bluuebunny/crossref_metadata_2025 huggingface dataset:
The KK‐Periome database for transcripts of periodontal ligament development
Authors: Saito Masahiro , Nishida Eisaku , Sasaki Takashi , Yoneda Toshiyuki , Shimizu Nobuyoshi
Published: January 2009

The periodontal ligament (PDL) is a strong connective tissue that surrounds the tooth root, absorbs occlusal forces, and functions as a sense organ. PDL originated from dental follicle (DF), which possessed mesenchymal progenitors in the developing tooth germ. However, as specific marker genes for PDL and DF are currently unavailable, the molecular mechanisms of PDL development are yet to be clarified. To facilitate the identification of such genes, we have previously established a transcriptome database of the human PDL (the KK‐Periome database) and screened for specific genes expressed during PDL development. Initial screening of the database revealed two marker genes for distinguishing DF and PDL. The KK‐Periome database thus appears to offer a useful resource for investigating genes involved in PDL development. J. Exp. Zool. (Mol. Dev. Evol.) 312B:495–502, 2009. © 2009 Wiley‐Liss, Inc.
Spermiogenic nuclear protein transitions and chromatin condensation. Proposal for an ancestral model of nuclear spermiogenesis
Authors: Kurtz Kathryn , Saperas Núria , Ausió Juan , Chiva Manel
Published: January 2009

We have chosen three species (Sparus aurata, Dicentrarchus labrax, and Monodonta turbinata) that represent different transition patterns in the composition and structure of spermiogenic nuclei. The transition patterns of these species are representative of spermiogenesis in a large number of animal species. We analyze: (a) nuclear protein exchange; (b) chromatin condensation pattern; and (c) histone acetylation during spermiogenic development. In the simplest spermiogenesis histones and nucleosomes remain in mature sperm. Chromatin of spermatids is organized into 20 nm granules, simultaneous with a nuclear volume reduction. The granules coalesce in the final stage of spermiogenesis. Granular chromatin is correlated with acetylation of histones H3 and H4, whereas final coalescence is associated with histone deacetylation. We also studied two other spermiogenesis where a basic protein substitutes histones. Each species has a very different substituting protein. One has a typical protamine of 34 amino acids; the other has a sperm nuclear basic proteins (SNBP) of 106 amino acids. In both, the structural transitions and histone acetylation pattern are similar: in early spermiogenesis chromatin is organized into 20 nm granules, and histones are significantly acetylated, while the nuclear volume decreases. Subsequently, acetylated histones are displaced by the protamine or SNBP. Histone substitution causes chromatin remodelling and additional reduction in nuclear volume. We analyze these three cases together with earlier works and propose that the formation of 20 nm granules containing acetylated H3 and H4 accomplishes the minimum functional requirement to be considered the most evolutionarily ancestral chromatin conformation preceding condensation in animal spermiogenesis. J. Exp. Zool. (Mol. Dev. Evol.) 312B:149–163, 2009. © 2009 Wiley‐Liss, Inc.
Synthesis and biodistribution in mice of 99mTcN–DBODC–DMSEt
Authors: Yang Shuye , Wang Xuebin , Guo Haixun , Liu Jian , Wang Fenglong , Zhang Xianzhong
Published: January 2009

Nitrido technetium(V)‐mixed ligand complex of 99mTcN–DBODC–DMSEt [DMSEt: Monoethyl ester of (meso) 2,3‐dimercaptosuccinic acid, DBODC: bis(2‐ethoxyethyl)carbamodithioate] has been prepared in a two‐step procedure by first reaction of 99mTcO with succinic dihydrazede in the presence of stannous chloride as a reducing agent and propylenediamine tetraacetic acid as a complexant, followed by the addition of DMSEt and DBODC. The complex was stable over 6 h at room temperature. The partition coefficient indicated that it was a hydrophilic complex. Biodistribution in mice demonstrated that the complex accumulated mainly in liver, lungs and kidneys. Copyright © 2009 John Wiley & Sons, Ltd.
Transition metals as electron traps. I. Structures, energetics, electron capture, and electron‐transfer‐induced dissociations of ternary copper–peptide complexes in the gas phase
Authors: Tureček František , Jones Jace W. , Holm Anne I. S. , Panja Subhasis , Nielsen Steen Brøndsted , Hvelplund Preben
Published: January 2009

Electron‐induced dissociations of gas‐phase ternary copper‐2,2′‐bipyridine complexes of Gly‐Gly‐Gly and Gly‐Gly‐Leu were studied on a time scale ranging from 130 ns to several milliseconds using a combination of charge‐reversal (+CR−) and electron‐capture‐induced dissociation (ECID) measured on a beam instrument and electron capture dissociation (ECD) measured in a Penning trap. Charge‐reduced intermediates were observed on the short time scale in the +CR− and ECID experiments but not in ECD. Ion dissociations following electron transfer or capture mostly occurred by competitive bpy or peptide ligand loss, whereas peptide backbone fragmentations were suppressed in the presence of the ligated metal ion. Extensive electron structure theory calculations using density functional theory and large basis sets provided optimized structures and energies for the precursor ions, charge‐reduced intermediates, and dissociation products. The Cu complexes underwent substantial structure changes upon electron capture. Cu was calculated to be pentacoordinated in the most stable singly charged complexes of the [Cu(peptide − H)bpy]+ • type where it carried a ∼+ 1 atomic charge. Cu coordination in charge‐reduced [Cu(peptide − H)bpy] intermediates depended on the spin state. The themodynamically more stable singlet states had tricoordinated Cu, whereas triplet states had a tetracoordinated Cu. Cu was tricoordinated in stable [Cu(peptide − H)bpy]− • products of electron transfer. [Cu(peptide)bpy]2 + • complexes contained the peptide ligand in a zwitterionic form while Cu was tetracoordinated. Upon electron capture, Cu was tri‐ or tetracoordinated in the [Cu(peptide)bpy]+ charge‐reduced analogs and the peptide ligands underwent prototropic isomerization to canonical forms. The role of excited singlet and triplet electronic states is assessed. Copyright © 2009 John Wiley & Sons, Ltd.
Statistical‐dynamical prediction of the Madden–Julian oscillation using NCEP Climate Forecast System (CFS)
Authors: Seo Kyong‐Hwan
Published: January 2009

