bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPICKER: A clustering approach to identify near‐native protein folds
Authors: Zhang Yang , Skolnick Jeffrey 
Published: March 2004

AbstractWe have developed SPICKER, a simple and efficient strategy to identify near‐native folds by clustering protein structures generated during computer simulations. In general, the most populated clusters tend to be closer to the native conformation than the lowest energy structures. To assess the generality of the approach, we applied SPICKER to 1489 representative benchmark proteins ≤200 residues that cover the PDB at the level of 35% sequence identity; each contains up to 280,000 structure decoys generated using the recently developed TASSER (Threading ASSembly Refinement) algorithm. The best of the top five identified folds has a root‐mean‐square deviation from native (RMSD) in the top 1.4% of all decoys. For 78% of the proteins, the difference in RMSD from native to the identified models and RMSD from native to the absolutely best individual decoy is below 1 Å; the majority belong to the targets with converged conformational distributions. Although native fold identification from divergent decoy structures remains a challenge, our overall results show significant improvement over our previous clustering algorithms. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 865–871, 2004
A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)
Authors: Fedorov Dmitri G. , Olson Ryan M. , Kitaura Kazuo , Gordon Mark S. , Koseki Shiro 
Published: March 2004

AbstractA two‐level hierarchical scheme, generalized distributed data interface (GDDI), implemented into GAMESS is presented. Parallelization is accomplished first at the upper level by assigning computational tasks to groups. Then each group does parallelization at the lower level, by dividing its task into smaller work loads. The types of computations that can be used with this scheme are limited to those for which nearly independent tasks and subtasks can be assigned. Typical examples implemented, tested, and analyzed in this work are numeric derivatives and the fragment molecular orbital method (FMO) that is used to compute large molecules quantum mechanically by dividing them into fragments. Numeric derivatives can be used for algorithms based on them, such as geometry optimizations, saddle‐point searches, frequency analyses, etc. This new hierarchical scheme is found to be a flexible tool easily utilizing network topology and delivering excellent performance even on slow networks. In one of the typical tests, on 16 nodes the scalability of GDDI is 1.7 times better than that of the standard parallelization scheme DDI and on 128 nodes GDDI is 93 times faster than DDI (on a multihub Fast Ethernet network). FMO delivered scalability of 80–90% on 128 nodes, depending on the molecular system (water clusters and a protein). A numerical gradient calculation for a water cluster achieved a scalability of 70% on 128 nodes. It is expected that GDDI will become a preferred tool on massively parallel computers for appropriate computational tasks. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 872–880, 2004
Ligand–protein docking using a quantum stochastic tunneling optimization method
Authors: Mancera Ricardo L. , Källblad Per , Todorov Nikolay P. 
Published: March 2004

AbstractA novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand–protein complexes using the PLP score to represent the ligand–protein potential energy surface and ScreenScore to score the ligand–protein binding energies. When taking the top energy‐ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 858–864, 2004
Kinetics and mechanism of esterification of epoxy resin in presence of triphenylphosphine
Authors: Pal Neelam , Srivastava Akanksha , Rai J. S. P. 
Published: March 2004

AbstractThe kinetics of esterification of bisphenol‐A based epoxy resin with acrylic acid in presence of triphenylphosphine has been studied. The reaction exhibits a first‐order rate dependence with respect to [Epoxy] and [Catalyst]. A first‐order dependence of rate with respect to [Acid] has been observed during a particular kinetic run. However, a retarding effect of [Acid] on the rate has been observed by increasing the initial concentration of acid. A suitable mechanism consistent with the kinetic data is proposed and discussed. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36: 280–285, 2004
Dynamic scaling for Eley‐Rideal reactions over rough surface
Authors: Chaudhari Ajay , Yan Ching‐Cher Sanders , Lee Shyi‐Long 
Published: March 2004

AbstractEley‐Rideal reaction mechanism is studied over rough surface of random deposition model. Two types of rough surface are considered: (1) different rough surface with same surface density and (2) different rough surface with different surface density. Dynamic scaling theory, which is generally applied to the growing surface, is applied for this reaction mechanism to obtain the temporal and spatial scaling parameters α and β. The scaling parameters are found to be negative in contrast to the positive scaling parameters in surface growth model. The values of β are the same for both types of surface whereas the values of α are different. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36: 286–292, 2004
Pitting and crevice corrosion of superaustenitic stainless steels
Authors: Mori G. , Bauernfeind D. 
Published: March 2004

