bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consensus scoring for enriching near‐native structures from protein–protein docking decoys
Authors: Liang Shide , Meroueh Samy O. , Wang Guangce , Qiu Chao , Zhou Yaoqi 
Published: September 2008

AbstractThe identification of near native protein–protein complexes among a set of decoys remains highly challenging. A strategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near‐native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near‐native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu. Proteins 2009. © 2008 Wiley‐Liss, Inc.
An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields
Authors: Whitford Paul C. , Noel Jeffrey K. , Gosavi Shachi , Schug Alexander , Sanbonmatsu Kevin Y. , Onuchic José N. 
Published: September 2008

AbstractProtein dynamics take place on many time and length scales. Coarse‐grained structure‐based$ {\bf (G{\overline o})} $models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All‐atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure‐based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all‐atom model. Results for the B domain of Protein A, the SH3 domain of C‐Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cαstructure‐based model and an all‐atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free‐energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a Cαmodel and the all‐atom model agree, although differences can be attributed to energetic heterogeneity in the all‐atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure‐based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Visualizing molecular wavefunctions using Monte Carlo methods
Authors: Alexander S. A. , Coldwell R. L. 
Published: September 2008

AbstractUsing explicitly correlated wavefunctions and variational Monte Carlo we calculate the electron density, the electron density difference, the intracule density, the extracule density, two forms of the kinetic energy density, the Laplacian of the electron density, the Laplacian of the intracule density, and the Laplacian of the extracule density on a dense grid of points for the ground state of the hydrogen molecule at three internuclear distances (0.6, 1.4, 8.0). With these values we construct a contour plot of each function and describe how it can be used to visualize the distribution of electrons in this molecule. We also examine the influence of electron correlation on each expectation value by calculating each function with a Hartree–Fock wavefunction and then comparing these values with our explicitly correlated values. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
The role of resonances in building cross sections: The Mittag‐Leffler expansion in a two‐channel scattering
Authors: Shilyaeva Ksenia , Elander Nils , Yarevsky Evgeny 
Published: September 2008

AbstractThe Mittag‐Leffler formalism for identifying resonance contributions to a two‐body scattering cross section is extended here from the one channel case to the two channel case. The reduced partial wave cross sections based on subtracting S‐matrix residues are compared with expressions which can be derived from the Breit‐Wigner approximation. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Developing and assessing a force and motion learning progression
Authors: Alonzo Alicia C. , Steedle Jeffrey T. 
Published: September 2008

AbstractLearning progressions are ordered descriptions of students' understanding of a given concept. In this paper, we describe the iterative process of developing a force and motion learning progression and associated assessment items. We report on a pair of studies designed to explore the diagnosis of students' learning progression levels. First, we compare the use of ordered multiple‐choice (OMC) and open‐ended (OE) items for assessing students relative to the learning progression. OMC items appear to provide more precise diagnoses of students' learning progression levels and to be more valid, eliciting students' conceptions more similarly to cognitive interviews. Second, we explore evidence bearing on two challenges concerning reliability and validity of level diagnoses: the consistency with which students respond to items set in different contexts and the ways in which students interpret and use language in responding to items. As predicted, students do not respond consistently to similar problems set in different contexts. Although the language used in OMC items generally seems to reflect student thinking, misinterpretation of the language in items may lead to inaccurate diagnoses for a subset of students. Both issues are less problematic for classroom applications than for use of learning progressions in large‐scale testing. © 2008 Wiley Periodicals, Inc. Sci Ed 93: 389–421, 2009
Adsorption of water on JSC‐1A (simulated moon dust samples)—a surface science study
Authors: Goering J. , Sah Shweta , Burghaus U. , Street K. W. 
Published: September 2008

