are found mainly (0.64e) in the lone pairs of oxygen Vi
= 1,2 (O) from the OH group. The β‐spin electrons are delocalized over the ONO group, with the largest concentration (0.34e) on the lone pair of nitrogen V(N). © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Conformational searching using a population‐based incremental learning algorithm
Authors: Long Stephen M. , Tran Tran T. , Adams Peter , Darwen Paul , Smythe Mark L.
Published: February 2011

A new population‐based incremental learning algorithm for conformational searching of molecules is presented. This algorithm is particularly effective at determining, by relatively small number of energy minimizations, global energy minima of large flexible molecules. The algorithm is also able to find a large set of low energy conformations of more rigid small molecules. The performance of the algorithm is relation to other algorithm is examined via the test molecules: C18H38, C39H80, cycloheptadecane and a set of five drug‐like molecules. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Enumeration and classification of benzenoid hydrocarbons
Authors: Brunvoll J. , Cyvin S. J. , Cyvin B. N.
Published: February 2011

The enumeration of benzenoids is studied with the aid of different modifications of a computer program. Known values for the number of cata‐condensed and of all benzenoids with h (number of hexagons) up to eight are reproduced. These benzenoids are classified into (a) unbranched of different symmetries and branched cata‐condensed, and (b) normal, essentially disconnected and non‐Kekuléan peri‐condensed. Within the normal benzenoids a more detailed classification is performed: basic benzenoids, fused, or annelated. For h = 9 an almost complete classification along the same lines was achieved.
Electronic structure of clusters modeling silica
Authors: Lopez Jesus P. , Yang Cary Y. , Helms C. R.
Published: February 2011

Self‐consistent‐field‐Xα‐scattered wave calculations on clusters Si2O76− and H6Si2O7 modeling silica have been performed. Incorporation of Si 3d orbitals produces significant changes in the overall valence structure. In addition to σ Si — O bonds, there exists a bonding π character due to the participation of O 2p and Si 3d. Hydrogen terminators do not seem to correct edge effects for these π states.
Small imines and oximes as model compounds in the optimization of a consistent force field potential energy function
Authors: Huige C. J. M. , Hezemans A. M. F. , Rasmussen Kjeld
Published: February 2011

Parameters have been optimized for a potential energy function to be used in molecular mechanics calculations of small imines as a preliminary step to calculations on larger systems. A consistent force field (CFF) program was used, and a new damping algorithm due to Sundius was introduced in the optimization procedure. Optimization of parameters has been done on structural and vibrational data of five small imines and one oxime. The quality of the derived potential energy function is examined by calculations on larger oximes.
Model potentials for molecular calculations. II. The spd‐MP set for transition metal atoms Sc through Hg
Authors: Sakai Yoshiko , Miyoshi Eisaku , Klobukowski Mariusz , Huzinaga Sigeru
Published: February 2011

Model potential parameters and valence orbitals were generated for the transition metal atoms Sc through Hg. They are named the spd‐MPs and are supplementary to the sd‐MPs presented in the preceding article. The outermost core np electrons were treated explicitly together with valence nd and (n + 1)s electrons, and the remaining electrons were replaced by a model potential. The model potential parameters and valence orbitals were determined in the same way as the sd‐MPs. Major relativistic effects (via the mass velocity and Darwin terms) were also incorporated in the spd‐MPs for the second‐and third‐row transition metal atoms. The results of numerical nonrelativistic Hartree‐Fock (HF) calculations for the first‐row transition metal atoms and of the quasirelativistic HF calculations with Cowan and Griffin's method for the second‐row and third‐row transition metal atoms were used as reference data in determination of the spd‐MPs.
Interaction energy studies of 8‐azapurine during transcription
Authors: Sanyal Nitish K. , Ojha Rajendra Prasad , Roychoudhury M.
Published: February 2011