AbstractSuperaustenites are mainly used in offshore applications, oil production and chemical industry. Most important types of localised corrosion of these steels are pitting and crevice corrosion. Investigated materials were N08028, S31254 and three modified alloys. Chromium content of investigated alloys varied between 20 and 27%, molybdenum between 3.2 and 6.0%, nitrogen between 0.1 and 0.36% and copper between 0 and 1.1%. For means of comparison stainless steel AISI 316L has been included in the study.Pitting and crevice corrosion of these highly corrosion resistant steels has been investigated by use of standardized tests. Critical pitting temperature and critical crevice temperatures were determined according to ASTM G 48, Methods C and D, respectively. Electrochemical measurements for determination of pitting potentials were done according to ASTM G 61 as well as for determination of critical pitting temperatures according to ASTM G 150.Results are presented as function of MARC (Measure of alloying for resistance to corrosion) defined by Speidel since linear correlation coefficients were higher when compared to conventional PREN. Results obtained by different testing methods must not be compared directly. Every test however is sensitive to microstructural defects like precipitations and segregations that decrease corrosion resistance. The higher alloyed a material is, the higher is its tendency to form microstructural defects, and the more difficult is it to reach its theoretical corrosion resistance at given chemical composition.
Application limits of stainless steels in the petroleum industry
Authors: Oberndorfer M. , Thayer K. , Kästenbauer M. 
Published: March 2004

AbstractStainless steels have a great variety of potential applications in the petroleum industry, mainly as an alternative to carbon steel in corrosive environments. Within a number of media that can cause corrosion problems with these materials, only chloride solutions and hydrogen sulfide are of importance in oilfield service.A reliable tool that permits the proper selection of stainless steels has yet been missing. In order to provide engineering diagrams for this purpose, pitting and stress corrosion cracking (SCC) tests were performed. Specimens were exposed to NaCl solutions containing from 3 to 100,000 ppm Cl− at temperatures from 40 to 200 °C. This test configuration was chosen to give a better representation of actual service conditions than accelerated standard test procedures do.Tested materials were the austenitic stainless steel grades 321, 316Ti (API LC30‐1812) and 254 SMO, and 22Cr duplex (austenitic‐ferritic) steel (API LC65‐2205). Based on an optical examination of the specimens, no‐risk regions of chloride concentration vs. temperature have been identified. Subsequently, service temperature limits have been deduced for each tested material.Thus, material failures by pitting and SCC can be prevented without overdesigning. The results of the testing series are applicable to all chloride environments without presence of H2S, as they have to be handled by primary production equipment, as well as transportation and gas processing facilities.
Microbially influenced corrosion of stainless steel by manganese oxidizing microorganisms
Authors: Linhardt P. 
Published: March 2004

AbstractBased on the corrosion behaviour of stainless steels in fresh water and on the electrochemical properties of higher manganese oxides, the mechanism “Microbially influenced corrosion by manganese oxidizing microorganisms” (MIC by MOMOs) is presented as the consequence of biomineralized manganese oxides in contact with the metal. Localized corrosion may develop at elevated but normally undercritical chloride concentration in the water. The mechanism was found useful in the analysis of certain cases of unexpected failure of stainless steel in fresh water.
Influence of shot peening on the corrosion fatigue properties of a stainless steel for surgical implants
Authors: Wieser H. 
Published: March 2004

