bluuebunny/crossref_metadata_2025_split huggingface dataset:
FLIM ‐ A Variant of FEM based on Line Integration
Authors: Synka Josef , Kraus Johannes 
Published: December 2005

AbstractA variant of the finite element method (FEM) for modelling and solving partial differential equations based on triangular and tetrahedral meshes is proposed. While FEM is based on integration over finite elements, the new approach ‐ briefly denoted as FLIM hereafter ‐ uses integration along edges (finite lines). The stiffness matrix, which ‐ for linear triangles and tetrahedra ‐ is identical with the one obtained with FEM, as well as the load vector can solely be obtained by summing up the edge contributions. This new variant requires much lower storage than FEM, especially for three‐dimensional problems, but yields the same approximation error and convergence rate as the finite element method. It is shown that its performance, when applied to linear problems, is in close agreement with the performance of the finite element method. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The numerical methods in the field of operators
Authors: Takači Djurdjica , Štrboja Mirjana 
Published: December 2005

AbstractThe approximate solution of a class of nonlinear differential equations, in the field of Mikusiński operators is constructed by using the Euler method. The obtained results are applied to a class of partial integro–differential equations. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Proteomics profiling of epidermal mucus secretion of a cichlid (Symphysodon aequifasciata) demonstrating parental care behavior
Authors: Chong Kenny , Joshi Shashikant , Jin Lam Toong , Shu‐Chien Alexander Chong 
Published: December 2005

AbstractThe discus fish (Symphysodon aequifasciata) is a cichlid demonstrating advanced mode of parental care towards fry. Both male and female fish utilized epidermal mucus secreted from specialized epidermal cells to feed developing fry. We utilized proteomics to compare protein profile from parental and nonparental fish. Gel analysis revealed a total of 35 spots that were up‐regulated in parental mucus. In tandem, another 18 spots were uniquely expressed in parental mucus. MS analysis of these spots identified proteins such as fructose biphosphate aldolase, nucleoside diphosphate kinase, and heat shock proteins, which are essential to support energy provision, cell repair and proliferation, stress mediation, and defense mechanism in parental fish during parental‐care period. Concurrently, the detection of several antioxidant‐related proteins such as thioredoxin peroxidase and hemopexin suggests a need to overcome oxidative stress during hypermucosal production in parental‐care behavior. A C‐type lectin was also found to be uniquely expressed in parental mucus and could have important role in providing antimicrobial defense to both parental fish and fry. In summary, our study shows that discus mucus proteome undergoes changes in protein expression during parental‐care period.
Spectroscopic Diagnostics of Atmospheric Pressure Helium Dielectric Barrier Discharges in Divergent Fields
Authors: Poenariu Viorel , Wertheimer Michael R. , Bartnikas Raymond 
Published: December 2005

AbstractSummary: We present optical emission spectroscopy studies of atmospheric pressure glow discharges in flowing pure helium (He), and He/nitrogen (N2) mixtures. Two different metallic high‐voltage electrode geometries have been examined, namely needle and cylindrical, the grounded dielectric‐covered electrode being planar. The axial and radial distributions of gas temperature have been evaluated from rotational spectra of molecular nitrogen ion emissions as a function of the electrode geometries, the gap spacings and the partial pressure of N2 in He. Also, the spatiotemporal distribution of discharge species in the needle‐plane geometry and the link between gas temperature and light emission intensity are presented. The physical interpretations of these results are discussed with reference to recent work reported by the present authors and by others.Axial and time‐dependent intensity distribution of the total light emission during the positive voltage half‐cycle, across a needle‐ (dielectric) plane gap.magnified imageAxial and time‐dependent intensity distribution of the total light emission during the positive voltage half‐cycle, across a needle‐ (dielectric) plane gap.
Parametric Study of Zirconium Oxide Films Using Plasma‐Based Ion Implantation and Deposition
Authors: Yukimura Ken , Ono Hiroyuki , Akashi Shuhei , Ma Xinxin 
Published: December 2005