The quantum mechanical perturbation method has been utilized to explain the biological function of 8‐azapurine nucleoside analogs. The possibility of binding of the analog has been discussed in terms of interaction energy, which includes the electrostatic, polarization, dispersion, and repulsion terms. The stacking and the hydrogen bonding energy of the analog with nucleic acid bases and base pairs have been computed in all possible orientations. The model developed by Sanyal et al. for the incorporation of nucleoside analogs has been used to find out the inhibitory effect of the drug on nucleic acid and protein synthesis. It has been observed that these results are in broad agreement with the experimental observations.
Knock‐down of amphiregulin inhibits cellular invasion in inflammatory breast cancer
Authors: Baillo Andrea , Giroux Craig , Ethier Stephen P.
Published: February 2011

We have previously shown that SUM‐149 human breast cancer cells require an amphiregulin (AREG) autocrine loop for cell proliferation. We also demonstrated that AREG can increase epidermal growth factor receptor (EGFR) stability and promote EGFR localization to the plasma membrane. In the present studies we successfully knocked‐down AREG expression in SUM‐149 cells by lentiviral infection of AREG shRNA. In the absence of AREG expression, SUM‐149 cell growth was slowed, but not completely inhibited. Furthermore, cells infected with AREG shRNA constructs showed an increase in EGFR protein expression by Western blot. Immunofluorescence and confocal microscopy showed that following AREG knock‐down, EGFR continued to localize to the cell surface. Soft agar assays demonstrated that AREG knock‐down cells retain anchorage‐independent growth capacity. Additionally mammosphere forming assays and Adefluor staining analysis showed that knock‐down of AREG expression did not affect the expression of stem cell phenotypes. However, following AREG knock‐down, SUM‐149 cells demonstrated a dramatic decrease in their ability to invade a Matrigel matrix. Consistent with this observation, microarray analysis comparing cells infected with a non‐silencing vector to the AREG knock‐down cells, identified genes associated with the invasive phenotype such as RHOB and DKK1, and networks associated with cell motility such as integrin‐linked kinase signaling, and focal adhesion kinase signaling. AREG was also found to modulate WNT and Notch signaling in these cells. Thus, AREG functions in regulating the invasive phenotype, and we propose that this regulation may be through altered signaling that occurs when AREG activates plasma membrane localized EGFR. J. Cell. Physiol. 226: 2691–2701, 2011. © 2011 Wiley‐Liss, Inc.
Characterization of the differential response of endothelial cells exposed to normal and elevated laminar shear stress
Authors: White Stephen J. , Hayes Elaine M. , Lehoux Stéphanie , Jeremy Jamie Y. , Horrevoets Anton J.G. , Newby Andrew C.
Published: February 2011

Most acute coronary events occur in the upstream region of stenotic atherosclerotic plaques that experience laminar shear stress (LSS) elevated above normal physiological levels. Many studies have described the atheroprotective effect on endothelial behavior of normal physiological LSS (approximately 15 dynes/cm2) compared to static or oscillatory shear stress (OSS), but it is unknown whether the levels of elevated shear stress imposed by a stenotic plaque would preserve, enhance or reverse this effect. Therefore we used transcriptomics and related functional analyses to compare human endothelial cells exposed to laminar shear stress of 15 (LSS15‐normal) or 75 dynes/cm2 (LSS75‐elevated). LSS75 upregulated expression of 145 and downregulated expression of 158 genes more than twofold relative to LSS15. Modulation of the metallothioneins (MT1‐G, ‐M, ‐X) and NADPH oxidase subunits (NOX2, NOX4, NOX5, and p67phox) accompanied suppression of reactive oxygen species production at LSS75. Shear induced changes in dual specificity phosphatases (DUSPs 1, 5, 8, and 16 increasing and DUSPs 6 and 23 decreasing) were observed as well as reduced ERK1/2 but increased p38 MAP kinase phosphorylation. Amongst vasoactive substances, endothelin‐1 expression decreased whereas vasoactive intestinal peptide (VIP) and prostacyclin expression increased, despite which intracellular cAMP levels were reduced. Promoter analysis by rVISTA identified a significant over representation of ATF and Nrf2 transcription factor binding sites in genes upregulated by LSS75 compared to LSS15. In summary, LSS75 induced a specific change in behavior, modifying gene expression, reducing ROS levels, altering MAP kinase signaling and reducing cAMP levels, opening multiple avenues for future study. J. Cell. Physiol. 226: 2841–2848, 2011. © 2011 Wiley‐Liss, Inc.
Insulin‐stimulated L‐arginine transport requires SLC7A1 gene expression and is associated with human umbilical vein relaxation
Authors: González Marcelo , Gallardo Victoria , Rodríguez Natalia , Salomón Carlos , Westermeier Francisco , Gutiérrez Enrique Guzmán‐ , Abarzúa Fernando , Leiva Andrea , Casanello Paola , Sobrevia Luis
Published: February 2011

