bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation and ranking of enzyme designs
Authors: Kiss Gert , Röthlisberger Daniela , Baker David , Houk K. N. 
Published: July 2010

AbstractIn 2008, a successful computational design procedure was reported that yielded active enzyme catalysts for the Kemp elimination. Here, we studied these proteins together with a set of previously unpublished inactive designs to determine the sources of activity or lack thereof, and to predict which of the designed structures are most likely to be catalytic. Methods that range from quantum mechanics (QM) on truncated model systems to the treatment of the full protein with ONIOM QM/MM and AMBER molecular dynamics (MD) were explored. The most effective procedure involved molecular dynamics, and a general MD protocol was established. Substantial deviations from the ideal catalytic geometries were observed for a number of designs. Penetration of water into the catalytic site and insufficient residue‐packing around the active site are the main factors that can cause enzyme designs to be inactive. Where in the past, computational evaluations of designed enzymes were too time‐extensive for practical considerations, it has now become feasible to rank and refine candidates computationally prior to and in conjunction with experimentation, thus markedly increasing the efficiency of the enzyme design process.
Crystal structure of Bacillus subtilis SPP1 phage gp23.1, a putative chaperone
Authors: Veesler David , Blangy Stéphanie , Lichière Julie , Ortiz‐Lombardía Miguel , Tavares Paulo , Campanacci Valérie , Cambillau Christian 
Published: July 2010

AbstractSPP1 is a siphophage infecting the gram‐positive bacterium Bacillus subtilis. The SPP1 tail electron microscopy (EM) reconstruction revealed that it is mainly constituted by conserved structural proteins such as the major tail proteins (gp17.1), the tape measure protein (gp18), the Distal tail protein (Dit, gp19.1), and the Tail associated lysin (gp21). A group of five small genes (22–24.1) follows in the genome but it remains to be elucidated whether their protein products belong or not to the tail. Noteworthy, an unassigned EM density accounting for ∼245 kDa is present at the distal end of the SPP1 tail‐tip. We report here the gp23.1 crystal structure at 1.6 Å resolution, a protein that lacks sequence identity to any known protein. We found that gp23.1 forms a hexamer both in the crystal lattice and in solution as revealed by light scattering measurements. The gp23.1 hexamer does not fit well in the unassigned SPP1 tail‐tip EM density and we hypothesize that this protein might act as a chaperone.
L‐Arginine hydrochloride increases the solubility of folded and unfolded recombinant plasminogen activator rPA
Authors: Tischer Alexander , Lilie Hauke , Rudolph Rainer , Lange Christian 
Published: July 2010

AbstractL‐Arginine hydrochloride (L‐ArgHCl) was found to be an effective enhancer for in vitro protein refolding more than two decades ago. A detailed understanding of the mechanism of action, by which L‐ArgHCl as co‐solvent is capable to effectively suppress protein aggregation, while protein stability is preserved, has remained elusive. Concepts for the effects of co‐solvents, which have been established over the last decades, were found to be insufficient to completely explain the effects of L‐ArgHCl on protein refolding. In this article, we present data, which clearly establish that L‐ArgHCl acts on the equilibrium solubility of the native model protein recombinant plasminogen activator (rPA), while for S‐carboxymethylated rPA (IAA‐rPA) that served as a model protein for denatured protein states, equilibrium solubilities could not be obtained. Solid to solute free transfer energies for native rPA were lowered by up to 14 kJ mol‐1 under the tested conditions. This finding is in marked contrast to a previously proposed model in which L‐ArgHCl acts as a neutral crowder which exclusively has an influence on the stability of the transition state of aggregation. The effects on the apparent solubility of IAA‐rPA, as well as on the aggregation kinetics of all studied protein species, that were observed in the present work could tentatively be explained within the framework of a nucleation‐aggregation scheme, in which L‐ArgHCl exerts a strong effect on the pre‐equilibria leading to formation of the aggregation seed.
Two glutathione S‐transferase inhibitors from Radix Angelicae sinensis
Authors: Huang Feng , Li Shaojing , Lu Xinhua , Liu Ailin , Du Guanhua , Shi Ganggang 
Published: July 2010