AbstractJSC‐1a (a simulated lunar dust sample) supported on a silica wafer (SiO2/Si(111)) has been characterized by scanning electron microscopy (SEM), energy dispersive x‐ray (EDX) spectroscopy, and Auger electron spectroscopy (AES). The adsorption kinetics of water has been studied primarily by thermal desorption spectroscopy (TDS) and in addition by collecting isothermal adsorption transients. Blind experiments on the silica support have been performed as well. JSC‐1a consists mostly of aluminosilicate glass and other minerals containing Fe, Na, Ca, and Mg, as characterized in detail in prior studies, for example, at NASA. The particle sizes span the range from a few micrometers up to 100 µm. At small exposures, H2O TDS is characterized by broad (100–450) K structures; at large exposures, distinct TDS peaks emerge, which are assigned to amorphous solid water (ASW) (145 K) and crystalline ice (CI) (165 K). Water dissociates on JSC‐1a at small exposures but not on the bare silica support. Coadsorption TDS data (alkane–water mixtures) indicate that rather porous condensed ice layers form at large exposures, with the mineral particles acting most likely as nucleation sites. At thermal impact energies, the initial adsorption probability amounts to 0.92 ± 0.05. It is evident that the drop‐and‐dry technique, developed in studies about nanoparticles/tubes, can be extended to obtain samples for surface science studies based on powders consisting of particles with rather large diameters. Copyright © 2008 John Wiley & Sons, Ltd.
Tragverhalten von Stahlgussbauteilen in Offshore‐Windenergie‐Anlagen unter vorwiegend ruhender und nicht ruhender Beanspruchung
Authors: Lüddecke Falk , Rücker Werner , Seidel Marc , Assheuer Jens 
Published: September 2008

AbstractFür die Installation von Offshore‐Windenergie‐Anlagen der 5‐Megawattklasse vor der Küste Deutschlands in der Nordsee ist es erforderlich, Gründungsstrukturen in hoher Stückzahl wirtschaftlich herstellen zu können. Für den Wassertiefenbereich der Nordsee wird im Rahmen dieses Aufsatzes der Konstruktions‐typ Jacket hinsichtlich dynamischer Eigenschaften untersucht.Darüber hinaus wird über Stahlgussbauteile berichtet, die in den hochbelasteten Knotenpunkten des Jackets verbaut werden. Derzeit ist es üblich, Jackets aus handelsüblichen Stahlhohlprofilen zu fertigen, die an den Enden zu einer Knotenverbindung miteinander verschweißt werden. Diese Lösung besitzt jedoch eine Vielzahl von Nachteilen, über die nachfolgend berichtet wird.Bauteile aus Stahlguss hingegen weisen unter anderem die Vorteile auf, universell einsetzbar und in Form bzw. Gestaltung völlig frei wählbar zu sein. Um das komplexe Tragverhalten dieser Stahlgussbauteile bewerten zu können, wurden neben Simulationsrechnungen auch Laborversuche durchgeführt. Es wurde das Tragverhalten unter statischer Belastung am Stahlgussbauteil im 1:1‐Modell und das Ermüdungsverhalten an Stahlgussproben getestet.
Die Ingenieurbauwerke für die Verkehrserschließung der Neuen Landesmesse in Stuttgart
Authors: Angelmaier Volkhard , Andelfinger Joachim , Herrmann Jörg , Sandner Dieter 
Published: September 2008

AbstractDas weithin sichtbare Parkhaus gilt mittlerweile als Erkennungszeichen der Neuen Landesmesse Stuttgart und bietet mit einer Gesamtfläche von 125000 m2 4100 Fahrzeugen eine Parkmöglichkeit. Das wesentliche Prinzip der Stahl‐Verbundkonstruktion besteht in einem weitgehend lager‐ und fugenlosen Bauwerk. Die fachwerkartigen Hauptträger mit Spannweiten von knapp 100 m sind dabei in ein räumliches Gesamtsystem ähnlich dem Chassis‐Prinzip im Fahrzeugbau integriert und annähernd biegesteif mit den Hauptstützen verbunden. Dieser Grundgedanke der semi‐integralen Bauweise war für die Stahlverbundbrücken der Messe‐erschließung ebenfalls entwurfsbestimmend. Wiederkehrende Gestaltungselemente vermitteln einen in sich geschlossenen Gesamteindruck der Ingenieurbauwerke für die Verkehrserschließung der neuen Landesmesse.
Drillknicken einfach‐symmetrischer Stahlstützen mit erzwungener Drehachse
Authors: Gosowski Bronisław 
Published: September 2008

