bluuebunny/crossref_metadata_2025 huggingface dataset:
In vivo performance of a sol–gel glass‐coated collagen
Authors: Andrade Ângela Leão , Andrade Sílvia Passos , Domingues Rosana Zacarias
Published: April 2006

Synthetic bioactive materials offer possibilities to repair large tissue defects. It is well known that bioactivity, angiogenesis, and inflammation are key events in implant incorporation. Using glass‐coated and glass‐free collagen as potential bone graft substitutes, we carried out in vitro bioactivity and an in vivo angiogenesis and inflammation studies. The in vitro study showed bioactivity when the glass‐coated samples were left in SBF for 5 days. This was confirmed by FTIR results, which presented PO vibration bands characteristic of hydroxyapatite close to 1060 cm−1 and 600 cm−1. The in vivo response was evaluated following subcutaneous implantation of the biomaterial in the mouse dorsa. Angiogenesis, as determined by hemoglobin content extracted from implants 7 and 14 days after implantation, increased progressively in both glass‐coated and glass‐free collagen implants. However, vascularization was higher in the glass‐coated collagen implants 14 days after implantation (μg Hb per mg wet tissue 6.0 ± 0.3) compared with the glass‐free group (1.6 ± 0.1). The inflammatory process, determined by the levels of myeloperoxidase and N‐acetylglucosaminidase, was similar for both implants. This study shows that glass‐coated collagen implants hold osteogenic and angiogenic potential and may be used in clinical conditions requiring improvement of these biological processes. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Tissue response to in situ polymerization of a new two‐solution bone cement: Evaluation in a sheep model
Authors: Allen Matthew J. , Leone Kendall A. , Hasenwinkel Julie M. , Gilbert Jeremy L.
Published: April 2006

A two‐solution bone cement (2‐SC) was evaluated in a non‐load bearing sheep model that simulated insertion of a cemented total joint replacement. A commercial powder–liquid bone cement formulation (Palacos® R) was used as the control. The systemic response to the two cements was determined by monitoring changes in arterial blood pressure (ABP) and serum concentrations of methyl methacrylate monomer at intervals after insertion of the cement. The short‐term tissue response to the two cements was assessed by quantifying histomorphometric parameters of new bone formation at 2, 4, and 12 weeks postsurgery. Intraoperatively, injection and pressurization of bone cement were well tolerated, with no significant changes in ABP in either group and no detectable circulating monomer in any animal. Several interesting trends were identified in the histomorphometry data. In the trabecular specimens, new bone formation immediately adjacent to the cement mantle was apparently suppressed in the first 2 weeks postsurgery, increased dramatically at 4 weeks, and then returned to baseline values by 12 weeks. This pattern was seen with both Palacos® and 2‐SC. In the cortical specimens, new bone formation was reduced on the endosteal surface when compared with the periosteal surface, with this effect being more noticeable at 2 and 4 weeks than at 12 weeks. There were no significant histopathological findings in either the bone or the draining lymph nodes. These data indicate that the biological response to 2‐SC is substantially equivalent to that of Palacos® R. Additional testing in a functional, load‐bearing animal model is now recommended to more fully characterize the long‐term biological response to 2‐SC and to determine the mechanical performance of this new cement in vivo. © 2006 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2006
Hydromediastinum associated with a peripherally inserted central venous catheter in a newborn infant
Authors: Maruyama Kenichi , Koizumi Takenobu
Published: April 2006

We report a case of hydromediastinum in a newborn associated with a peripherally inserted central venous catheter. A 9‐day‐old male infant with total parenteral nutrition via a peripherally inserted central venous catheter had acute respiratory distress. A chest radiograph showed a widened mediastinal shadow and left pleural effusion, and sonography revealed fluid collection in the mediastinum and bilateral hydrothorax. Sonography is useful in the diagnosis of hydromediastinum when infants treated with peripherally inserted central venous catheters have acute respiratory distress. © 2006 Wiley Periodicals, Inc. J Clin Ultrasound 34:195–198, 2006
Accuracy of sonographic volume measurements of kidney transplant
Authors: Mancini Marcello , Mainenti Pier Paolo , Speranza Antonio , Liuzzi Raffaele , Soscia Ernesto , Sabbatini Massimo , Ferrara Liberato Aldo , Federico Stefano , Salvatore Marco
Published: April 2006

Purpose.

Sonographic measurement of renal volume is one of the parameters used in the diagnosis of renal transplant dysfunction and in follow‐up of patients with renal transplant. The aim of this study was to compare the prolate ellipsoid formula with a new formula in calculating the volume of a transplanted kidney.

Methods.

The renal volumes in 24 patients with a stable renal transplant were determined sonographically with the ellipsoid formula and via helical CT with the voxel‐count method, which is the gold standard. A new formula that uses renal length and the cross‐sectional area at the maximum transverse section has been evaluated in a small series of transplanted kidneys.

Results.

Renal volume was underestimated with the sonographic ellipsoid formula and the new formula. The new formula yielded the lowest underestimation of the mean renal volume, and the measurements obtained with it were not significantly different from those obtained with CT.

Conclusions.

The use of sonography is appropriate for accurate calculation of renal volume, and the new formula that uses only 2 ultrasound parameters best represents the volume of a renal transplant. © 2006 Wiley Periodicals, Inc. J Clin Ultrasound34:184–189, 2006
Delineation of brain tumor margins using intraoperative sononavigation: Implications for tumor resection
Authors: Shinoura Nobusada , Takahashi Masamichi , Yamada Ryozi
Published: April 2006

Purpose.