AbstractChemotherapy for malignant tumors fails because of multidrug resistance (MDR). The overexpression of glutathione S‐transferase (GST) with MDR is considered one of the major obstacles to successful cancer chemotherapy. High‐throughput screening was performed to search for inhibitors of GST from natural products. Two compounds isolated from Radix Angelicae sinensis had an inhibitory effect on GST, with 50% inhibitory concentration (IC50) values of 16.80 and 7.30μm. Kinetic analyses showed that the two compounds acted as reversible noncompetitive inhibitors of GST. They also increased apoptosis of B‐MD‐C1 (ADR+/+) cells induced by adriamycin with low cytotoxic activity. Radix Angelicae sinensis may be a potential source of GST inhibition for pharmaceutical use. Copyright © 2010 John Wiley & Sons, Ltd.
Augmented state–extended Kalman filter combined framework for topology estimation in large‐area underwater mapping
Authors: Elibol Armagan , Gracias Nuno , Garcia Rafael 
Published: July 2010

AbstractOver the past few years, underwater vehicles have greatly improved as a tool for undersea exploration and navigation. In particular, autonomous navigation, localization, and mapping through optical imaging have become topics of interest for researchers in both underwater robotics and marine science. Underwater imagery can be used to construct image composites (photomosaics) used in many different application areas such as underwater surveying and navigation. For surveying operations with a low‐cost robot limited to a down‐looking camera and a sonar altimeter, it is common practice to ensure that there is enough overlap between time‐consecutive images as this is the only data source of navigation. When the robot revisits a previously surveyed area, it is essential to detect and match the non‐time‐consecutive images to close a loop and, thus, improve trajectory estimation. While creating the mosaic, most of the existing algorithms try to match all image pairs to detect the non‐time‐consecutive overlapping images when there is no additional navigation information. We present a framework to obtain a two‐dimensional mosaic with minimum image matching attempts and simultaneously get the best possible trajectory estimation by exploring the contribution of the image pairs matching to the whole system. Different strategies for choosing match candidates have been tested, and the results are given in different challenging underwater image sequences. © 2010 Wiley Periodicals, Inc.
Surface characterization of dead microalgae‐based biomass using methylene blue adsorption
Authors: Tsai Wen‐Tien , Chen Huei‐Ru , Kuo Kuan‐Chi 
Published: July 2010

AbstractTo examine the surface characterization of dead chlorella biomass, the chlorella‐manufacturing residue was used as an adsorbent for removal of cationic dye (i.e. methylene blue) from aqueous solutions at low concentrations (less than 5 mg dm−3). It could be elucidated by considering the ion‐exchange adsorption phenomena on the negative‐charged surface of the adsorbent based on the characterization of functional groups by the Fourier transform infrared (FTIR) analysis. On the basis of monolayer dye adsorption capacity, the specific surface area of this spherical biomass powder was estimated as 11.8 m2 g−1, which was consistent with the rigid cell wall structure of the dead chlorella particles as shown in the SEM observation. Copyright © 2010 John Wiley & Sons, Ltd.
The influence of Ni(II) ion on the properties of NiOAl2O3 catalyst prepared by impregnation method
Authors: Kiurski Jelena S. , Obadović Dušanka Ž. , Marinković‐Nedučin Radmila P. , Cvetinov Miroslav J. 
Published: July 2010

AbstractThe behavior of the NiOAl2O3 catalysts is strongly dependent on the preparation method and pretreatment conditions. In the present work, we investigate the influence of Ni(II) content and various treatment temperatures on the properties of NiOAl2O3 catalysts prepared by impregnation method. On the basis of experimental diffuse reflectance spectroscopy data of electronic d–d transitions of Ni(II) promoter ion, the energies of electronic states in spinel‐like structure were calculated and the most probable scheme of molecular orbital have been proposed. The results of studying the system model allowed the conclusion that the type of contact between the starting phases has a decisive influence on the coordination of Ni(II) ions. Copyright © 2010 John Wiley & Sons, Ltd.
Retinoic Acid Synthesis Promotes Development of Neural Progenitors from Mouse Embryonic Stem Cells by Suppressing Endogenous, Wnt-Dependent Nodal Signaling
Authors: Engberg Nina , Kahn Morten , Petersen Dorthe Rønn , Hansson Mattias , Serup Palle 
Published: July 2010