The predictive performance of the Madden–Julian Oscillation (MJO) in the National Centers for Environmental Prediction's (NCEP's) operational coupled, Climate Forecast System (CFS) model is assessed and statistical‐dynamical hybrid models are developed based on this numerical model to improve forecasting skill. By projecting ENSO‐removed variables onto the principal patterns of the MJO convection and upper‐ and lower‐level circulations, MJO‐related signals in the dynamical model forecasts are extracted. It is found that the coupled model exhibits useful predictability out to 2 and 3 pentads when the initial MJO convection is located over the Maritime Continent and the Indian Ocean, respectively. The first hybrid model (HYBRID1) developed is a lagged multiple linear regression scheme, where the previous values of the first two leading principal components (PCs) from the coupled model are used as predictors along with the latest observed PC values. The other hybrid model (HYBRID2) is constructed to fit the predicted PC time series from the coupled model to the observed PCs at each lead time using 13 years of training data fields. HYBRID2 does not produce persistent improvement in forecast skill compared to CFS, whereas for HYBRID1, the resulting correlation coefficient and root mean square (RMS) skills are considerably enhanced due to the incorporation of lagged correlation information between the two PCs. The skill improvement of HYBRID1 ranges from 15 to 50% relative to the CFS forecast and the improvement in the correlation skill is greater than the RMS error correction. When the MJO convection is located initially over the Maritime Continent during the northern summer, the CFS forecast skill is as small as the persistence forecast, whereas HYBRID1 demonstrates the greatest skill improvement. During ENSO winters, the forecast skill is enhanced by ∼30% by HYBRID1. In particular, the skill improvement in La Niña years is noticeably greater than in El Niño years. Copyright © 2009 Royal Meteorological Society
Length change patterns of the extensor retinaculum and the effect of total knee replacement
Authors: Ghosh Kanishka M. , Merican Azhar M. , Iranpour‐Boroujeni Farhad , Deehan David J. , Amis Andrew A.
Published: January 2009

Patellofemoral dysfunction following total knee replacement (TKR) is a significant clinical problem, but little information exists on the mechanics of the patellofemoral retinacula or the effects of TKR on these structures. We hypothesized that TKR would cause significant elongation of the retinacula. Retinacular length changes were measured by threading sutures along the retinacula, fixing the sutures to the patella and the iliotibial band (ITB), and attaching the femoral ends to displacement transducers. The intact knee was flexed‐extended while the quadriceps and ITB were tensed and the retinacular length change patterns were recorded. The measurements were repeated post‐TKR. The medial patellofemoral ligament (MPFL) was close to isometric, stretching 2 mm in terminal knee extension, whereas the lateral retinaculum slackened 8 mm from 110° to 0° flexion. TKR did not cause significant elongation of either of the retinacula, the largest change being 3 mm elongation of the MPFL around 40°, which stretched the MPFL by 1.4 mm above its maximum natural length. Thus, this work did not support the hypothesis that TKR causes significant elongation of the retinacula sufficient to affect knee function. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 865–870, 2009
Cobalt ions induce chemokine secretion in primary human osteoblasts
Authors: Queally J.M. , Devitt B.M. , Butler J.S. , Malizia A.P. , Murray D. , Doran P.P. , O'Byrne J.M.
Published: January 2009

Chemokines are major regulators of the inflammatory response and have been shown to play an important role in periprosthetic osteolysis. Titanium particles have previously been shown to induce IL‐8 and MCP‐1 secretion in osteoblasts. These chemokines result in the chemotaxis and activation of neutrophils and macrophages, respectively. Despite a resurgence in the use of cobalt‐chromium‐molybdenum alloys in metal‐on‐metal arthroplasty, cobalt and chromium ion toxicity in the periprosthetic area has been insufficiently studied. In this study we investigate the in vitro effect of cobalt ions on primary human osteoblast activity. We demonstrate that cobalt ions rapidly induce the protein secretion of IL‐8 and MCP‐1 in primary human osteoblasts. This elevated chemokine secretion is preceded by an increase in the transcription of the corresponding chemokine gene. Using a Transwell migration chemotaxis assay we also demonstrate that the chemokines secreted are capable of inducing neutrophil and macrophage migration. Furthermore, cobalt ions significantly inhibit osteoblast function as demonstrated by reduced alkaline phosphatase activity and calcium deposition. In aggregate these data demonstrate that cobalt ions can activate transcription of the chemokine genes IL‐8 and MCP‐1 in primary human osteoblasts. Cobalt ions are not benign and may play an important role in the pathogenesis of osteolysis by suppressing osteoblast function and stimulating the production and secretion of chemokines that attract inflammatory and osteoclastic cells to the periprosthetic area. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 855–864, 2009
Vocal cord immobility caused by the long‐standing impaction of a fishbone in the hypopharynx
Authors: Hung Chung‐Ching , Lee Jih‐Chin , Hsiao Li‐Chun , Lin Yaoh‐Shiang
Published: January 2009