Insulin causes endothelium‐derived nitric oxide (NO)‐dependent vascular relaxation, and increases L‐arginine transport via cationic amino acid transporter 1 (hCAT‐1) and endothelial NO synthase (eNOS) expression and activity in human umbilical vein endothelium (HUVEC). We studied insulin effect on SLC7A1 gene (hCAT‐1) expression and hCAT‐transport activity role in insulin‐modulated human fetal vascular reactivity. HUVEC were used for L‐arginine transport and L‐[3H]citrulline formation (NOS activity) assays in absence or presence of N‐ethylmaleimide (NEM) or L‐lysine (L‐arginine transport inhibitors). hCAT‐1 protein abundance was estimated by Western blot, mRNA quantification by real time PCR, and SLC7A1 promoter activity by Luciferase activity (−1,606 and −650 bp promoter fragments from ATG). Specific protein 1 (Sp1), and total or phosphorylated eNOS protein was determined by Western blot. Sp1 activity (at four sites between −177 and −105 bp from ATG) was assayed by chromatin immunoprecipitation (ChIP) and vascular reactivity in umbilical vein rings. Insulin increased hCATs–L‐arginine transport, maximal transport capacity (Vmax/Km), and hCAT‐1 expression. NEM and L‐lysine blocked L‐arginine transport. In addition, it was trans‐stimulated (∼7.8‐fold) by L‐lysine in absence of insulin, but unaltered (∼1.4‐fold) in presence of insulin. Sp1 nuclear protein abundance and binding to DNA, and SLC7A1 promoter activity was increased by insulin. Insulin increased NO synthesis and caused endothelium‐dependent vessel relaxation and reduced U46619‐induced contraction, effects blocked by NEM and L‐lysine, and dependent on extracellular L‐arginine. We suggest that insulin induces human umbilical vein relaxation by increasing HUVEC L‐arginine transport via hCATs (likely hCAT‐1) most likely requiring Sp1‐activated SLC7A1 expression. J. Cell. Physiol. 226: 2916–2924, 2011. © 2011 Wiley‐Liss, Inc.
Importance of serum source for the in vitro replicative senescence of human bone marrow derived mesenchymal stem cells
Authors: Duggal Shivali , Brinchmann Jan E.
Published: February 2011

Human mesenchymal stem cells (hMSCs) may be used for therapeutic applications. Culture conditions such as the serum source may impact on cell quality and the onset of replicative senescence. We have examined the effect of culturing hMSCs in autologous serum (AS) versus fetal bovine serum (FBS) on factors involved in in vitro replicative senescence. hMSCs from four donors were cultured in 10% FBS or 10% AS until they reached senescence. Cells were harvested at early passage and near senescence to study factors known to be involved in cellular senescence. The number of population doublings till senescence was similar for cells cultured in FBS, but varied greatly for hMSCs cultured in AS. FBS cells accumulated in S phase of cell cycle. This could not be explained by increased expression of cell cycle inhibitor proteins. Heat shock proteins were upregulated in AS compared to FBS cells. Reactive oxygen species and nitric oxide were upregulated in senescent FBS cells. Telomeres were shorter in senescent cells, more significantly in FBS cells. The source of serum was a determinant for the time till senescence in cultured hMSC. Serum source affected aspects of cell cycle regulation and the levels of heat shock proteins. Several mechanisms are likely to be responsible for replicative senescence in hMSC. Insight into the molecular details of how serum factors impacts on these mechanisms is important for the safe use of hMSCs in clinical applications. J. Cell. Physiol. 226: 2908–2915, 2011. © 2011 Wiley‐Liss, Inc.
HAX‐1: A family of apoptotic regulators in health and disease
Authors: Yap Solomon V. , Koontz Jason M. , Kontrogianni‐Konstantopoulos Aikaterini
Published: February 2011