AbstractSummary: Zirconium oxide films were prepared using a zirconium arc discharge in a gas mixture of argon‐diluted with oxygen, where the gas flow rate was varied from 100 sccm to 600 sccm, which corresponded to a gas pressure of 1.9 to 4.6 Pa. The voltage applied to the target was, unless otherwise specified, set to a value of −5 kV, with a pulse width of 20 µs at a repetition rate of 400 Hz. It was observed from XPS measurements that the oxygen and zirconium were mostly present in the deposited film in a stoichiometric state. The prepared films changed from amorphous state to orthorhombic structure by increasing the pressure of the gas mixture. At an applied voltage as high as −9 kV, the crystal size becomes small due to high energy ion bombardment. Thus, the structure of the prepared film is changed into a micro‐structural state. By applying a pulse voltage of −5 kV to the substrate, the deposited film shows a smooth surface, with roughness which is smaller by a factor of 1/7 compared to that in the absence of the applied voltage.Films surface morphology as measured by AFM.magnified imageFilms surface morphology as measured by AFM.
Graft Polymerisation of Functional Acrylic Monomers onto Cotton Fibres Activated by Continuous Ar Plasma
Authors: Castelvetro Valter , Fatarella Enrico , Corsi Leopoldo , Giaiacopi Simone , Ciardelli Gianluca 
Published: December 2005

AbstractSummary: Continuous cold Ar plasmas were used to activate the mercerised cotton fabric towards surface‐initiated graft polymerisation of glycidyl methacrylate, 2‐hydroxyethyl methacrylate (HEMA) and 1,1,2,2‐tetrahydroperfluorodecyl methacrylate (XFDMA). Single and multi‐step processes, carried out either in the plasma chamber (one‐step and two‐step processes) or ex situ after plasma treatment, were explored to optimise the grafting efficiency. The mechanical properties of the grafted cotton were substantially unaffected. Grafting with XFDMA gave good results only when the plasma activation was performed on monomer‐impregnated fabrics, as shown by gravimetry, ATR FT‐IR spectroscopy, and water and oil repellence tests. On the contrary, with HEMA better results were obtained by in situ grafting from monomer vapours.Mercerized cotton fabric before (left) and after (right) graft polymerisation of the fluorinated methacrylate XFDMA from the plasma‐activated surface.magnified imageMercerized cotton fabric before (left) and after (right) graft polymerisation of the fluorinated methacrylate XFDMA from the plasma‐activated surface.
Structure/function of KRAB repression domains: Structural properties of KRAB modules inferred from hydrodynamic, circular dichroism, and FTIR spectroscopic analyses
Authors: Mannini Riccardo , Rivieccio Vincenzo , D'Auria Sabato , Tanfani Fabio , Ausili Alessio , Facchiano Aangelo , Pedone Carlo , Grimaldi Giovanna 
Published: December 2005

AbstractThe abundant zinc finger proteins (ZFPs) sharing the KRAB motif, a potent transcription repression domain, direct the assembly on templates of multiprotein repression complexes. A pivotal step in this pathway is the assembly of a KRAB domain‐directed complex with a primary corepressor, KAP1/KRIP‐1/TIF1β. The structure/function dependence of KRAB/TIF1β protein–protein interaction and properties of the complex, therefore, play pivotal roles in diverse cellular processes depending on KRAB‐ZFPs regulation. KRAB domains are functionally bipartite. The 42 amino acid‐long KRAB‐A module, indeed, is necessary and sufficient for transcriptional repression and for the interaction with the tripartite RBCC region of TIF1β, while the KRAB‐B motif seems to potentiate the assembly of the complex. The structural properties of KRAB‐A and KRAB‐AB domains from the human ZNF2 protein have been investigated by characterizing highly purified lone (A) and composite (AB) modules. Hydrodynamic and spectroscopic features, investigated by means of gel filtration, circular dichroism, and infrared spectroscopy, provide evidence that both KRAB‐A and KRAB‐AB domains present low compactness, structural disorder, residual secondary structure content, flexibility, and tendency to molecular aggregation. Comparative analysis among KRAB‐A and KRAB‐AB modules suggests that the presence of the ‐B module may influence the properties of lone KRAB‐A by affecting the structural flexibility and stability of the conformers. The combined experimental data and the intrinsic features of KRAB‐A and KRAB‐AB primary structures indicate a potential role of specific subregions within the modules in driving structural flexibility, which is proposed to be of importance for their function. Proteins 2006. © 2005 Wiley‐Liss, Inc.
A folding inhibitor of the HIV‐1 protease
Authors: Broglia R. A. , Provasi D. , Vasile F. , Ottolina G. , Longhi R. , Tiana G. 
Published: December 2005