Vocal cord immobility is a rare presentation of an impacted fishbone in the pharynx. The mechanisms can be classified into either mechanical articular fixation or direct/indirect neuropathy of the recurrent laryngeal nerve. We report a case of vocal cord immobility secondary to long‐standing impaction of a fishbone in the hypopharynx for at least 9 months. The diagnosis was made by computed tomography (CT) and rigid laryngoscopy because no reliable history was available. The cricoarytenoid joint was not fixed and the function of the vocal cords returned one month after removal of the fishbone. The mechanism of the vocal cord immobility was an injury to the recurrent laryngeal nerve due to the chronic inflammatory reaction in the paraglottic space. Laryngoscope, 119:228–230, 2009
Confusion over different types of n‐3 polyunsaturated fatty acids
Authors: Stanley John C.
Published: January 2009

There are two kinds of n‐3 polyunsaturated fatty acid (PUFA). Alpha‐linolenic acid (ALA) is the parent n‐3 PUFA; it cannot be synthesized by the human body and as a result is an essential fatty acid. The two long chain n‐3 PUFA eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) can in principle be synthesized from ALA or obtained from the diet. While the cardioprotective effects of long chain n‐3 PUFA are well established the effects of ALA on the cardiovascular system are more controversial. The Lyon Diet Heart Study which it is claimed provides evidence for beneficial effects of ALA on the cardiovascular system is flawed. The argument that ALA conversion into EPA and DHA provides significant quantities of the two long chain n‐3 PUFA is unsustainable as rates of conversion are too low. To avoid confusion a distinction needs to be drawn between ALA and the long chain n‐3 PUFA. Health claims for foods rich in EPA and DHA cannot be extended to foods rich in ALA nor is ALA a substitute for EPA and DHA in vegetarian diets.
Physico‐Mechanical Properties of Biodegradable Starch Nanocomposites
Authors: García Nancy L. , Ribba Laura , Dufresne Alain , Aranguren Mirta I. , Goyanes Silvia
Published: January 2009

Nanocomposites of cassava starch reinforced with waxy starch nanocrystals were prepared. They showed a 380% increase of the rubbery storage modulus (at 50 °C) and a 40% decrease in the water vapor permeability. X‐ray spectra show that the composite was more amorphous than the neat matrix, which was attributed to higher equilibrium water content in the composites. TGA confirmed this result and its thermal derivative suggested the formation of hydrogen bonding between glycerol and the nanocrystals. The reinforcing effect of starch nanocrystals was attributed to strong filler/matrix interactions due to the hydrogen bonding. The decrease of the permeability suggests that the nanocrystals were well dispersed, with few filler/filler interactions.

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On Processing and Impact Deformation Behavior of High Density Polyethylene (HDPE)–Calcium Carbonate Nanocomposites
Authors: Yuan Qiang , Shah Jinesh S. , Bertrand Kennith J. , Misra R. Devesh K.
Published: January 2009

Different processing approaches were adopted to obtain the best combination of strength and toughness. The approach that yielded superior properties was examined in detail to study the mechanical response of nanoscale calcium carbonate‐reinforced high density polyethylene in conjunction with unreinforced high density polyethylene. The reinforcement of high density polyethylene with nanoscale calcium carbonate increases impact strength and is not accompanied by decrease in yield strength. The addition of nanoscale calcium carbonate to high density polyethylene alters the micromechanism of deformation from crazing‐tearing in high density polyethylene to fibrillation in high density polyethylene–calcium carbonate nanocomposite.

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Ultra‐Fast Fabrication of Colloidal Photonic Crystals by Spray Coating
Authors: Cui Liying , Zhang Youzhuan , Wang Jingxia , Ren Yibing , Song Yanlin , Jiang Lei
Published: January 2009

An ultra‐fast fabrication of large‐scale colloidal PCs via spray coating was demonstrated. The latex spheres with hydrophobic core and hydrophilic shell were designed, and the latex shell with abundant COOH groups resulted in strong hydrogen bonding interaction among latex spheres, which boosted latex arrangement during the spray procedure. The resultant samples with area of 7 × 12 cm2 were easily fabricated within 1 min on different substrates. This ultra‐fast fabrication procedure would be of great importance for the practical application of PCs for optic devices and functional coatings.

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Understanding and Optimizing the SMX Static Mixer
Authors: Singh Mrityunjay K. , Anderson Patrick D. , Meijer Han E. H.
Published: January 2009

Using the Mapping Method different designs of SMX motionless mixers are analyzed and optimized. The three design parameters that constitute a specific SMX design are: The number of cross‐bars over the width of channel,Nx, the number of parallel cross‐bars per element,Np, and the angle between opposite cross‐barsθ. OptimizingNx, somewhat surprisingly reveals that in the standard design withNp = 3,Nx = 6 is the optimum using both energy efficiency as well as compactness as criteria. IncreasingNxresults in under‐stretching and decreasingNxleads to over‐stretching of the interface. IncreasingNpmakes interfacial stretching more effective by co‐operating vortices. Comparing realized to optimal stretching, we find the optimum series for all possible SMX(n) designs to obey the universal design ruleNp = (2/3)Nx−1, forNx = 3, 6, 9, 12, ….