Sonography has been employed for real‐time intraoperative delineation of tumor boundaries during resection of brain tumors. However, the variably hyperechoic appearance of brain edema or gliosis surrounding the brain may interfere with accurate depiction of tumor margins. The goal of the present study was to use sononavigation, which provides coregistration between real‐time sonograms and MRI scans, to assess the accuracy of sonographic determination of tumor margins.

Methods.

Sononavigation was performed on 12 brain tumors (7 metastatic brain tumors, 2 meningiomas, 1 anaplastic oligodendroglioma, 1 anaplastic pilocytic astrocytoma, and 1 anaplastic astrocytoma). Sonograms of tumor margins were categorized into 1 of 3 types: in type 1, the tumor margin was clearly visualized and corresponded to the margin of the enhanced lesion on MR scan in all areas; in type 2, the tumor margin was clearly seen in some areas but was obscure in others due to hyperechoic edema; and in type 3, the tumor margin was indistinguishable from surrounding tissues in all areas.

Results.

Three metastatic brain tumors and 1 meningioma were categorized as type 1. Three metastatic brain tumors, 1 meningioma, and 1 anaplastic oligodendroglioma were categorized as type 2. The anaplastic pilocytic astrocytoma, 1 metastatic brain tumor (which consisted mainly of necrotic tissue), and the anaplastic astrocytoma were categorized as type 3. These data assist in determining whether the sonographic appearance of tumor margins is accurate and whether to rely on information from either sonography (type 1) or the sononavigation system when resecting tumor types 1, 2, and 3.

Conclusions.

Sononavigation can help categorize the sonographic tumor margins into 3 different patterns, and this categorization can assist in determining which imaging modalities are needed to better delineate the tumor margins for subsequent resection. © 2006 Wiley Periodicals, Inc. J Clin Ultrasound 34:177–183, 2006
Transmembrane signaling through phospholipase C‐β in the developing human prefrontal cortex
Authors: Ruiz de Azúa Iñigo , del Olmo Elena , Pazos Angel , Sallés Joan
Published: April 2006

To investigate changes in muscarinic receptor‐stimulated phospholipase C‐β (PLC‐β) activity during brain development, we examined the functional coupling of each of the three major protein components of the phosphoinositide system (M1, M3, and M5 muscarinic receptor subtypes; Gq/11 proteins; PLC‐β1–4 isoforms) in membrane preparations from post‐mortem human prefrontal cerebral cortex collected at several stages of prenatal and postnatal development. In human prenatal brain membranes, PLC was found to be present and could be activated by calcium, but the ability of guanosine‐5′‐o‐3 thiotriphosphate (GTPγS) or carbachol (in the presence of GTPγS) to modulate prenatal PLC‐β was significantly weaker than that associated with postnatal PLC‐β. Western blot analysis revealed that the levels of Gαq/11 did not change significantly during development. In contrast, dramatically higher levels of expression of PLC‐β1–4 isoforms and of M1, M3, and M5 muscarinic receptors were detected in the child vs. the fetal brain, a finding that might underlie the observed increased activity of PLC. Thus, inositol phosphate production may be more efficiently regulated by altering the amount of effectors (PLC‐β1–4) and receptors (M1,3,5 subtypes) than by altering the level of Gαq/11 subunits. These results demonstrate that different PLC isoforms are expressed in the prefrontal cortex of the developing human brain in an age‐specific manner, suggesting specific roles not only in synaptic transmission but also in the differentiation and maturation of neurons in the developing brain. © 2006 Wiley‐Liss, Inc.
Fluorescence staining of human ovarian cancer tissue following application of 5‐aminolevulinic acid: Fluorescence microscopy studies
Authors: Löning Martin C. , Diddens Heyke C. , Holl‐Ulrich Konstanze , Löning Uta , Küpker Wolfgang , Diedrich Klaus , Hüttmann Gereon
Published: April 2006

Background and Objectives

Application of 5‐aminolevulinic acid (ALA) for fluorescence‐guided second‐look laparoscopy has been shown to be a promising new procedure in the early diagnosis of ovarian carcinoma metastases. However, for assessing the reliability of this method, information on the microscopic distribution of protoporphyrin IX (PP IX) in the tissue is needed. Additionally, the selectivity of PP IX uptake is essential for a potential photodynamic therapy (PDT) of ovarian cancer metastases.

Study Design/Materials and Methods

Thirty‐six patients with epithelial ovarian cancer and two patients suffering from fallopian tube carcinoma underwent a laparoscopic second‐look procedure 5 hours after the application of ALA. In 17 patients 36 fluorescence‐guided biopsies were taken from fluorescing and non‐fluorescing tissues for further evaluation. Fluorescence microscopy and digital image processing were utilized to determine the presence of PP IX fluorescence.

Results

A specificity of 88% and a sensitivity of 100% with a negative predictive value of 100% and a positive predictive value of 91% were calculated for PP IX fluorescence on a microscopic level as marker for ovarian cancer metastases.