AbstractDargestellt wird die Lösung des elastischen räumlichen Stabili‐tätsproblems von einfach‐symmetrischen I‐Stahlstützen mit erzwungener Drehachse – gelegen in der Symmetrieebene des Querschnitts und parallel zur Stützenlängsachse. Dabei wurden einfeldrige Stützen mit elastischen Punktbindungen in Längsrichtung auf Verdrehung und auf Verwölbung hin untersucht. Die Punktbindungen wurden in den Berechnungsmodellen unter Anwendung der Distributionsrechnung erfasst. Die Druckkraft sowie das Biegemoment, das in der Symmetrieebene des Querschnitts wirkt, bilden die Stützenlast. Bei Stützen mit festem Biegemoment und beliebigen Lagerungsbedingungen an den Stützenenden wurde die Stabilität in geschlossener Form gelöst. Für die Lösungen von Stützen mit beliebigem Biegemoment und festgelegten Lagerungsbedingungen an den Stützenenden wurde das Bubnow‐Galerkin ‐Verfahren genutzt. Die Lösungen werden im vorliegenden Beitrag an Rechenbeispielen veranschaulicht, in denen die kritischen Lasten der elastischen Drillknickung bei erzwungener Drehachse für längsversteifte Stahlstützen ermittelt werden. Die Berechnungen wurden unter Anwendung selbst ausgearbeiteter EDV‐Programme durchgeführt.Des weiteren werden im Beitrag die durchgeführten experimentellen Untersuchungen gebogener und gedrückter, quer‐ und längsversteifter I‐Stützen beschrieben, an denen die kritischen Lasten der elastischen räumlichen Knickung ermittelt wurden. Diese Untersuchungen stellen eine experimentelle Überprüfung der theoretischen, mittels approximativer Methode hergeleiteten Lösung dar. Der Beitrag wird mit allgemeinen Anmerkungen und praktischen Schlussfolgerungen abgeschlossen.
In vitro Starch Digestibility and Nutritionally Important Starch Fractions in Processed Roots and Tubers
Authors: Ahmed Faiyaz , Urooj Asna 
Published: September 2008

AbstractIn view of the nutritionally important starch fractions it has become essential to generate data on starch digestibility of commonly used foods. The present investigation was aimed at evaluating the effect of processing on the nutritionally important starch fractions and the extent of in vitro starch digestibility in six roots and tubers commonly consumed in the Indian cuisine, using controlled enzymatic digestion with pancreatin and amyloglucosidase. The samples were subjected to open‐pan and pressure cooking. Rapidly available glucose (RAG) was also measured to derive a starch digestion index (SDI), a measure of the relative rate of starch digestion. The total starch and amylose content in the raw samples ranged from 41% (w/w) to 80% (w/w) (dry basis) and 0.91 to 26.80% (w/w) (dry basis), respectively. Pressure cooking of roots and tubers significantly (p<0.05) decreased the amylose content. The levels of the individual starch fractions varied depending on the cooking method and were characteristic for each sample. Processing significantly influenced the various starch fractions in yam and knollkohl. The SDI of samples subjected to the two cooking methods was only different for beet root and radish. Radish and carrot contained the highest dietary fiber content. The simple in vitro measurement of starch fractions could serve as a tool for characterizing dietary carbohydrates with respect to their digestion in the intestine.
Novel Nanoporous Superabsorbent Hydrogel Based on Poly(acrylic acid) Grafted onto Salep: Synthesis and Swelling Behavior
Authors: Pourjavadi Ali , Soleyman Rouhollah , Barajee Ghasem Rezanejade 
Published: September 2008