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Functionalized Graphenes and Thermoplastic Nanocomposites Based upon Expanded Graphite Oxide
Authors: Steurer Peter , Wissert Rainer , Thomann Ralf , Mülhaupt Rolf
Published: January 2009

Exfoliation of expanded GO represents an attractive route to functionalized graphenes as versatile 2D carbon nanomaterials and components of a wide variety of polymer nanocomposites. Thermally reduced graphite oxides (TrGO) with specific surface areas of 600 to 950 m2 · g−1 were obtained by oxidation of graphite followed by thermal expansion at 600 °C. Thermal post treatment at 700 °C and 1 000 °C increased carbon content (81 to 97 wt.‐%) and lowered resistivity (1 600 to 50 Ω · cm). During melt extrusion with PC, iPP, SAN and PA6, exfoliation afforded uniformly dispersed graphenes with aspect ratio > 200. In comparison to conventional 0D and 1D carbon nanoparticles, TrGO afforded nanocomposites with improved stiffness and lower percolation threshold. Recent progress and new strategies in development of functionalized graphenes and graphene‐based nanocomposites are highlighted.

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Measuring RF‐induced currents inside implants: Impact of device configuration on MRI safety of cardiac pacemaker leads
Authors: Nordbeck Peter , Weiss Ingo , Ehses Philipp , Ritter Oliver , Warmuth Marcus , Fidler Florian , Herold Volker , Jakob Peter M. , Ladd Mark E. , Quick Harald H. , Bauer Wolfgang R.
Published: January 2009

Radiofrequency (RF)‐related heating of cardiac pacemaker leads is a serious concern in magnetic resonance imaging (MRI). Recent investigations suggest such heating to be strongly dependent on an implant's position within the surrounding medium, but this issue is currently poorly understood. In this study, phantom measurements of the RF‐induced electric currents inside a pacemaker lead were performed to investigate the impact of the device position and lead configuration on the amount of MRI‐related heating at the lead tip. Seven hundred twenty device position/lead path configurations were investigated. The results show that certain configurations are associated with a highly increased risk to develop MRI‐induced heating, whereas various configurations do not show any significant heating. It was possible to precisely infer implant heating on the basis of current intensity values measured inside a pacemaker lead. Device position and lead configuration relative to the surrounding medium are crucial to the amount of RF‐induced heating in MRI. This indicates that a considerable number of implanted devices may incidentally not develop severe heating in MRI because of their specific configuration in the body. Small variations in configuration can, however, strongly increase the risk for such heating effects, meaning that hazardous situations might appear during MRI. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Functional changes in CSF volume estimated using measurement of water T2 relaxation
Authors: Piechnik S.K. , Evans J. , Bary L.H. , Wise R.G. , Jezzard P.
Published: January 2009

Cerebrospinal fluid (CSF) provides hydraulic suspension for the brain. The general concept of bulk CSF production, circulation, and reabsorption is well established, but the mechanisms of momentary CSF volume variation corresponding to vasoreactive changes are far less understood. Nine individuals were studied in a 3T MR scanner with a protocol that included visual stimulation using a 10‐Hz reversing checkerboard and administration of a 5% CO2 mix in air. We acquired PRESS‐localized spin‐echoes (TR = 12 sec, TE = 26 ms to 1.5 sec) from an 8‐mL voxel located in the visual cortex. Echo amplitudes were fitted to a two‐compartmental model of relaxation to estimate the partial volume of CSF and the T2 relaxation times of the tissues. CSF signal contributed 10.7 ± 3% of the total, with T2,csf = 503.0 ± 64.3 [ms], T2,brain = 61.0 ± 2 [ms]. The relaxation time of tissue increased during physiological stimulation, while the fraction of signal contributed by CSF decreased significantly by 5–6% with visual stimulation (P < 0.03) and by 3% under CO2 inhalation (P < 0.08). The CSF signal fraction is shown to represent well the volume changes under viable physiological scenarios. In conclusion, CSF plays a significant role in buffering the changes in cerebral blood volume, especially during rapid functional stimuli. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Backcalculating pavement structural properties using a Nelder–Mead simplex search
Authors: Yi Jin‐Hak , Mun Sungho
Published: January 2009

A structural integrity assessment technique of pavements that considers the backcalculation of material properties is herein proposed. In order to carry out the backcalculation, a Nelder–Mead simplex (NMS) search is applied to estimate the elastic moduli of layered structures using the deflection data simulated by falling weight deflectometer (FWD) tests. In order to utilize a forward calculation engine of the numerical simulation in the FWD testing, a wave analysis program of layered pavement systems is used based on a spectral element method. The performance of the NMS inversion technique is evaluated based on a comparison with the Levenberg–Marquardt method. Copyright © 2009 John Wiley & Sons, Ltd.
Solving the reaction–diffusion equations with nonlocal boundary conditions based on reproducing kernel space
Authors: Lin Yingzhen , Zhou Yongfang
Published: January 2009

The reaction–diffusion equations with initial condition and nonlocal boundary conditions are discussed in this article. A reproducing kernel space is constructed, in which an arbitrary function satisfies the initial condition and nonlocal boundary conditions of the reaction‐diffusion equations. Based on the reproducing kernel space, a new algorithm for solving the reaction–diffusion equations with initial condition and nonlocal boundary conditions is presented. Some examples are displayed to demonstrate the validity and applicability of the proposed method. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2009
Erratum zu “Antitussiva und Expektorantien”, Pharmazie in unserer Zeit 6/2008
Authors: Sander Kerstin , Zettl Heiko , Schubert‐Zsilavecz Manfred , Stark Holger
Published: January 2009

Leider ist uns in der Ausgabe 6/2008 “Antitussiva/Expektorantien” in dem Artikel “Medizinisch‐chemische Aspekte – Antitussiva und Expektorantien” in Abb. 2, Seite 463, ein Formelfehler unterlaufen. Die Abbildung enthält die Struktur von Levomethorphan statt der des beschriebenen antitussiven Dextromethorphans. Zur Sicherheit haben wir beide Strukturen hier nochmals aufgeführt (Abb.).