Conclusions

On a microscopic scale, ALA‐induced PP IX fluorescence is confined to ovarian cancer tumor tissue sparing stromal tissues. Lasers Surg. Med. © 2006 Wiley‐Liss, Inc.
Microvascular blood flow dynamics associated with photodynamic therapy, pulsed dye laser irradiation and combined regimens
Authors: Smith Tia K. , Choi Bernard , Ramirez‐San‐Juan Julio C. , Nelson J. Stuart , Osann Kathryn , Kelly Kristen M.
Published: April 2006

Background and Objectives

Previous in vitro studies demonstrated the potential utility of benzoporphyrin derivative monoacid ring A (BPD) photodynamic therapy (PDT) for vascular destruction. Moreover, the effects of PDT were enhanced when this intervention was followed immediately by pulsed dye laser (PDL) irradiation (PDT/PDL). We further evaluate vascular effects of PDT alone, PDL alone and PDT/PDL in an in vivo rodent dorsal skinfold model.

Study Design/Materials and Methods

A dorsal skinfold window chamber was installed surgically on female Sprague–Dawley rats. One milligram per kilogram of BPD solution was administered intravenously via a jugular venous catheter. Evaluated interventions were: control (no BPD, no light), PDT alone (576 nm, 16 minutes exposure time, 15 minutes post‐BPD injection, 10 mm spot), PDL alone at 7 J/cm2 (585 nm, 1.5 ms pulse duration, 7 mm spot), PDL alone at 10 J/cm2, PDT/PDL (PDL at 7 J/cm2), and PDT/PDL (PDL at 10 J/cm2). To assess changes in microvascular blood flow, laser speckle imaging was performed before, immediately after, and 18 hours post‐intervention.

Results

Epidermal irradiation was accomplished without blistering, scabbing or ulceration. A reduction in perfusion was achieved in all intervention groups. PDT/PDL at 7 J/cm2 resulted in the greatest reduction in vascular perfusion (56%).

Conclusions

BPD PDT can achieve safe and selective vascular flow reduction. PDT/PDL can enhance diminution of microvascular blood flow. Our results suggest that PDT and PDT/PDL should be evaluated as alternative therapeutic options for treatment of hypervascular skin lesions including port wine stain birthmarks. Lasers Surg. Med. © 2006 Wiley‐Liss, Inc.
Recessive Parkinson's disease
Authors: Kubo Shin‐Ichiro , Hattori Nobutaka , Mizuno Yoshikuni
Published: April 2006

Parkinson's disease (PD) is a progressive neurodegenerative disease caused by loss of dopaminergic neurons in the substantia nigra pars compacta. Although the etiology of PD remains unclear, it is now clear that genetic factors contribute to the pathogenesis of the disease. Recently, several causative genes have been identified in monogenic forms of PD. Accumulating evidence indicates that their gene products play important roles in mitochondrial function, oxidative stress response, and the ubiquitin–proteasome system, which are also implicated in sporadic PD, suggesting that these gene products share a common pathway to nigral degeneration in both familial and sporadic PD. Here, we review recent advances in knowledge about genes associated with recessive PD, including parkin, PINK1, and DJ‐1. © 2006 Movement Disorder Society
A survey of language barriers from the perspective of pediatric oncologists, interpreters, and parents
Authors: Abbe Marisa , Simon Christian , Angiolillo Anne , Ruccione Kathy , Kodish Eric D
Published: April 2006

Background

Oncologists in the US increasingly face the challenge of communicating with non‐English speaking parents of children with cancer. This study explores this challenge from the perspectives of a sample of pediatric oncologists, interpreters, and Spanish‐speaking parents of children with newly diagnosed leukemia.

Procedure

Thirty‐seven oncologists and 17 professional language interpreters based at two non‐profit pediatric hospitals in the US were surveyed on the topic of language barriers in pediatric care. Seventeen parents who communicated with their child's oncologist through an interpreter were also surveyed.

Results

All groups expressed considerable concern over the process of communicating across a language barrier. For oncologists, these concerns included the accuracy and completeness of interpretations, complexity of information, and loss of confidence and control over the communication process. For interpreters, they included complexity of information, information overload, and lack of clinician sensitivity toward the cultural and socioeconomic backgrounds of limited English proficiency (LEP) families. Parent concerns included difficulties comprehending information and anxiety over the possibility of missing out on important information. All groups provided multiple suggestions for improving communication across a language barrier.

Conclusions

Oncologists, interpreters, and parents expressed considerable concern over the process of communicating across a language barrier. Some of these concerns could be minimized through efforts to boost interpreter accuracy and completeness, including the use of more simple, easy to understand language. Other issues, such as differences in culture and socioeconomic background, warrant consideration of the intercultural knowledge and skills of interpreters. Pediatric Blood Cancer 2006;47:819–824. © 2006 Wiley‐Liss, Inc.
Intracerebral hematoma as a complication of intrathecal methotrexate administration
Authors: Boran Perran , Tokuc Gulnur , Boran Burak O. , Oktem Sedat
Published: April 2006

Neurotoxicity of methotrexate is a well‐documented issue, but development of an intracerebral hematoma following administration of intrathecal methotrexate is an extremely rare entity. A 6‐year‐old male with the diagnosis of non‐Hodgkin lymphoma was put on a treatment regimen, including intrathecal methotrexate. Six days following the last intrathecal methotrexate administration, the patient developed a deteriorating state of consciousness. There was no history of trauma. Coagulation studies and platelet count were normal. Magnetic resonance imaging of the brain demonstrated a large left frontoparietal hematoma. Intracerebral hematoma may be a very rare, but serious, complication of intrathecal methotrexate administration. Pediatr Blood Cancer 2008;50:152–154. © 2006 Wiley‐Liss, Inc.
Comparison of validity of assessment methods using indices of adjusted agreement
Authors: Nam Jun‐mo
Published: April 2006