AbstractFor some applications in surgical implants a rough surface is desired, since the jagged surface structure assists the adhesion of bone material or surface coatings. Some implants are peened with coarse and sharp edged peening media. In order to avoid a distinct loss of fatigue strength, spherical peening balls should be used. The present paper shows for stainless steel X2CrNiMo18‐15‐3 that the effect of surface roughening can be compensated by the effect of compressive residual stresses in the surface layer.However, the effect of surface flaws must not be ignored. For this reason, the shape and depth of surface flaws in shot peened surfaces has been examined and a classification of different types of surface flaws is presented.Fatigue tests in laboratory air and in physiological NaCl solution showed that there is a distinct influence of the depth and shape of surface flaws on the fatigue strength. The use of coarser peening balls and a subsequent electrolytic polishing treatment leads to an increase of fatigue strength.Furthermore, it is shown that shot peening may have a positive or negative effect on corrosion fatigue strength.
Versagensverhalten keramischer Faserverbundwerkstoffe mit poröser Matrix – experimentelle Untersuchungen und Modellierung
Authors: Tushtev K. , Horvath J. , Koch D. , Grathwohl G. 
Published: March 2004

AbstractBidirektional verstärkte Carbon/Carbon‐Verbundwerkstoffe besitzen eine poröse Matrix, die unter Beanspruchung das Versagensverhalten entscheidend mitbestimmt. Zur Klärung der Schädigungsmechanismen werden Zugversuche durchgeführt, bei denen die Proben in Richtung 0° und 45° zur Faserorientierung beansprucht werden. Die experimentellen Ergebnisse werden in einem makroskopischen Modell unter Berücksichtigung des nichtlinearen Spannungs‐Dehnungs‐Verhaltens der Komposite erfasst. Das Modell basiert auf den Konzepten der Schädigungs‐ und Plastizitätstheorie und ist auf das mechanische Werkstoffverhalten unter quasistatischer Belastung begrenzt. Das vorgeschlagene Modell wird mit Hilfe zusätzlicher Zugexperimente, bei denen die Fasern in verschiedenen Belastungsrichtungen orientiert sind, verifiziert.
Micromechanical Modelling of Shape Memory Alloy Composites
Authors: Wang YF , Wang XM , Yue ZF 
Published: March 2004

AbstractAn isothermal finite element method (FEM) model has been applied to study the behavior of two kinds of shape memory alloy (SMA) composites. For SMA‐fiber reinforced normal metal composites, the FEM analysis shows that the mechanical behavior of the composites depends on the SMA volume fraction. For normal metal‐fiber reinforced SMA matrix composites, the SMA phase transformation is affected by the increasing Young’s modulus of the metal fiber. The phase transformation was also treated using a simple numerical analysis, which assumes that there are uniform stresses and strains distributions in the fiber and the matrix respectively. It is found that there is an obvious difference between the FEM analysis and the simple numerical assessment. Only FEM can provide reasonable predictions of phase transformations in SMA/normal metal composites.
Large‐scale identification and characterization of genes with asymmetric expression patterns in the developing chick retina
Authors: Shintani Takafumi , Kato Akira , Yuasa‐Kawada Junichi , Sakuta Hiraki , Takahashi Masakazu , Suzuki Ryoko , Ohkawara Takeshi , Takahashi Hiroo , Noda Masaharu 
Published: March 2004

AbstractTo understand the molecular basis of topographic retinotectal projection, an overall view of the asymmetrically expressed molecules in the developing retina is needed. We performed a large‐scale screening using restriction landmark cDNA scanning (RLCS) in the embryonic day 8 (E8) chick retina. RLCS is a cDNA display system, in which a large number of cDNA species are displayed as two‐dimensional spots with intensities reflecting their expression levels as mRNA. We searched for spots that gave different signal intensities between the nasal and temporal retinas or between the dorsal and ventral retinas, and detected about 200 spots that were preferential on one side in the retina. The asymmetric expression of each gene was verified by Northern blotting and in situ hybridization. By subsequent analyses using molecular cloning, DNA sequencing, and database searching, 33 asymmetric molecules along the nasotemporal (N‐T) axis and 20 along the dorsoventral (D‐V) axis were identified. These included transcription factors, secretory factors, transmembrane proteins, and intracellular proteins with various putative functions. Their expression profiles revealed by in situ hybridization are highly diverse and individual. Moreover, many of them begin to be expressed in the retina from the early developmental stages, suggesting that they are implicated in the establishment and maintenance of regional specificity in the developing retina. The molecular repertoire revealed by this work will provide candidates for future studies to elucidate the molecular mechanisms of topographic retinotectal map formation. © 2004 Wiley Periodicals, Inc. J Neurobiol 59: 34–47, 2004
Polarity and laminar formation of the optic tectum in relation to retinal projection
Authors: Nakamura Harukazu , Sugiyama Sayaka 
Published: March 2004