HAX‐1 comprises a family of ubiquitously expressed proteins that play important roles in the regulation of programmed cell death. Herein, we provide a comprehensive review of the expression profile of HAX‐1 and its functional implications during health and disease, highlighting its direct involvement in the development of congenital neutropenia and neural abnormalities, when absent, and its contribution to the progression of psoriasis and cancer, when overexpressed. Moreover, we provide new information on the differential expression of the HAX‐1 subfamily in three distinct types of epithelial cancers, including breast, skin, and colon. Our results demonstrate a significant up‐regulation of the anti‐apoptotic HAX‐1 variant 001 in skin and colon, but not in breast and cancer cells, indicating tissue‐specific differences in its expression pattern and properties during cancer formation and progression. Our findings further reveal a considerable down‐regulation, if not abrogation, of three distinct, yet to be characterized, HAX‐1 isoforms in breast cancer cells, suggesting that they may function in an opposite manner to the anti‐apoptotic variant 001. This study aims to summarize our current knowledge on the physiological implications of the expression profile of the HAX‐1 subfamily in health and disease, and provide new information on the differential expression and activities of HAX‐1 members in three distinct types of cancer. J. Cell. Physiol. 226: 2752–2761, 2011. © 2011 Wiley‐Liss, Inc.
Exposure to 50 Hz electromagnetic field raises the levels of the anti‐apoptotic protein BAG3 in melanoma cells
Authors: Basile Anna , Zeppa Rosario , Pasquino Nicola , Arra Claudio , Ammirante Massimo , Festa Michelina , Barbieri Antonio , Giudice Aldo , Pascale Maria , Turco Maria Caterina , Rosati Alessandra
Published: February 2011

The expression of the anti‐apoptotic protein BAG3 is induced in several cell types by exposure to high temperature, oxidants, and other stressful agents. We investigated whether exposure to 50 Hz electromagnetic fields raised BAG3 levels in the human melanoma cell line M14, in vitro and in orthotopic xenografts. Exposure of cultured cells or xenografts for 6 h or 4 weeks, respectively, produced a significant (P < 0.01) increase in BAG3 protein amounts. Interestingly, at the same times, we could not detect any significant variation in the levels of HSP70/72 protein or cell apoptosis. These results confirm the stressful effect of exposure to ELF in human cells, by identifying BAG3 protein as a marker of ELF‐induced stress. Furthermore, they suggest that BAG3 induction by ELF may contribute to melanoma cell survival and/or resistance to therapy. J. Cell. Physiol. 226: 2901–2907, 2011. © 2011 Wiley‐Liss, Inc.
Apo‐ and holo‐lactoferrin are both internalized by lactoferrin receptor via clathrin‐mediated endocytosis but differentially affect ERK‐signaling and cell proliferation in caco‐2 cells
Authors: Jiang Rulan , Lopez Veronica , Kelleher Shannon L. , Lönnerdal Bo
Published: February 2011

Lactoferrin (Lf) is a major iron‐binding and multi‐functional protein in exocrine fluids such as breast milk and mucosal secretions. The functions of Lf appear dependent upon the iron saturation of the Lf protein and are postulated to be mediated through Lf internalization by a Lf receptor (LfR). However, mechanisms by which LfR mediates Lf internalization in enterocytes are unknown. We now demonstrate that a LfR previously cloned from the small intestine mediates Lf endocytosis in a human enterocyte model (Caco‐2 cells). LfR was detected at the plasma membrane by cell surface biotinylation; both apo‐Lf and holo‐Lf uptake were significantly inhibited in cells transfected with LfR siRNA. Treatments of hypertonic sucrose and clathrin siRNA and co‐immunoprecipitation of LfR with clathrin adaptor AP2 indicate that LfR regulates Lf endocytosis via clathrin‐mediated endocytosis. Although both iron‐free Lf (apo‐Lf) and iron‐saturated Lf (holo‐Lf) enter Caco‐2 cells via a similar mechanism and no significant differences were observed in the binding and uptake of apo‐ and holo‐Lf in Caco‐2 cells, apo‐Lf but not holo‐Lf stimulates proliferation of Caco‐2 cells. Interestingly, apo‐Lf stimulated extracellular signal‐regulated mitogen‐activated protein kinase (ERK) cascade to a significantly greater extent than holo‐Lf and the apo‐Lf induced proliferation was significantly inhibited by an ERK cascade inhibitor (U0126) and clathrin siRNA. Taken together, our data suggest that LfR is a major pathway through which Lf is taken up by enterocytes, which occurs independently of iron saturation through clathrin‐mediated endocytosis. The differential effects of apo‐ and holo‐Lf are not due to differences in cellular internalization mechanisms. J. Cell. Physiol. 226: 3022–3031, 2011. © 2011 Wiley‐Liss, Inc.
Normal atmospheric oxygen tension and the use of antioxidants improve hepatocyte spheroid viability and function
Authors: Lillegard Joseph B. , Fisher James E. , Nedredal Geir , Luebke‐Wheeler Jennifer , Bao Ji , Wang William , Amoit Bruce , Nyberg Scott L.
Published: February 2011