AbstractBecause the human immunodeficiency virus type 1 protease (HIV‐1‐PR) is an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single‐domain proteins, like each of the monomers forming the HIV‐1‐PR homodimer, is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved, as a rule hydrophobic, amino acids). These LES have evolved over myriad generations to recognize and strongly attract each other, so as to make the protein fold fast and be stable in its native conformation. Consequently, peptides displaying a sequence identical to those segments of the monomers associated with LES are expected to act as competitive inhibitors and thus destabilize the native structure of the enzyme. These inhibitors are unlikely to lead to escape mutants as they bind to the protease monomers through highly conserved amino acids, which play an essential role in the folding process. The properties of one of the most promising inhibitors of the folding of the HIV‐1‐PR monomers found among these peptides are demonstrated with the help of spectrophotometric assays and circular dichroism spectroscopy. Proteins 2006. © 2005 Wiley‐Liss, Inc.
SSALN: An alignment algorithm using structure‐dependent substitution matrices and gap penalties learned from structurally aligned protein pairs
Authors: Qiu Jian , Elber Ron 
Published: December 2005

AbstractIn template‐based modeling of protein structures, the generation of the alignment between the target and the template is a critical step that significantly affects the accuracy of the final model. This paper proposes an alignment algorithm SSALN that learns substitution matrices and position‐specific gap penalties from a database of structurally aligned protein pairs. In addition to the amino acid sequence information, secondary structure and solvent accessibility information of a position are used to derive substitution scores and position‐specific gap penalties. In a test set of CASP5 targets, SSALN outperforms sequence alignment methods such as a Smith‐Waterman algorithm with BLOSUM50 and PSI_BLAST. SSALN also generates better alignments than PSI_BLAST in the CASP6 test set. LOOPP server prediction based on an SSALN alignment is ranked the best for target T0280_1 in CASP6. SSALN is also compared with several threading methods and sequence alignment methods on the ProSup benchmark. SSALN has the highest alignment accuracy among the methods compared. On the Fischer's benchmark, SSALN performs better than CLUSTALW and GenTHREADER, and generates more alignments with accuracy >50%, >60% or >70% than FUGUE, but fewer alignments with accuracy >80% than FUGUE. All the supplemental materials can be found at http://www.cs.cornell.edu/∼jianq/research.htm. Proteins 2006. © 2005 Wiley‐Liss, Inc.
Optimal design of protein docking potentials: Efficiency and limitations
Authors: Tobi Dror , Bahar Ivet 
Published: December 2005

AbstractProtein–protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s) upon binding. The major challenge is to define scoring function soft enough to tolerate these changes and specific enough to distinguish between near‐native and “misdocked” conformations. Using a linear programming technique, we derived protein docking potentials (PDPs) that comply with this requirement. We considered a set of 63 nonredundant complexes to this aim, and generated 400,000 putative docked complexes (decoys) based on shape complementarity criterion for each complex. The PDPs were required to yield for the native (correctly docked) structure a potential energy lower than those of all the nonnative (misdocked) structures. The energy constraints applied to all complexes led to ca. 25 million inequalities, the simultaneous solution of which yielded an optimal set of PDPs that discriminated the correctly docked (up to 4.0 Å root‐mean‐square deviation from known complex structure) structure among the 85 top‐ranking (0.02%) decoys in 59/63 examined bound–bound cases. The high performance of the potentials was further verified in jackknife tests and by ranking putative docked conformation submitted to CAPRI. In addition to their utility in identifying correctly folded complexes, the PDPs reveal biologically meaningful features that distinguish docking potentials from folding potentials. Proteins 2006. © 2005 Wiley‐Liss, Inc.
The astroglial cell that guides nerve fibers from growth cone to synapse in organotypic cultures of the fetal mouse spinal cord
Authors: Sobkowicz Hanna M. , Waclawik Andrew J. , August Benjamin K. 
Published: December 2005