AbstractThe mes‐metencephalic boundary (isthmus) works as an organizer for the tectum, and the organizing molecule may be Fgf8. The region where Otx2, En1, and Pax2 are expressed overlappingly may differentiate into the mesencephalon. The di‐mesencephalic and mes‐metencephalic boundaries are determined by repressive interaction of Pax6 and En1/Pax2 and of Otx2 and Gbx2, respectively. The optic tectum is a visual center in lower vertebrates. The tectum and the retina should be regionalized and be positionally specialized for the proper retinotopic projection. Gradient of En2 plays a crucial role in rostrocaudal polarity formation of the tectum. En2 confers caudal characteristics of the retina by inducing ephrinA2 and A5, which are the repellant molecules for the growth cones of temporal retinal ganglion cells. Grg4 antagonizes the isthmus‐related genes, and is involved in the formation of di‐mesencephalic boundary and tectal polarity formation at an early phase of development. Then, Grg4 plays a role in tectal laminar formation by controlling the migration pathway. Migration pathway of tectal postmitotic cells changes after E5. The late migratory cells split the early migratory neurons to form laminae h–j of SGFS. Grg4 is expressed in the ventricular layer after E5, and forces postmitotic cells to follow the late migratory pathway, though retinal fibers terminate at laminae a–f of SGFS. Misexpression of Grg4 disrupts the lamina g, and in such tecta retinal arbors invade deep into the tectal layer, indicating that lamina g is a nonpermissive lamina for the retinal arbors. © 2004 Wiley Periodicals, Inc. J Neurobiol 59: 48–56, 2004
EphrinB2a in the zebrafish retinotectal system
Authors: Wagle Mahendra , Grunewald Barbara , Subburaju Sivan , Barzaghi Cristiana , Le Guyader Sylvie , Chan Joanne , Jesuthasan Suresh 
Published: March 2004

AbstractMembers of the Eph‐B family of receptors tyrosine kinase and their transmembrane ligands have been implicated in dorsoventral patterning of the vertebrate retinotectal projection. In the zebrafish retinotectal system, however, ephrinB2a is expressed strongly in the posterior tectum, in tectal neurons that form physical contacts with retinal ganglion cell (RGC) axons. In the gnarled mutant, where tectal neurons form ectopically in the pretectum, RGC axons stall before entering the tectum, or else are misrouted or branch aberrantly in the tectal neuropil. Ectopic expression of ephrinB2a in the anterior midbrain of wild‐type embryos, with the aid of baculovirus, also inhibits RGC axon entry into the tectum. In vitro, zebrafish RGC axons are repelled by stripes of purified ephrinB2a. It is proposed that ephrinB2a may signal a subpopulation of RGC axons that they have reached their target neurons in the tectum. © 2004 Wiley Periodicals, Inc. J Neurobiol 59: 57–65, 2004
Computational modeling of retinotopic map development to define contributions of EphA‐ephrinA gradients, axon‐axon interactions, and patterned activity
Authors: Yates Paul A. , Holub Alex D. , McLaughlin Todd , Sejnowski Terrence J. , O'Leary Dennis D.M. 
Published: March 2004