For comparing the validity of rating methods, the adjustedκ(Scoefficient) and Yule'sYindex are better than Cohen'sκwhich is affected by marginal probabilities. We consider a validity study in which a subject is assessed as exposed or not‐exposed by two competing rating methods and the gold standard. We are interested in one of the methods, which is closer in agreement with the gold standard. We present statistical methods taking correlations into account for comparing the validity of the rating methods usingScoefficient andYindex. We show how theScoefficient and Yule'sYindex are related to sensitivity and specificity. In comparing the two rating methods, the preference is clear when the inference is the same for bothSandY. If the inference usingSdiffers from that usingY, then it is not obvious how to decide a preference. This may occur when one rating method is better than the other in sensitivity but not in specificity. Numerical examples for comparing asbestos‐exposure assessment methods are illustrated. Copyright © 2006 John Wiley & Sons, Ltd.
A knowledge warehouse system for enterprise resource planning systems
Authors: Zhang Hong , Liang Yin
Published: April 2006

In this paper, a model of a data warehouse based on an ERP system is presented. A traditional data warehouse has the function of providing data to decision support systems (DSS) or online analytical processing systems (OLAP) but not knowledge. This paper proposes that an existing data warehouse can be extended to create a knowledge warehouse for knowledge management. The knowledge warehouse can manage not only data and information but also the knowledge assets of an enterprise. Both tacit knowledge and explicit knowledge can be analysed, integrated, and converted; new knowledge can be created through the synergistic interactions within the knowledge warehouse. In this paper, knowledge warehouse architecture based on ERP, how it works, and related technologies are discussed. The knowledge warehouse will provide more effective support for DSS and OLAP. Copyright © 2006 John Wiley & Sons, Ltd.
Molecular pathology of breast apocrine carcinomas: A protein expression signature specific for benign apocrine metaplasia
Authors: Celis Julio E. , Gromova Irina , Gromov Pavel , Moreira José M.A. , Cabezón Teresa , Friis Esbern , Rank Fritz
Published: April 2006

Breast cancer is a heterogeneous disease that encompasses a wide range of histopathological types including: invasive ductal carcinoma, lobular carcinoma, medullary carcinoma, mucinous carcinoma, tubular carcinoma, and apocrine carcinoma among others. Pure apocrine carcinomas represent about 0.5% of all invasive breast cancers according to the Danish Breast Cancer Cooperative Group Registry, and despite the fact that they are morphologically distinct from other breast lesions, there are at present no standard molecular criteria available for their diagnosis. In addition, the relationship between benign apocrine changes and breast carcinoma is unclear and has been a matter of discussion for many years. Recent proteome expression profiling studies of breast apocrine macrocysts, normal breast tissue, and breast tumours have identified specific apocrine biomarkers [15‐hydroxyprostaglandin dehydrogenase (15‐PGDH) and hydroxymethylglutaryl coenzyme A reductase (HMG‐CoA reductase)] present in early and advanced apocrine lesions. These biomarkers in combination with proteins found to be characteristically upregulated in pure apocrine carcinomas (psoriasin, S100A9, and p53) provide a protein expression signature distinctive for benign apocrine metaplasias and apocrine cystic lesions. These studies have also presented compelling evidence for a direct link, through the expression of the prostaglandin degrading enzyme 15‐PGDH, between early apocrine lesions and pure apocrine carcinomas. Moreover, specific antibodies against the components of the expression signature have identified precursor lesions in the linear histological progression to apocrine carcinoma. Finally, the identification of proteins that characterize the early stages of mammary apocrine differentiation such as 15‐PGDH, HMG‐CoA reductase, and cyclooxygenase 2 (COX‐2) has opened a window of opportunity for pharmacological intervention, not only in a therapeutic manner but also in a chemopreventive setting. Here we review published and recent results in the context of the current state of research on breast apocrine cancer.
Cyclic nucleotide‐gated ion channels in sensory transduction
Authors: Pifferi Simone , Boccaccio Anna , Menini Anna
Published: April 2006

Cyclic nucleotide‐gated (CNG) channels, directly activated by the binding of cyclic nucleotides, were first discovered in retinal rods, cones and olfactory sensory neurons. In the visual and olfactory systems, CNG channels mediate sensory transduction by conducting cationic currents carried primarily by sodium and calcium ions. In olfactory transduction, calcium in combination with calmodulin exerts a negative feedback on CNG channels that is the main molecular mechanism responsible for fast adaptation in olfactory sensory neurons. Six mammalian CNG channel genes are known and some human visual disorders are caused by mutations in retinal rod or cone CNG genes.
A COMPARISON OF FEMALE- AND MALE-HEADED HOUSEHOLDS IN TANZANIA AND POVERTY IMPLICATIONS
Authors: KATAPA R. S.
Published: April 2006

Female- and male-headed households were compared using data from a Demographic and Health Survey conducted in Tanzania in 1996. Chi-squared tests showed that sex of head of household was highly significantly associated with: residence, household size and composition, radio ownership, having enough food to eat, and age and marital status of head of household. An analysis by the logit regression model showed that female-headed households were more likely than male-headed households to be in rural areas, be small, have fewer men, not have radios and not have enough food to eat. The majority of female heads of households were unmarried and older than male heads of households. The implication is that female-headed households are poorer than male-headed households.
CHILDREN OF HOMOSEXUALS AND TRANSSEXUALS MORE APT TO BE HOMOSEXUAL
Authors: CAMERON PAUL
Published: April 2006