Die Autoren
Nobelviren
Authors: Zündorf Ilse , Dingermann Theo , Winckler Thomas
Published: January 2009

Zwei spannende und zugleich lehrreiche Wissenschaftsgeschichten wurden mit dem jüngsten Nobelpreis für Physiologie und Medizin ausgezeichnet: Zum einen die Entdeckung des HI‐Virus als Ursache für AIDS, zum anderen die Identifizierung der Humanen Papillomaviren (HPV) als Auslöser des Gebärmutterhalskrebses. Natürlich freut es die deutsche Wissenschaftswelt besonders, dass die Hälfte des Preises an den langjährigen Leiter des Deutschen Krebsforschungszentrums in Heidelberg, Harald zur Hausen ging.
Pharmacokinetics of high‐dose methotrexate in infants treated for acute lymphoblastic leukemia
Authors: Lönnerholm Gudmar , Valsecchi Maria Grazia , De Lorenzo Paola , Schrappe Martin , Hovi Liisa , Campbell Myriam , Mann Georg , Janka‐Schaub Gritta , Li Chi‐Kong , Stary Jan , Hann Ian , Pieters Rob
Published: January 2009

Background

Interfant‐99 was an international collaborative treatment protocol for infants with acute lymphoblastic leukemia (ALL).

Procedure

We collected data on 103 infants at the time of their first treatment with high‐dose methotrexate (HD MTX), 5 g/m2. Children <6 months of age received two‐third of the calculated dose based on body surface area (BSA), children 6–12 months three‐fourth of the calculated dose, and children >12 months full dose.

Results

The median steady‐state MTX concentration at the end of the 24‐hr infusion was 57.8 µM (range 9.5–313). The median systemic clearance was 6.22 L/hr/m2 BSA, and tended to increase with age (P = 0.099). Boys had higher clearance than girls, 6.77 and 5.28 L/hr/m2 (P = 0.030), and tended to have lower median MTX concentration at 24 hr. Eight infants had MTX levels below 20 µM, a level judged to be sufficient in B‐lineage ALL in children >1 year of age. All infants tolerated the dose well enough to receive a second dose of HD MTX without dose reduction. We found no significant effect on disease‐free survival for MTX steady‐state concentration, MTX clearance, or time to MTX below 0.2 µM.

Conclusions

Our data provide no support for a change in the dosing rules for MTX used in Interfant‐99. However, in view of the poor treatment results for infants, one might consider increase in the dose for patients who reach plasma levels below median after the first MTX dose. Pediatr Blood Cancer 2009;52:596–601. © 2009 Wiley‐Liss, Inc.
Mass spectrometric and computational analysis of cytokine‐induced alterations in the astrocyte secretome
Authors: Keene Sarah Dunn , Greco Todd M. , Parastatidis Ioannis , Lee Seon‐Hwa , Hughes Ethan G. , Balice‐Gordon Rita J. , Speicher David W. , Ischiropoulos Harry
Published: January 2009

The roles of astrocytes in the CNS have been expanding beyond the long held view of providing passive, supportive functions. Recent evidence has identified roles in neuronal development, extracellular matrix maintenance, and response to inflammatory challenges. Therefore, insights into astrocyte secretion are critically important for understanding physiological responses and pathological mechanisms in CNS diseases. Primary astrocyte cultures were treated with inflammatory cytokines for either a short (1 day) or sustained (7 days) exposure. Increased interleukin‐6 secretion, nitric oxide production, cyclooxygenase‐2 activation, and nerve growth factor (NGF) secretion confirmed the astrocytic response to cytokine treatment. MS/MS analysis, computational prediction algorithms, and functional classification were used to compare the astrocyte protein secretome from control and cytokine‐exposed cultures. In total, 169 secreted proteins were identified, including both classically and nonconventionally secreted proteins that comprised components of the extracellular matrix and enzymes involved in processing of glycoproteins and glycosaminoglycans. Twelve proteins were detected exclusively in the secretome from cytokine‐treated astrocytes, including matrix metalloproteinase‐3 (MMP‐3) and members of the chemokine ligand family. This compilation of secreted proteins provides a framework for identifying factors that influence the biochemical environment of the nervous system, regulate development, construct extracellular matrices, and coordinate the nervous system response to inflammation.
Proteomic profiling of tumor cells after induction of telomere dysfunction
Authors: Zimmermann Stefan , Biniossek Martin L. , Pantic Milena , Pfeifer Dietmar , Veelken Hendrik , Martens Uwe M.
Published: January 2009

Cell division in the absence of telomerase causes progressive telomere shortening which ultimately leads to telomere dysfunction and initiation of genome instability. In order to identify factors related to loss of telomere function, the effects of telomerase inhibition on the proteome of five tumor cell lines were followed by SELDI‐TOF‐MS. Five differentially expressed protein peaks (p<0.01) were found in a total of 60 clones of five cell lines representing four tissues (lung, breast, prostate, and colon) in which telomerase was inhibited by retroviral overexpression of a dominant negative (DN) mutant of human telomerase reverse transcriptase (hTERT). Among these, a 11.3 kDa peak diminished in DN‐hTERT clones was identified as histone H4 by nanoflow‐HPLC‐MS/MS. Immunoblot analysis not only confirmed the decline of histone H4, but also of other core histone proteins including histone H3. Furthermore, upregulation of several cytokeratins was found to be associated with telomere attrition. In conclusion, loss of telomere function is associated with alterations in the proteome which may represent novel biomarkers for the detection of replicative senescence.
Chemical de‐O‐glycosylation of glycoproteins for application in LC‐based proteomics
Authors: Hanisch Franz‐Georg , Teitz Sebastian , Schwientek Tilo , Müller Stefan
Published: January 2009