AbstractHydrogels of poly(acrylic acid) grafted onto salep with excellent water absorption and water retention abilities under neutral conditions were successfully synthesized for the first time and employed for different applications. The effect of reaction variables to achieve maximum swelling capacity was investigated. In our procedure, ammonium persulfate (APS) as a water‐soluble initiator and methylenebisacrylamide (MBA) as a suitable crosslinking agent were used and the best synthesis conditions described. The structure of the final product was confirmed by Fourier‐transform infrared (FTIR) spectroscopy, scanning electron microscopy SEM and TGA analysis and a mechanism for superabsorbent hydrogel formation was also suggested. The study of the surface morphology of hydrogels using SEM showed a highly nanoporous and cellular structure for the sample obtained under optimized condition. Furthermore, several factors which influence the water uptake of hydrogels, such as pH of water, sensitivity to salt solutions and solvent mixtures were examined.
Influence of Lipids Isolated from Soybean Seed on Different Properties of Cassava Starch
Authors: Radhika Gopinathan S. , Shanavas Salim , Moorthy Subramoney N. 
Published: September 2008

AbstractThe effect of lipids isolated from soybean seeds on the properties of cassava starch was investigated. Both polar and non‐polar lipid fractions were complexed with starch and the physicochemical and rheological properties were examined. The FTIR spectra of the complexed starches showed all the absorption bands characteristic of native starch with an extra minor peak at 2355 cm‐1.The complexes prepared using the polar lipid fraction in diethyl ether as solvent exhibited a swelling volume of 32.5 mL/g compared to 36.9 mL/g for petroleum ether as solvent. A similar effect was observed with the non‐polar fraction. The apparent amylose content of the complexes was found to be lowered as a result of complexation. Total and soluble amylose contents and water‐binding capacity of the complexes were higher while their enzyme digestibility was noticeably lowered. The peak viscosity of the complexes was suppressed as a result of complexation. The polar layer exhibited a greater influence on the viscometric properties of the complexes with a higher breakdown ratio and hence higher stability. When compared to native starch, the percentage light transmittance of the complexes was noticeably reduced. The results indicate a considerable influence of the isolated lipid fractions on starch properties which can be useful in food and industrial applications.
Using memes and memetic processes to explain social and conceptual influences on student understanding about complex socio‐scientific issues
Authors: Yoon Susan 
Published: August 2008

AbstractThis study investigated seventh grade learners' decision making about genetic engineering concepts and applications. A social network analyses supported by technology tracked changes in student understanding with a focus on social and conceptual influences. Results indicated that several social and conceptual mechanisms potentially affected how and why ideas were taken up in the learning system of the classroom. Mechanisms included copying or memetic processes such as “do as the smart students do” and friendship selection. Study outcomes are compared with the broader literature on memes and memetic processes to reveal general evolutionary ideas such as the development of prestige, identity versus problem‐solving strategies, extended phenotypes, and memeplexes. Educational implications for this research are also addressed. © 2008 Wiley Periodicals, Inc. J Res Sci Teach 45: 900–921, 2008
Assessing the toxicity of TBBPA and HBCD by zebrafish embryo toxicity assay and biomarker analysis
Authors: Hu Jun , Liang Yong , Chen Minjie , Wang Xiaorong 
Published: September 2008

AbstractTetrabromobisphenol A (TBBPA) and hexabromocyclododecane (HBCD) are two of the most widely used brominated flame retardants (BFRs). The biological toxicity effect of TBBPA and HBCD was studied by means of zebrafish embryo toxicity assays in combination with three biomarkers, including superoxide dismutase (SOD), lipid peroxidation, (LPO), and heat shock protein (Hsp70). The standard zebrafish embryo assay showed that high concentrations of TBBPA (≥0.75 mg/L) can cause lethality or malformation. For HBCD within the concentration range (0.002–10 mg/L), no endpoint was observed. Furthermore, SOD activities of zebrafish embryos exposed to TBBPA were increased with the increasing concentrations. SOD activities in the group treated by HBCD showed an increase followed by a decline. Regardless of TBBPA or HBCD, LPO were increased along with the increase of the concentration. The change pattern of Hsp70 levels was the same with LPO. All these results showed that TBBPA and HBCD could cause oxidative stress and Hsp70 overexpression, inducing acute toxicity to zebrafish embryo in a short‐term exposure. The study also indicates that the zebrafish embryo assay in combination with the biomarkers is effective in aquatic environmental toxicology and risk assessment. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Endoscopic Parathyroidectomy: Why and When?
Authors: Henry Jean‐François , Sebag Frédéric , Cherenko Mariya , Ippolito Giuseppe , Taieb David , Vaillant Josiane 
Published: August 2008