Do the sexual inclinations of parents influence those of their children? Of 77 adult children of homosexual parents who volunteered for three different investigations, at least 23 (30%) were currently homosexual: twelve (55%) of 22 daughters and three (21%) of fourteen sons of lesbians; five (29%) of seventeen daughters and three (17%) of eighteen sons of gays; none of six sons with both a gay and a lesbian parent. At least 25 (32%) were currently heterosexual. Of the ten with transsexual parents, one of nine daughters was currently lesbian, one was currently heterosexual, and one was transsexual. The son’s sexual preference was not reported. These findings suggest that parents’ sexual inclinations influence their children’s.
Modeling and prediction of the magnetospheric dynamics during intense geospace storms
Authors: Chen Jian , Sharma A. Surjalal
Published: April 2006

The nonlinear dynamical models of the coupled solar wind‐magnetosphere system derived from observational data have been used to yield efficient forecasts of the magnetospheric conditions. These data‐derived models have the advantage of capturing the essential features inherent in the data and thus can be improved as larger and better databases become available. Current models are based largely on the data of periods when the magnetosphere is weakly driven. For example, the widely used Bargatze et al. (1985) data set corresponds to a declining phase of the solar cycle and contains only a few weak storms. A correlated database of solar wind and magnetospheric time series data for the last solar cycle near its peak (year 2001) is compiled and used to model the magnetospheric dynamics under strong driving. The solar wind variables are obtained from ACE spacecraft, while the magnetospheric response consists of geomagnetic indices as well as magnetic perturbations measured by ground magnetometers. The dynamical models of the magnetosphere during superstorms developed with this database are used to forecast the geospace storms of October–November 2003 and April 2002 and yields improved forecasts of the intense storms. A new technique is introduced for data‐derived modeling based on the distances of the nearest neighbors from the current state. In this technique the contributions of the nearest neighbors are weighted by factors inversely proportional to the distances in the reconstructed phase space. This yields better predictions, especially during the strongly driven periods. The comparison of the models based on the year 2001 and Bargatze et al. (1985) databases show the similarities and differences in the magnetospheric states during solar maximum and minimum periods.
Angstrom exponent and bimodal aerosol size distributions
Authors: Schuster Gregory L. , Dubovik Oleg , Holben Brent N.
Published: April 2006

Power laws have long been used to describe the spectral dependence of aerosol extinction, and the wavelength exponent of the aerosol extinction law is commonly referred to as the Angstrom exponent. The Angstrom exponent is often used as a qualitative indicator of aerosol particle size, with values greater than 2 indicating small particles associated with combustion byproducts, and values less than 1 indicating large particles like sea salt and dust. In this study, we investigate the relationship between the Angstrom exponent and the mode parameters of bimodal aerosol size distributions using Mie theory calculations and Aerosol Robotic Network (AERONET) retrievals. We find that Angstrom exponents based upon seven wavelengths (0.34, 0.38, 0.44, 0.5, 0.67, 0.87, and 1.02 μm) are sensitive to the volume fraction of aerosols with radii less then 0.6 μm but not to the fine mode effective radius. The Angstrom exponent is also known to vary with wavelength, which is commonly referred to as curvature; we show how the spectral curvature can provide additional information about aerosol size distributions for intermediate values of the Angstrom exponent. Curvature also has a significant effect on the conclusions that can be drawn about two‐wavelength Angstrom exponents; long wavelengths (0.67, 0.87 μm) are sensitive to fine mode volume fraction of aerosols but not fine mode effective radius, while short wavelengths (0.38, 0.44 μm) are sensitive to the fine mode effective radius but not the fine mode volume fraction.
Endosomal hyperacidification in cystic fibrosis is due to defective nitric oxide–cylic GMP signalling cascade
Authors: Poschet Jens F , Fazio Joseph A , Timmins Graham S , Ornatowski Wojciech , Perkett Elizabeth , Delgado Monica , Deretic Vojo
Published: April 2006

Endosomal hyperacidification in cystic fibrosis (CF) respiratory epithelial cells is secondary to a loss of sodium transport control owing to a defective form of the CF transmembrane conductance regulator CFTR. Here, we show that endosomal hyperacidification can be corrected by activating the signalling cascade controlling sodium channels through cyclic GMP. Nitric oxide (NO) donors corrected the endosomal hyperacidification in CF cells. Stimulation of CF cells with guanylate cyclase agonists corrected the pH in endosomes. Exposure of CF cells to an inhibitor of cGMP‐specific phosphodiesterase PDE5, Sildenafil, normalized the endosomal pH. Treatment with Sildenafil reduced secretion by CF cells of the proinflammatory chemokine interleukin 8 following stimulation with Pseudomonas aeruginosa products. Thus, the endosomal hyperacidification and excessive proinflammatory response in CF are in part due to deficiencies in NO‐ and cGMP‐regulated processes and can be pharmacologically reversed using PDE5 inhibitors.
Dynamic bond constraints in protein Langevin dynamics
Authors: Franklin J. , Doniach S.
Published: April 2006