We describe a cyclic on‐column procedure for the sequential degradation of complex O‐glycans on proteins or peptides by periodate oxidation of sugars and cleavage of oxidation products by elimination. Desialylated glycoproteins were immobilized to alkali‐stable, reversed‐phase Poros 20 beads followed by two degradation cycles and the eluted apoproteins were either separated by SDS gel electrophoresis or digested with trypsin prior to LC/ESI‐MS. We demonstrate on the peptide and protein level that even complex glycan moieties are removed under mild conditions with only minimal effects on structural integrity of the peptide core by fragmentation, dehydration or by racemization of the Lys/Arg residues. The protocol is applicable on gel‐immobilized glycoproteins after SDS gel electrophoresis. Conversion of O‐glycoproteins into their corresponding apoproteins should result in facilitated accessibility of tryptic cleavage sites, increase the numbers of peptide fragments, and accordingly enhance protein coverage and identification rates within the subproteome of mucin‐type O‐glycoproteins.
HUPO World Congress Publication Committee Meeting August 2008, Amsterdam, The Netherlands
Authors: Orchard Sandra , Ping Peipei
Published: January 2009

The plenary session of the Publications Committee of the Human Proteome Organisation at the 7th annual HUPO world congress examined the relationship between journals, proteomics standardization initiatives, such as the work of the HUPO‐PSI, and the public domain data repositories. Delegates from industry, academia and the publishing houses discussed how best to bring these bodies closer to together and facilitate the publication process for the bench scientist.
Elucidation of high ring‐opening polymerizability of methylated 1,6‐anhydro glucose
Authors: Yoshida Dai , Yoshida Takashi
Published: January 2009

1,6‐Anhydro glucose was extracted from a wood tar that is a by‐product of charcoal manufacture. After methylation of the 1,6‐anhydro glucose, the starting monomer, 1,6‐anhydro‐2,3,4‐tri‐O‐methyl‐β‐D‐glucopyranose (LGTME), was obtained. We found that LGTME had high ring‐opening polymerizability and polymerized under mild conditions. With BF3OEt2 catalyst under ordinary pressure and N2 atmosphere at 0 °C, LGTME gave high molecular weight of polymer with 1,6‐α stereoregularity in a high yield, even though benzylated 1,6‐anhydro glucose monomer (LGTBE) gave no polymers by the same polymerization conditions. The GPC profile showed two absorptions corresponding to = 272 × 103 and = 390 × 104 in the proportion of 4.5:1. Furthermore, under high vacuum condition at 0 °C, LGTME gave the corresponding polymer and the lower molecular weight increased to = 364 × 103. To reveal the high polymerizability of LGTME, two‐step polymerization was performed. After the first stage of polymerization under ordinary pressure for 6 h at 0 °C, the second LGTME monomer was added to the polymerization mixture and then the polymerization was continued. It was found that the lower molecular weight of the resulting polymer increased to = 394 × 103 and the yield was 78%. These results suggest that poly(LGTME) after the first‐stage polymerization has stable propagating end which has a restarting ability for the ring‐opening polymerization. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1013–1022, 2009
Facile and quick synthesis of poly(N‐methylolacrylamide)/polyhedral oligomeric silsesquioxane graft copolymer hybrids via frontal polymerization
Authors: Fang Yuan , Chen Li , Chen Su
Published: January 2009

We report on a new strategy for fabricating well‐defined POSS‐based polymeric materials with and without solvent by frontal polymerization (FP) at ambient pressure. First, we functionalize polyhedral oligomeric silsesquioxane (POSS) with isophorone diisocyanate (IPDI). With these functionalized POSS‐containing isocyanate groups, POSS can be easily incorporated into a poly(N‐methylolacrylamide) (PNMA) matrix via FP in situ. Constant velocity FP is observed without significant bulk polymerization. The morphology and thermal properties of POSS‐based hybrid polymers prepared via FP are comparatively investigated on the basis of scanning electronic microscopy (SEM) and thermogravimetric analysis (TGA). Results show that the as‐prepared POSS‐based polymeric materials exhibit a higher glass transition temperature than that of pure PNMA, ascribing to modified POSS well‐dispersed in these hybrid polymers. Also, the products with different microstructures display different thermal properties. The pure PNMA exhibits a featureless morphology, whereas a hierarchical morphology is obtained for the POSS‐based polymeric materials. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1136–1147, 2009
Redox, ionic strength, and pH sensitive supramolecular polymer assemblies
Authors: Ghosh Suhrit , Yesilyurt Volkan , Savariar Elamprakash N. , Irvin Katharine , Thayumanavan S.
Published: January 2009

Formation of micelle‐type assembly from supramolecular complexation of a surfactant and an oppositely charged homopolymer is demonstrated. The lower CAC observed for these assemblies suggest that the electrostatic interaction provides an amphiphilic homopolymer‐like structure. The stimulus‐induced disassembly of these supramolecular structures has been accomplished with variations in redox characteristics, ionic strength, and pH of the medium. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1052–1060, 2009
Novel thermoplastic elastomers based on arborescent (dendritic) polyisobutylene with short copolymer end sequences
Authors: Puskas Judit E. , Dos Santos Lucas M. , Kaszas Gabor , Kulbaba Kevin
Published: January 2009