AbstractWe present electron microscopic and autoradiographic studies done using organotypic cultures of spinal cord explants excised from 15 days of gestation mouse embryos. Nerve fibers growing from the spinal cord explant carry at their tips immature mitotic astrocytic cells that lead their growth cones. These glial cells divide only during the active phase of neuronal growth, and correspond ultrastructurally to radial glia. They provide a specific cellular substrate for neuronal growth. Some growth cones form axoglial synapses with smooth membranes of immature glial cells. In contrast, maturing glial cells sprout cytoplasmic processes that tightly wrap individual growth cones and effectively arrest their growth. Next, the processes gather nerve endings into islets and nerve fibers into bundles. After internalizing nerve endings, the glial processes withdraw, bringing the endings into contact with each other. The direct neuronal appositions lead to the transformation of growth cones into presynaptic endings, signaled by their collection of presynaptic vesicles. Clustering of the vesicles at presynaptic axoglial or axodendritic membranes indicates the onset of synaptogenesis—completed by differentiation of spinous and compound synapses. Concomitant with the progress of synaptogenesis, astrocytic investment within the neuropil progressively diminishes. The differentiating astrocytic processes show secretory and tethering activity toward nerve fibers and their endings. Our observations demonstrate that astroglial cells—depending on their developmental stage—first promote and then arrest neuronal growth, and induce synaptogenesis. Thus, at any time, the growing nerve fibers are not only supported but also controlled by the astroglial cells. Synapse 59:183–200, 2006. © 2005 Wiley‐Liss, Inc.
Autoradiography of 2‐[18F]F‐A‐85380 on nicotinic acetylcholine receptors in the porcine brain in vitro
Authors: Deuther‐Conrad Winnie , Wevers Andrea , Becker Georg , Schildan Andreas , Patt Marianne , Sabri Osama , Steinbach Jörg , Brust Peter 
Published: December 2005

AbstractNoninvasive molecular imaging of subtypes of neuronal nicotinic acetylcholine receptors (nAChRs) will provide information on the role of these receptors in neurodegenerative diseases. The binding of the positron emission tomography ligand 2‐[18F]F‐A‐85380 to nAChRs was investigated in the porcine brain by quantitative autoradiography in vitro. The high‐affinity binding of 2‐[18F]F‐A‐85380 to each of the investigated 12 brain areas was saturable and apparently monophasic (e.g., apparentKDvalue of 1.72 nM in the thalamus). The highest density of specific binding sites was observed in the thalamus (1,158 fmol/mg protein), and the lowest density was measured in the cerebellar gray matter (11 fmol/mg protein). An attempt to assess nAChR subtype specificity of 2‐[18F]F‐A‐85380 was made by competitive autoradiography. Binding of 2‐[18F]F‐A‐85380 coincubated with 2‐F‐A‐85380, epibatidine, cytisine, or methyllycaconitine, respectively, indicated a specificity of 2‐[18F]F‐A‐85380 to β2‐containing nAChRs in the porcine brain. The autoradiographic data confirmed the suitability of swine as a model for the evaluation of radioligands designed for imaging of nAChR subtypes in the living brain. Synapse 59:201–210, 2006. © 2005 Wiley‐Liss, Inc.
Quantitative autoradiography of ligands for dopamine receptors and transporters in brain of Göttingen minipig: Comparison with results in vivo
Authors: Minuzzi Luciano , Olsen Aage Kristian , Bender Dirk , Arnfred Sidse , Grant Rebecca , Danielsen Erik H. , Cumming Paul 
Published: December 2005

AbstractThe pig has been used as animal model for positron emission tomography (PET) studies of dopamine (DA) receptors and pharmacological perturbations of DA neurotransmission. However, the binding properties of DA receptors and transporters in pig brain have not been characterized in vitro. Therefore, the saturation binding parameters of [3H]SCH 23390 for DA D1 receptors and [3H]raclopride for DA D2/3 receptors were measured by quantitative autoradiography in cryostat sections from brain of groups of 8 week old and adult female Göttingen minipigs. The magnitudes of Bmax and Kd for these ligands were similar in young and old pigs, and were close to those reported for rat and human brain. Furthermore, gradients in the concentrations of D1 and D2/3 sites in striatum measured in vitro agreed with earlier findings in PET studies. However, the dopamine transporter (DAT) ligand [3H]GBR12935 did not bind in pig brain cryostat sections. Whereas the tropane derivative [125I]RTI‐55 labeled serotonin transporters (serotonin transporter (SERT)) in pig brain, use of the same ligand under conditions specific for DAT, revealed a pattern of binding similar to that observed for SERT conditions. Parallel studies revealed the presence of DAT in rat and ferret brain. The distribution volume (Vd) of the selective DAT ligand [11C]NS2214 ([11C]Brasofensine) was mapped in groups of normal and MPTP‐lesioned Göttingen miniature pigs. The in vivo pattern of Vd matched the distribution of SERT in vitro, and did not differ between the normal pigs and the lesioned animals with documented 60% DA depletions. However, the pattern of specific binding of the selective noradrenaline transporter ligand (S,S)‐[11C]MeNER in a single Landrace pig showed that, of the three monoamine transporters, only DAT could not be detected in pig brain. We conclude that the pig is a suitable model for PET studies of DA D1 and D2/3 binding sites, which are fully developed on the eighth postnatal week. However, well‐characterized piperazine and tropane radioligands failed to recognize DAT in pig brain; the two tropane radioligands lacked pharmacological specificity for DAT and SERT in pig brain in vitro and in vivo. Synapse 59:211–219, 2006. © 2005 Wiley‐Liss, Inc.
The relation between identity status and romantic attachment style in middle and late adolescence
Authors: Berman Steven L. , Weems Carl F. , Rodriguez Eileen T. , Zamora Irving J. 
Published: December 2005