AbstractThe topographic projection of retinal ganglion cell (RGC) axons to mouse superior colliculus (SC) or chick optic tectum (OT) is formed in three phases: RGC axons overshoot their termination zone (TZ); they exhibit interstitial branching along the axon that is topographically biased for the correct location of their future TZ; and branches arborize preferentially at the TZ and the initial exuberant projection refines through axon and branch elimination to generate a precise retinotopic map. We present a computational model of map development that demonstrates that the countergradients of EphAs and ephrinAs in retina and the OT/SC and bidirectional repellent signaling between RGC axons and OT/SC cells are sufficient to direct an initial topographic bias in RGC axon branching. Our model also suggests that a proposed repellent action of EphAs/ephrinAs present on RGC branches and arbors added to that of EphAs/ephrinAs expressed by OT/SC cells is required to progressively restrict branching and arborization to topographically correct locations and eliminate axon overshoot. Simulations show that this molecular framework alone can develop considerable topographic order and refinement, including axon elimination, a feature not programmed into the model. Generating a refined map with a condensed TZ as in vivo requires an additional parameter that enhances branch formation along an RGC axon near sites that it has a higher branch density, and resembles an assumed role for patterned neural activity. The same computational model generates the phenotypes reported in ephrinA deficient mice and Isl2‐EphA3 knockin mice. This modeling suggests that gradients of counter‐repellents can establish a substantial degree of topographic order in the OT/SC, and that repellents present on RGC axon branches and arbors make a substantial contribution to map refinement. However, competitive interactions between RGC axons that enhance the probability of continued local branching are required to generate precise retinotopy. © 2004 Wiley Periodicals, Inc. J Neurobiol 59: 95–113, 2004
Convergent and divergent signaling mechanisms of growth cone collapse by ephrinA5 and slit2
Authors: Wong Eric V. , Kerner Julie A. , Jay Daniel G. 
Published: March 2004

AbstractEphrinA5 and slit2 are important repulsive guidance cues in the developing retinotectal system. Both ephrinA5 and slit2 cause growth cone collapse of embryonic chick retinal ganglion growth cones cultured on EHS laminin. However, the signaling mechanism that these guidance cues initiate to cause collapse remains unclear. Here we provide evidence that while both ephrinA5 and slit2 cause collapse in morphologically similar ways, the intracellular signaling leading to the collapse involves shared as well as divergent paths. Pharmacological inhibition of either phosphatidylinositol 3‐kinase (PI3K) or src family kinases prevented both ephrinA5‐mediated and slit2‐mediated growth cone collapse. In contrast, the inhibition of nonclassical protein kinase C (PKC) isoforms blocked ephrinA5‐mediated collapse, but did not interfere with slit2‐mediated collapse. PI3K was copurified by affinity chromatography with either the ephrinA5 receptors (ephAs) or the slit2 receptor (roundabout). Colocalization studies have also shown that src family kinase members are recruited to the ephA and roundabout receptors upon activation. In contrast, PKC members are recruited to the ephA receptors, but not to the roundabout receptors, upon activation. This demonstrates distinct points of convergence and divergence between the two signaling molecules, ephrinA5 and slit2, and their repulsive guidance in the chick retinotectal system. © 2004 Wiley Periodicals, Inc. J Neurobiol 59: 66–81, 2004
Activity‐driven sharpening of the retinotectal projection: The search for retrograde synaptic signaling pathways
Authors: Schmidt John T. 
Published: March 2004

AbstractPatterned visual activity, acting via NMDA receptors, refines developing retinotectal maps by shaping individual retinal arbors. Because NMDA receptors are postsynaptic but the retinal arbors are presynaptic, there must be retrograde signals generated downstream of Ca++ entry through NMDA receptors that direct the presynaptic retinal terminals to stabilize and grow or to withdraw. This review defines criteria for retrograde synaptic messengers, and then applies them to the leading candidates: nitric oxide (NO), brain‐derived neurotrophic factor (BDNF), and arachidonic acid (AA). NO is not likely to be a general mechanism, as it operates only in selected projections of warm blooded vertebrates to speed up synaptic refinement, but is not essential. BDNF is a neurotrophin with strong growth promoting properties and complex interactions with activity both in its release and receptor signaling, but may modulate rather than mediate the retrograde signaling. AA promotes growth and stabilization of synaptic terminals by tapping into a pre‐existing axonal growth‐promoting pathway that is utilized by L1, NCAM, N‐cadherin, and FGF and acts via PKC, GAP43, and F‐actin stabilization, and it shares some overlap with BDNF pathways. The actions of both are consistent with recent demonstrations that activity‐driven stabilization includes directed growth of new synaptic contacts. Certain nondiffusible factors (synapse‐specific CAMs, ephrins, neurexin/neuroligin, and matrix molecules) may also play a role in activity‐driven synapse stabilization. Interactions between these pathways are discussed. © 2004 Wiley Periodicals, Inc. J Neurobiol 59: 114–133, 2004