Hepatocyte spheroids have been proposed for drug metabolism studies and in bioartificial liver devices. However, the optimal conditions required to meet the aerobic demands of mitochondria‐rich hepatocyte spheroids is not well studied. We hypothesized that an optimal concentration of oxygen could be identified and that the health of hepatocyte spheroids might be further improved by antioxidant therapy. Rat hepatocyte spheroids were maintained in suspension culture for 7 days under a mixture of 5% CO2 plus O2:N2 to achieve fractional oxygen contents of 6% (C1), 21% (C2), 58% (C3), and 95% (C4). Spheroid health was assessed under each condition by vital staining, TEM, oxygen consumption, and mitochondrial counts. Hepatocyte differentiation was assessed by expression of 10 liver‐related genes (HNF4a, HNF6, Cyp1A1, albumin, Nags, Cps1, Otc, Ass, Asl, Arg1). Functional markers (albumin and urea) were measured. The influence of oxygen tension and antioxidant treatment on the production of reactive oxygen species (ROS) was assessed by confocal microscopy. We observed that the hepatocyte spheroids were healthiest under normal atmospheric (C2) conditions with antioxidants ascorbic acid and L‐carnitine. Cell death and reduced functionality of hepatocyte spheroids correlated with the formation of ROS. Normal atmospheric conditions provided the optimal oxygen tension for suspension culture of hepatocyte spheroids. The formation and deleterious effects of ROS were further reduced by adding antioxidants to the culture medium. These findings have direct application to development of the spheroid reservoir bioartificial liver and the use of hepatocyte spheroids in drug metabolism studies. J. Cell. Physiol. 226: 2987–2996, 2011. © 2011 Wiley‐Liss, Inc.
C/EBPβ binds the P1 promoter of the Runx2 gene and up‐regulates Runx2 transcription in osteoblastic cells
Authors: Henriquez Berta , Hepp Matias , Merino Paola , Sepulveda Hugo , van Wijnen Andre J. , Lian Jane B. , Stein Gary S. , Stein Janet L. , Montecino Martin
Published: February 2011

The Runx2 factor is an essential component of the regulatory mechanisms that control transcription during skeletogenesis. Runx2/p57 expression in osteoblastic cells is controlled by the P1 promoter, which is recognized by key regulators of osteoblast differentiation including homeodomain factors and Wnt‐ and BMP‐signaling mediators. Here, we report that the transcription factor C/EBPβ up‐regulates Runx2/p57 expression by directly binding to the Runx2 P1 promoter in mesenchymal, pre‐osteoblastic, and osteoblastic cells. This C/EBPβ‐mediated up‐regulation is principally dependent on C/EBP site II that is located within the first 180 bp of the proximal P1 promoter region and is highly conserved among mouse, rat, and human Runx2 genes. Our studies reveal how the C/EBPβ factor, known to have a key role during osteogenesis, contributes to regulating the expression of Runx2, the master regulator of osteoblast differentiation. J. Cell. Physiol. 226: 3043–3052, 2011. © 2011 Wiley‐Liss, Inc.