This article presents the synthesis and initial characterization of polymers having a high molecular weight dendritic (arborescent) polyisobutylene (arbPIB) core and short end sequences composed of copolymers of isobutylene with isoprene, p‐methyl styrene, or cyclopentadiene. The first stage of the polymerizations was controlled/living (i.e., no chain transfer or irreversible termination were detected) and the process was reproducible. The hydrodynamic radii of arbPIBs were measured by viscometry and quasi‐elastic light scattering, and good agreement between the two methods is demonstrated for the first time in this paper. Sequential addition of the second monomer(s) led to the formation of short copolymer end sequences. We have discovered that regardless of the Tg of the copolymer end blocks, the new block copolymers exhibited TPE properties, which were improved by carbon black and silica fillers to a great extent. These novel PIB‐based TPEs are promising new biomaterials. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1148–1158, 2009
The kinetics of enhanced spin capturing polymerization: Influence of the nitrone structure
Authors: Wong Edgar H. H. , Stenzel Martina H. , Junker Tanja , Barner‐Kowollik Christopher
Published: January 2009

Several nitrones and one nitroso compound have been evaluated for their ability to control the molecular weight of polystyrene via the recently introduced radical polymerization method of enhanced spin capturing polymerization (ESCP). In this technique, molecular weight control is achieved (at ambient or slightly elevated temperatures) via the reaction of a growing radical chain with a nitrone forming a macronitroxide. These nitroxides subsequently react rapidly and irreversibly with propagating macroradicals forming polymer of a certain chain length, which depends on the nitrone concentration in the system. Via evaluation of the resulting number‐average molecular weight, Mn, at low conversions, the addition rate coefficient of the growing radicals onto the different nitrones is determined and activation energies are obtained. For the nitrones N‐tert‐butyl‐α‐phenylnitrone (PBN), N‐methyl‐α‐phenylnitrone (PMN), and N‐methyl‐α‐(4‐bromo‐phenyl) nitrone (pB‐PMN), addition rate coefficients, kad,macro, in a similar magnitude to the styrene propagation rate coefficient, kp, are found with spin capturing constants CSC (with CSC = kad,macro/kp) ranging from 1 to 13 depending on the nitrone and on temperature. Activation energies between 23.6 and 27.7 kJ mol−1 were deduced for kad,macro, congruent with a decreasing CSC with increasing temperature. Almost constant Mn over up to high monomer to polymer conversions is found when CSC is close to unity, while increasing molecular weights can be observed when the CSC is large. From temperatures of 100 °C onward, reversible cleavage of the alkoxyamine group can occur, superimposing a reversible activation/deactivation mechanism onto the ESCP system. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1098–1107, 2009
Optimized water‐based ATRP of an anionic monomer: Comprehension and properties characterization
Authors: Mincheva Rosica , Paneva Dilyana , Mespouille Laetitia , Manolova Nevena , Rashkov Iliya , Dubois Philippe
Published: January 2009

The effect of pH and the ligand nature over the atom transfer radical polymerization (ATRP) of the anionic monomer sodium 2‐acrylamido‐2‐methylpropanesulfonate (AMPSNa) was investigated in aqueous medium by using ω‐halogenated poly(ethylene oxide) and CuBr, as macroinitiator and catalyst, respectively. The stability of both catalytic complexes and macroinitiator was investigated in function of pH, that is, fixed between 7.5 and 12. UV‐VIS spectroscopy confirmed a good catalytic complex stability in the studied conditions. Hydrolysis of the macroinitiator ester group at pH higher than 7.5 was detected by 1H NMR and GPC, yielding ill‐defined polymer samples when ATRP is performed in alkaline conditions. 2,2′‐Bipyridyl (Bpy), 1,1,4,7,10,10‐hexamethyltriethylenetetramine (HMTETA), and tris(2‐methylaminoethyl)amine (Me6‐TREN)‐based complexes were compared at the optimal pH (pH 7.5). When polymerization was carried out in the presence of CuBr · 2Me6‐TREN complex block copolymers with narrow molecular weight distribution (1.1 ≤ MW/Mn ≤ 1.3), and good agreement between theoretical and experimental molar masses was obtained. Moreover, increasing the PAMPSNa polymerization degrees (n) did not affect the control over the polymerization. Preliminary characterization of the diblock copolymers behavior in aqueous medium revealed a strong polyelectrolyte effect independently of n. Interestingly, occurrence of interactions between the PEO and PAMPSNa‐blocks was also evidenced by differential scanning calorimetry and thermogravimetric analyses. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1108–1119, 2009
pH and ionic strength responsive polyelectrolyte block copolymer micelles prepared by ring opening metathesis polymerization
Authors: Stubenrauch Kurt , Voets Ilja , Fritz‐Popovski Gerhard , Trimmel Gregor
Published: January 2009

Well‐defined amphiphilic block copolymers were prepared by ring opening metathesis polymerization and their stimuli responsive behavior of formed micelles in aqueous solution was investigated. The hydrophobic core of the micelles consists of either a poly[5,6‐bis(ethoxymethyl)bicyclo[2.2.1]hept‐2‐ene]‐block with a glass transition Tg at room temperature or a poly[endo,exo[2.2.1]bicyclohept‐5‐ene‐2,3‐diylbis (phenylmethanone)] with a Tg of 143 °C. For the polyelectrolyte shell, the precursor block poly[endo,exo[2.2.1]bicyclohept‐5‐ene‐2,3‐dicarboxyclic tert‐butylester] was transformed into the free acidic block by cleavage of the tert‐butyl groups using trifluoroacetic acid. Micellar solutions were prepared by dialysis, dissolving the copolymers in dimethyl sulfoxide which was subsequently replaced by water. All polymers form micelles with radii between 10 and 20 nm at a pH‐value below 5, where the carboxylic acid groups are in the protonated state. The block copolymer micelles show a strong increase of the hydrodynamic radius with increasing pH‐value, due to the repulsion among the formed carboxylate anions resulting in a stretching of the polymer chains. In this state, the micelles exhibit responsive behavior to ionic strength where a contraction of the micelles is observed as the carboxylate charges are balanced by sodium ions, whereas no changes of the hydrodynamic radius on addition of salt are observed at low pH. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1178–1191, 2009
Synthesis and self‐organization properties of copolyurethanes based on perylenediimide and naphthalenediimide units
Authors: Jancy B. , Asha S. K.
Published: January 2009