Bond constraint algorithms for molecular dynamics typically take, as the target constraint lengths, the values of the equilibrium bond lengths defined in the potential. In Langevin form, the equations of motion are temperature dependent, which gives the average value for the individual bond lengths a temperature dependence. In addition to this, locally constant force fields can shift the local equilibrium bond lengths. To restore the average bond lengths in constrained integration to their unconstrained values, we suggest changing the constraint length used by popular constraint methods such as RATTLE [H. C. Andersen, J. Comput. Phys. 52, 23 (1983)] at each step. This allows us to more accurately capture the equilibrium bond length changes (with respect to the potential) due to the local equilibration and temperature effects. In addition, the approximations to the unconstrained nonbonded energies are closer using the dynamic constraint method than a traditional fixed constraint algorithm. The mechanism for finding the new constrained lengths involves one extra calculation of the bonded components of the force, and therefore adds O(N) time to the constraint algorithm. Since most molecular dynamics calculations are dominated by the O(N2) nonbonded forces, this new method does not take significantly more time than a fixed constraint algorithm.
Electrical transport measurements on self-assembled organic molecular wires
Authors: Durkut M. , Mas-Torrent M. , Hadley P. , Jonkheijm P. , Schenning A. P. H. J. , Meijer E. W. , George S. , Ajayaghosh A.
Published: April 2006

The electrical properties of supermolecular assemblies of oligo(p-phenylene vinylene) were studied. These materials self-assemble into well-defined cylindrical structures in solution with lengths in the range of 100nm–10μm and diameters between 5 and 200nm. Atomic force microscopy showed that by adjusting the concentration, either individual molecular wires or a dense film could be deposited. The molecular wires showed poor electrical conduction. Several tests were performed that show that it was the molecular wires themselves, not the contacts, that limit the conductivity.
Reactive collisions between CH+ and O−
Authors: Le Padellec A. , Staicu-Casagrande E. M. , Nzeyimana T. , Naji E. A. , Urbain X.
Published: April 2006

Integral cross sections were measured for two reactions occurring in CH++O− collisions: the formation of the carbon monoxide cation CO+ via a reactive ionization process and the formation of the (iso)formyl cation HCO+ (HOC+) via the associative ionization process. Both carbon monoxide and formyl cations are present in the interstellar medium, the latter one being quite abundant in dense clouds. Provided the oxygen anion would also be present in the interstellar environment, the large efficiency of the two reactive processes reported here would justify their inclusion in astrochemical models. The whole set of data was obtained by means of a merged-beam setup operating with keV beams.
Absence of reptation in the high-temperature folding of the trpzip2 β-hairpin peptide
Authors: Pitera Jed W. , Haque Imran , Swope William C.
Published: April 2006

We have carried out extensive all atom explicit solvent simulations of the high-temperature folding and unfolding of the trpzip2 β-hairpin peptide and examined the resulting trajectories for evidence of folding via a reptation mechanism. Over 300 microcanonical simulations of 10 ns each were initiated from a Boltzmann ensemble of conformations at 425K. Though we observed numerous folding and unfolding events, no evidence of reptation was found. The diffusional dynamics of the peptide are orders of magnitude faster than any observed reptation-like motion. Our data suggest that the dominant mechanisms for β-hairpin folding under these conditions are hydrophobic collapse and turn formation, and that rearrangements occur via significant expansion of the polypeptide chain.
Negative bias temperature instability mechanism: The role of molecular hydrogen
Authors: Krishnan Anand T. , Chakravarthi Srinivasan , Nicollian Paul , Reddy Vijay , Krishnan Srikanth
Published: April 2006

The role of dimerization of atomic hydrogen to give molecular hydrogen in determining negative bias temperature instability (NBTI) kinetics is explored analytically. The time dependency of NBTI involving molecular hydrogen was found to obey a power law with a slope of 1∕6, as opposed to the 1∕4 slope derived for a reaction involving atomic hydrogen. The implications of this dimerization reaction for voltage and temperature acceleration are also discussed. Simulation results validating these predictions are also described. The higher slopes typically reported for NBTI are shown to be an artifact of measurement, and experimental data supporting this lower time dependency is shown.
Correlated wave functions for the ground and some excited states of the iron atom
Authors: Buendía E. , Gálvez F. J. , Sarsa A.
Published: April 2006

We study the states arising from the [Ar]4s23d6 and [Ar]4s13d7 configurations of iron atom with explicitly correlated wave functions. The variational wave function is the product of the Jastrow correlation factor times a model function obtained within the parametrized optimized effective potential framework. A systematic analysis of the dependence of both the effective potential and the correlation factor on the configuration and on the term is carried out. The ground state of both, the cation, Fe+, and anion, Fe−, are calculated with correlated wave functions and the ionization potential and the electron affinity are obtained.
In situ resonant x-ray study of vertical correlation and capping effects during GaN∕AlN quantum dot growth
Authors: Coraux J. , Renevier H. , Favre-Nicolin V. , Renaud G. , Daudin B.
Published: April 2006