ABSTRACTThis study examined the linkages between identity formation and romantic attachment in an ethnically diverse sample of high school () and college students (). Individuals in the foreclosed identity status group had significantly lower relationship avoidance scores than the diffused identity status group, and the foreclosed group had significantly lower relationship anxiety scores than both the achieved identity and moratorium groups. Identity status and romantic attachment style were significantly related among the college sample, but not among the high school sample. Some ethnic differences in attachment style were noted. Developmental implications are discussed.
Differentially expressed cortical genes contribute to perivascular deposition in transgenic mice with inducible neuron‐specific expression of TGF‐β1
Authors: Ueberham Uwe , Zobiak Bernd , Ueberham Elke , Brückner Martina K. , Boriss Hinnerk , Arendt Thomas 
Published: December 2005

AbstractIn the brain the expression of transforming growth factor β1 (TGF‐β1) is involved both in neuroprotective and neurodegenerative processes. Recently, we have established a transgenic mouse model with inducible neuron‐specific expression of TGF‐β1 based on the tetracycline‐regulated gene expression system. A long‐term expression of TGF‐β1 results in persisting perivascular thioflavin‐positive depositions, which did not disappear even though the transgene synthesis was repressed completely by administration of doxycycline. Formation and composition of these depositions are hardly elucidated. The aim of this study was to identify TGF‐β1 responding genes potentially participating in forming these depositions. To address this problem we have compared the cortical mRNA expression pattern of TGF‐β1 expressing mice with mice impeded to express the transgenic protein using oligonucleotide microarray analysis. Differential gene expression was further characterized by quantitative real‐time reverse transcription‐polymerase chain reaction including animals, where the long‐lasting TGF‐β1 expression was repressed. While no change of amyloid precursor protein RNA expression level was detected, various genes strongly involved in calcium homeostasis, tissue mineralization or vascular calcification were identified differentially expressed. It is suggested, that these genes might contribute to the perivascular depositions in the TGF‐β1 expressing mice.
Thioflavins released from nanoparticles target fibrillar amyloid β in the hippocampus of APP/PS1 transgenic mice
Authors: Siegemund T. , Paulke B.‐R. , Schmiedel H. , Bordag N. , Hoffmann A. , Harkany T. , Tanila H. , Kacza J. , Härtig W. 
Published: December 2005

AbstractFor the delivery of drugs into the brain, the use of nanoparticles as carriers has been described as a promising approach. Here, we prepared nanoparticles as carriers for the model drugs thioflavin T and thioflavin S that bind fibrillar amyloid β peptides (Aβ). These polymer colloids are composed of a polystyrene core and a degradable PBCA [poly(butyl‐2‐cyanoacrylate)] shell with a diameter of 90–100 nm as shown by dynamic light scattering. Fluorescence spectrophotometric analysis revealed that encapsulated thioflavin T exhibited significantly stronger fluorescence than the free fluorophore. The enzymatic degradation of core‐shell nanoparticles, as required in vivo, was shown after their treatment with porcine liver esterase, a non‐specific esterase, in vitro. Shells of nanoparticles were dose‐dependently degraded while their polystyrene cores remained intact. In the cortices of 7–14 months old APP/PS1 mice with age‐dependent β‐amyloidosis, thioflavins selectively targeted fibrillar Aβ after biodegradation‐induced release from their nanoparticulate carriers upon intracerebral injection. Collectively, our data suggest that core‐shell nanoparticles with controlled degradation in vivo can become versatile tools to trace and clear Aβ in the brain.