A series of perylene and naphthalene diimide‐containing random copolyurethanes with different ratios of perylene/naphthalene diimide content was synthesized and characterized. Copolymerization improved the solubility of these rigid aromatic diimides, and the copolymers were soluble in common organic solvents like chloroform, tetrahydrofuran, and so forth. The absorption spectra of perylene‐based copolymers showed a red‐shifted peak at a wavelength of 557 nm corresponding to J‐type aggregates. For naphthalene copolymers, the quenching of fluorescence at higher naphthalene incorporation suggested the presence of aggregates because of the extensive π‐π stacking of the aromatic core. FTIR spectroscopic analysis showed that the hydrogen bonding tendency of the polymer decreased with increase in perylene/naphthalene incorporation. The fluorescence spectra of the perylene polymers were exactly a mirror image of the absorption spectra. The fluorescence spectra of the naphthalene polymers at higher naphthalene incorporation showed a red‐shifted excimer like emission peak, which was assigned as static excimers based on their excitation spectra. These polymers could exhibit two types of secondary interaction modes, namely, hydrogen bonding (via urethane linkage) and π‐stacking (via aromatic perylene or naphthalene units) thus highlighting the importance of polymer design in inducing self‐organization at both low and high incorporation of the rigid bisimide moieties. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1224–1235, 2009
Design and synthesis of new trehalose‐conjugated pentapeptides as inhibitors of Aβ(1–42) fibrillogenesis and toxicity
Authors: De Bona Paolo , Laura Giuffrida Maria , Caraci Filippo , Copani Agata , Pignataro Bruno , Attanasio Francesco , Cataldo Sebastiano , Pappalardo Giuseppe , Rizzarelli Enrico
Published: January 2009

Aggregation of the amyloid Aβ peptide and its accumulation into insoluble deposits (plaques) are believed to be the main cause of neuronal dysfunction associated with Alzheimer's disease (AD); small molecules that can interfere with the Aβ amyloid fibril formation are therefore of interest for a potential therapeutic strategy. Three new trehalose‐conjugated peptides of the well known β‐sheet breaker peptide iAβ5p, were synthesized. The disaccharide was covalently attached to different sites of the LPFFD peptide chain, i.e. at the N‐terminus, C‐terminus or at the Asp side chain. CD spectroscopy in different solvents was used to assess changes in the peptide conformation of these compounds. The effects of these glycopeptides on the self‐assembly and morphology of Aβ aggregates were investigated by ThT fluorescence assay and dynamic Scanning Force Microscopy, respectively. All the synthesized compounds were tested as inhibitors of Aβ toxicity toward pure cultures of rat cortical neurons. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Knowledge‐based reliability assessments for time‐varying climates
Authors: Monroe Eric M. , Pan Rong
Published: January 2009

A method of obtaining a set of closed‐form solutions for reliability acceleration factors under time‐varying temperature/humidity environments is presented. This paper outlines the procedure for generating such equations based on National Oceanographic and Atmospheric Administration climatic data. Results from Phoenix, Arizona are used as a case study. Predictions from these closed‐form solutions are compared with traditional reliability assessments and exact solutions using raw ambient temperature and humidity values. Copyright © 2008 John Wiley & Sons, Ltd.
Dynamics simulation on the flexibility and backbone motions of HP1 chromodomain bound to free and lysine 9‐methylated histone H3 tails
Authors: Jiang Yanke , Zou Jianwei , Zeng Min , Zhang Na , Yu Qingsen
Published: January 2009

Histone methylation has emerged as a central epigenetic modification with both activating and repressive roles in eukaryotic chromatin. Drosophila HP1 (heterochromatin‐associated protein 1) is one of the chromodomain proteins that contain the essential aromatic residues as the recognition pocket for lysine methylated histone H3 tail. The aromatic cage indicates that the complex of chromodomain protein binding lysine methylated histone H3 tail can be seen as a typical host–guest system between protein and protein. About 10‐ns molecular dynamics simulations have been carried out in this study to examine how the presence of mono‐, trimethylated lysine 9 histone H3 tail (Me1K9, Me3K9 H3) influences the motions of HP1 protein receptor. The study shows that the conformation of HP1 protein free of H3 tail easily changes, whereas that of HP1 protein bound to methylated H3 tail does not. But the conformation of inserted Me1K9 H3 changes obviously as the Me1K recognition makes hydrogen‐bonded interactions associated with the aromatic cage even more unstable than those in free HP1 protein. The conformational change of Me1K9 H3 is correlated with the motions of HP1 protein. As the recognition factor going from Me1K to Me3K produces a more favorable interaction for aromatic ring, hydrogen‐bonded interactions associated with aromatic cage in Me3K9 H3‐HP1 complex were observed to be much more stable than those in Me1K9 H3‐HP1 complex and free HP1. Because of correlation, the flexibility of Me3K9 H3 decreases. The simulations indicate that both the MeK and the surrounding histone tail sequence are necessary features of recognition which significantly affect the flexibility and backbone motions of HP1 chromodomain. These findings confirm a regulatory mechanism of protein–protein interactions through a trimethylated post‐translational modification. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009