Grazing incidence anomalous x-ray scattering was used to monitor in situ the molecular beam epitaxy growth of GaN∕AlN quantum dots (QDs). The strain state was studied by means of grazing incidence multiwavelength anomalous diffraction (MAD) in both the QDs and the AlN during the progressive coverage of QDs by AlN monolayers. Vertical correlation in the position of the GaN QDs was also studied by both grazing incidence MAD and anomalous grazing incidence small angle scattering as a function of the number of GaN planes and of the AlN spacer thickness. In a regime where the GaN QDs and the AlN capping are mutually strain influenced, a vertical correlation in the position of QDs is found with as a side effect an average increase in the QD width.
Potential performance of indium-nitride-based devices
Authors: O’Leary Stephen K. , Foutz Brian E. , Shur Michael S. , Eastman Lester F.
Published: April 2006

We study how electrons, initially in thermal equilibrium, drift under the action of an applied electric field within bulk wurtzite indium nitride. We find that the optimal cutoff frequency for an ideal indium-nitride-based device ranges from around 10GHz when the device thickness is set to 10μm to about 2.5THz when the device thickness is set to 0.1μm. We thus suggest that indium nitride offers great promise for future high-speed device applications.
Optimized effective potentials yielding Hartree–Fock energies and densities
Authors: Staroverov Viktor N. , Scuseria Gustavo E. , Davidson Ernest R.
Published: April 2006

It is commonly believed that the exchange-only optimized effective potential (OEP) method must yield total energies that are above corresponding ground-state Hartree–Fock (HF) energies except for one- and two-electron systems. We present a simple procedure for constructing local (multiplicative) exchange potentials that reproduce exactly the HF energy and density in any finite basis set for any number of electrons. For any finite basis set, no matter how large, there exist infinitely many such OEPs, which questions their suitability for practical applications.
Growth of nanographite on Pt(111) and its edge state
Authors: Entani Shiro , Ikeda Susumu , Kiguchi Manabu , Saiki Koichiro , Yoshikawa Genki , Nakai Ikuyo , Kondoh Hiroshi , Ohta Toshiaki
Published: April 2006

The nanographite grains, the diameter of which was around 5nm, were formed on Pt(111) by exposing the Pt(111) substrate to benzene gas at room temperature and annealing it up to 850K. The increase of relative number of edge atoms enabled the observation of edge-derived electronic states. The measurement of ultraviolet photoelectron spectroscopy and near edge x-ray absorption fine structure on the nanographite revealed the appearance of the edge state located at the Fermi level.
Ubiquitylation of yeast proliferating cell nuclear antigen and its implications for translesion DNA synthesis
Authors: Haracska Lajos , Unk Ildiko , Prakash Louise , Prakash Satya
Published: April 2006

The Rad6–Rad18 ubiquitin-conjugating enzyme complex promotes replication through DNA lesions by means of at least three different pathways: the DNA polymerase (Pol) η- and ζ-dependent translesion DNA synthesis (TLS) and a Rad5–Mms2–Ubc13-dependent pathway. In DNA-damaged yeast cells proliferating cell nuclear antigen (PCNA) becomes monoubiquitylated at the K164 residue, and genetic studies in yeast have indicated a requirement for this modification in TLS mediated by Polη and Polζ. To be able to decipher the role of PCNA monoubiquitylation in the TLS process, we have reconstituted this PCNA modification
in vitro
from purified yeast proteins. We show that, in addition to the requirement for Rad6–Rad18, the reaction depends on the loading of the PCNA homotrimeric ring onto the DNA by replication factor C and that all three PCNA monomers become efficiently ubiquitylated. The availability of PCNA monoubiquitylated on all of its three monomers has enabled us to examine the effects of this PCNA modification on DNA synthesis by Pols δ, η, ζ, and Rev1. Contrary to the prevailing ideas that presume a role for PCNA ubiquitylation in the disruption of Polδ’s binding to PCNA or in the enhancement of the binding affinity of the TLS Pols for PCNA, we find that PCNA ubiquitylation does not affect any of these processes. These observations lead us to suggest a role for PCNA monoubiquitylation in disrupting the PCNA binding of a protein(s) that otherwise is inhibitory to the binding of PCNA by TLS Pols.
Glucocorticoid enhancement of memory requires arousal-induced noradrenergic activation in the basolateral amygdala
Authors: Roozendaal Benno , Okuda Shoki , Van der Zee Eddy A. , McGaugh James L.
Published: April 2006

Considerable evidence indicates that glucocorticoid hormones enhance the consolidation of long-term memories for emotionally arousing experiences but not that for less arousing or neutral information. However, previous studies have not determined the basis of such arousal-induced selectivity. Here we report the finding that endogenous noradrenergic activation of the basolateral complex of the amygdala (BLA) induced by emotional arousal is essential in enabling glucocorticoid memory enhancement. Corticosterone administered immediately after object recognition training enhanced 24-h memory of naïve male rats but not that of rats previously habituated to the training context in order to reduce novelty-induced emotional arousal. The β-adrenoceptor antagonist propranolol administered either systemically or into the BLA blocked the corticosterone-induced memory enhancement. Further, in habituated rats, corticosterone activated BLA neurons, as assessed by phosphorylated cAMP response element binding (pCREB) immunoreactivity levels, and enhanced memory only when norepinephrine release was stimulated by administration of the α
2
-adrenoceptor antagonist yohimbine. These findings strongly suggest that synergistic actions of glucocorticoids and emotional arousal-induced noradrenergic activation of the BLA constitute a neural mechanism by which glucocorticoids may selectively enhance memory consolidation for emotionally arousing experiences.
A Discoidin Domain Receptor 1/SHP-2 Signaling Complex Inhibits α2β1-Integrin–mediated Signal Transducers and Activators of Transcription 1/3 Activation and Cell Migration
Authors: Wang Chau-Zen , Su Hsiao-Wen , Hsu Yu-Chih , Shen Meng-Ru , Tang Ming-Jer
Published: April 2006