AbstractBackgroundIn recent years, several new minimally invasive techniques for parathyroidectomy (MIP) have been developed. There was a rapid worldwide acceptance of mini‐open procedures by most surgeons. However, the use of an endoscope remains debatable. This study was designed to determine the role of preoperative imaging studies in the decision‐making for using an endoscope during MIP.MethodsAll patients with sporadic primary hyperparathyroidism (PHPT) and candidate for MIP underwent localizing studies. MIP was proposed only for patients in whom a single adenoma was localized by both ultrasonography and sestamibi scanning. Three locations were described: (1) posterior to the two superior thirds of the thyroid lobe; (2) at the level of or below the inferior pole of the thyroid lobe but in a plane posterior to it; (3) at the level of or below the tip of the inferior pole of the thyroid lobe but in a superficial plane. In locations 1 and 2, the nerve was considered to be at risk and an endoscopic lateral approach was indicated. In location 3, a mini‐open approach was indicated.ResultsOf the 165 patients operated on for PHPT in 2006, 86 underwent MIP. According to the results of imaging studies, 39 patients presented an adenoma in location 1, 21 in location 2, and 26 in location 3. In locations 1 and 2, 59 patients (1 false‐positive) had an adenoma that was located posteriorly, in close proximity to the nerve; all were cured. In location 3, 25 patients (1 false‐positive) presented an inferior parathyroid adenoma superficially located; all were cured. There was no transient or permanent laryngeal nerve palsy.ConclusionsIn patients who are candidates for MIP, we recommend the use of the endoscope for the resection of parathyroid adenomas that are located deeply in the neck.
Enzymes used in molecular biology: a useful guide
Authors: Rittié Laure , Perbal Bernard 
Published: September 2008

AbstractSince molecular cloning has become routine laboratory technique, manufacturers offer countless sources of enzymes to generate and manipulate nucleic acids. Thus, selecting the appropriate enzyme for a specific task may seem difficult to the novice. This review aims at providing the readers with some cues for understanding the function and specificities of the different sources of polymerases, ligases, nucleases, phosphatases, methylases, and topoisomerases used for molecular cloning. We provide a description of the most commonly used enzymes of each group, and explain their properties and mechanism of action. By pointing out key requirements for each enzymatic activity and clarifying their limitations, we aim at guiding the reader in selecting appropriate enzymatic source and optimal experimental conditions for molecular cloning experiments.
Maternal heart disease and pregnancy outcome: A single‐centre experience
Authors: Stangl Verena , Schad Johanna , Gossing Gabriele , Borges Adrian , Baumann Gert , Stangl Karl 
Published: August 2008

AbstractBackground:Maternal and neonatal complication rates are increased in pregnant women with heart disease. Cardiac risk assessment may be improved by defining low and high‐risk groups.Aims:To analyze pregnancy risks in low and high‐risk women with cardiovascular diseases.Methods and results:Pregnancy outcomes were analyzed in 93 consecutive women with heart disease, monitored in a single‐centre cohort between 1996 and 2006. Women were classified according to pre‐defined risk predictors as high‐risk (left ventricular [LV] ejection fraction <50%, NYHA class>II or cyanosis, peak LV outflow gradient >60 mmHg) or low‐risk (not meeting these criteria). Mean age was 28.1±5.7 years. 81.7% presented with congenital, 10.8% with acquired heart disease, and 7.5% with myocardial diseases. Severe maternal complications developed in 12.9% of all women: 6.5% heart failure, 3.2% arrhythmias, and 2.2% thrombotic complications. Maternal mortality was 1.1%. Women at high‐risk (24.7%) had a 6.1‐fold higher maternal complication rate and a 6.1 times higher foetal/neonatal event rate (abortion and stillbirth). 64.7% of the high‐risk women delivered prematurely, before the 37th week, compared to 16.4% in the low‐risk group.Conclusions:Despite pronounced clinical variability of congenital and acquired heart diseases, a small number of risk conditions can effectively characterize women in whom pregnancy is associated with appreciably increased maternal and foetal risk.