Regulation of cell migration is an important step for the development of branching tubule morphogenesis in collagen gel. Here, we showed that discoidin domain receptor (DDR) 1a/b inhibited collagen-induced tyrosine phosphorylation of signal transducers and activators of transcription (Stat) 1/3 and cell migration triggered by α2β1-integrin. Overexpression of DDR1a/b increased the interaction of DDR1 with SHP-2 and up-regulated the tyrosine phosphatase activity of SHP-2. Expression of catalytically inactive SHP-2 in DDR1-transfected cells restored the tyrosine phosphorylation of Stat3 and cell migration. We demonstrated that the Src homology-2 (SH2)-SH2 and phosphotyrosyl phosphatase (PTP) domains of SHP-2 were responsible for interaction with DDR1 and that both tyrosine phosphorylation sites 703 and 796 of DDR1 were essential for it to bind with SHP-2. Mutation of tyrosine 703 or 796 of DDR1 abolished the ability of DDR1 to inhibit the tyrosine phosphorylation of Stat1 and Stat3 and restored collagen-induced cell migration and hepatocyte growth factor-induced branching tubulogenesis in collagen gel. Together, these results demonstrate that SHP-2 is required for the DDR1-induced suppression of Stat1 and Stat3 tyrosine phosphorylation, cell migration, and branching tubulogenesis.
Aip1 and Cofilin Promote Rapid Turnover of Yeast Actin Patches and Cables: A Coordinated Mechanism for Severing and Capping Filaments
Authors: Okada Kyoko , Ravi Harini , Smith Ellen M. , Goode Bruce L.
Published: April 2006

Rapid turnover of actin structures is required for dynamic remodeling of the cytoskeleton and cell morphogenesis, but the mechanisms driving actin disassembly are poorly defined. Cofilin plays a central role in promoting actin turnover by severing/depolymerizing filaments. Here, we analyze the in vivo function of a ubiquitous actin-interacting protein, Aip1, suggested to work with cofilin. We provide the first demonstration that Aip1 promotes actin turnover in living cells. Further, we reveal an unanticipated role for Aip1 and cofilin in promoting rapid turnover of yeast actin cables, dynamic structures that are decorated and stabilized by tropomyosin. Through systematic mutagenesis of Aip1 surfaces, we identify two well-separated F-actin–binding sites, one of which contributes to actin filament binding and disassembly specifically in the presence of cofilin. We also observe a close correlation between mutations disrupting capping of severed filaments in vitro and reducing rates of actin turnover in vivo. We propose a model for balanced regulation of actin cable turnover, in which Aip1 and cofilin function together to “prune” tropomyosin-decorated cables along their lengths. Consistent with this model, deletion of AIP1 rescues the temperature-sensitive growth and loss of actin cable defects of tpm1Δ mutants.
Cortactin Has an Essential and Specific Role in Osteoclast Actin Assembly
Authors: Tehrani Shandiz , Faccio Roberta , Chandrasekar Indra , Ross F. Patrick , Cooper John A.
Published: April 2006

Osteoclasts are essential for bone dynamics and calcium homeostasis. The cells form a tight seal on the bone surface, onto which they secrete acid and proteases to resorb bone. The seal is associated with a ring of actin filaments. Cortactin, a c-Src substrate known to promote Arp2/3-mediated actin assembly in vitro, is expressed in osteoclasts and localizes to the sealing ring. To address the role of cortactin and actin assembly in osteoclasts, we depleted cortactin by RNA interference. Cortactin-depleted osteoclasts displayed a complete loss of bone resorption with no formation of sealing zones. On nonosteoid surfaces, osteoclasts flatten with a dynamic, actin-rich peripheral edge that contains podosomes, filopodia, and lamellipodia. Cortactin depletion led to a specific loss of podosomes, revealing a tight spatial compartmentalization of actin assembly. Podosome formation was restored in cortactin-depleted cells by expression of wild-type cortactin or a Src homology 3 point mutant of cortactin. In contrast, expression of a cortactin mutant lacking tyrosine residues phosphorylated by Src did not restore podosome formation. Cortactin was found to be an early component of the nascent podosome belt, along with dynamin, supporting a role for cortactin in actin assembly.
Prediction of chirality- and size-dependent elastic properties of single-walled carbon nanotubes via a molecular mechanics model
Authors: Chang Tienchong , Geng Jingyan , Guo Xingming
Published: April 2006

Molecular mechanics has been widely used to analytically study mechanical behaviour of carbon nanotubes. However, explicit expressions for elastic properties of carbon nanotubes are so far confined to some special cases due to the lack of fully constructed governing equations for the molecular mechanics model. In this paper, governing equations for an analytical molecular mechanics model are fully established. The explicit expressions for five in-plane elastic properties of a chiral single-walled carbon nanotube are derived, which make properties at different length-scales directly connected. The effects of tube chirality and tube diameter are investigated. In particular, the present results show that the classic relationship from the isotropic elastic theory of continuum mechanics between Young's modulus and shear modulus of a single-walled carbon nanotube is not retained. The present analytical results are helpful to the understanding of elastic properties of carbon nanotubes, and also useful to the topic of linking molecular mechanics with continuum mechanics.