Abstract
Embryonic stem (ES) cells differentiate spontaneously toward a neuroectodermal fate in serum-free, adherent monocultures. Here, we show that this spontaneous neural fate requires retinoic acid (RA) synthesis. We monitor ES cells containing reporter genes for markers of the early neural plate as well as the primitive streak and its progeny to determine the cell fates induced when RA signaling is perturbed. We demonstrate that the spontaneous neural commitment of mouse ES cells requires endogenous RA production from vitamin A (vitA) in the medium. Formation of neural progenitors is inhibited by removing vitA from the medium, by inhibiting the enzymes that catalyze the synthesis of RA, or by inhibiting RA receptors. We show that subnanomolar concentrations of RA restore neuroectodermal differentiation when RA synthesis is blocked. We demonstrate that a neural to mesodermal fate change occurring when RA signaling is inhibited is dependent on Nodal-, Wnt-, and fibroblast growth factor-signaling. We show that Nodal suppresses neural development in a Wnt-dependent manner and that Wnt-mediated inhibition of neural development is reversed by inhibition of Nodal signaling. Together, our results show that neural induction in ES cells requires RA at subnanomolar levels to suppress Nodal signaling and suggest that the mechanism by which Wnt signaling suppresses neural development is through facilitation of Nodal signaling.
miR-124a Is Important for Migratory Cell Fate Transition During Gastrulation of Human Embryonic Stem Cells
Authors: Ryul Lee Man , Soo Kim Jong , Kim Kye-Seong 
Published: July 2010

Abstract
Precise control of gene expression is of paramount importance for proper embryonic development. Although a number of microRNAs (miRNAs) has been implicated in fine-tuning mRNA translation during development, their exact roles for gastrulation, particularly in connection with functional targets, have yet to be clarified, with regard to stage-specific cell migration to form three embryonic germ layers. We found that miR-124a is expressed in human embryonic stem cells (hESC), but is gradually downregulated during embryoid body (EB) formation in vitro. We also provide evidence that SLUG and IQGAP1, which modulates rearrangement of the migratory cytoskeleton, are specific targets for miR-124a during EB formation. Furthermore, we show that the beginning of cell migration, a hallmark event in gastrulation, is tightly coupled with downregulation of miR-124a during EB formation and induction of SLUG and IQGAP1. Overexpressed miR-124a in hESC reduced expression of SLUG and IQGAP1 and blocked migratory cell behavior in EB. An expression level of MIXL1, associated with gastulation process, was also inversely correlated with expression of miR-124a. Taken together, our results strongly suggest that miR-124a may play an active role in inhibiting hESCs from differentiation into EB by downregulating expression of SLUG and IQGAP1, thereby maintaining stemness.
Mode shape linearization and correction in coupled dynamic analysis of wind‐excited tall buildings
Authors: Huang Mingfeng , Tse Kam‐Tim , Chan Chun‐Man , Kwok Kenny C. S. , Hitchcock Peter A. , Lou Wenjuan 
Published: July 2010

AbstractThe three‐dimensional mode shapes found in modern tall buildings complicate the use of the high‐frequency base balance (HFBB) technique in wind tunnel testing for predicting their wind‐induced loads and effects. The linearized‐mode‐shape (LMS) method was recently proposed to address some of the complications in the calculation of the generalized wind forces, which serve as the input to modal analysis for predicting wind‐induced dynamic responses of tall buildings. An improved LMS method, called the advanced linearized‐mode‐shape (ALMS) method, is developed in this paper by introducing torsional mode shape corrections to account for the partial correlation of torques over building height. The ALMS method has been incorporated into the accurate complete quadratic combination method in the coupled dynamic analysis to form a comprehensive procedure for the determination of equivalent static wind loads (ESWLs) for structural design of complex tall buildings. The improved accuracy in the prediction of generalized forces by the ALMS method has been validated by a 60‐storey benchmark building with multiple‐point simultaneous pressure measurements. A practical 40‐storey residential building with significant swaying and torsional effects is presented to demonstrate the effectiveness of the proposed wind load and response analysis procedure based on the HFBB data. Copyright © 2010 John Wiley & Sons, Ltd.
Long‐term potentiation (LTP) of human sensory‐evoked potentials
Authors: Kirk Ian J. , McNair Nicolas A. , Hamm Jeffrey P. , Clapp Wesley C. , Mathalon Daniel H. , Cavus Idil , Teyler Timothy J. 
Published: July 2010

AbstractLong‐term potentiation (LTP) is the principal candidate synaptic mechanism underlying learning and memory, and has been studied extensively at the cellular and molecular level in laboratory animals. Inquiry into the functional significance of LTP has been hindered by the absence of a human model as, until recently, LTP has only been directly demonstrated in humans in isolated cortical tissue obtained from patients undergoing surgery, where it displays properties identical to those seen in non‐human preparations. In this brief review, we describe the results of paradigms recently developed in our laboratory for inducing LTP‐like changes in visual‐, and auditory‐evoked potentials. We describe how rapid, repetitive presentation of sensory stimuli leads to a persistent enhancement of components of sensory‐evoked potential in normal humans. Experiments to date, investigating the locus, stimulus specificity, and NMDA receptor dependence of these LTP‐like changes suggest that they have the essential characteristics of LTP seen in experimental animals. The ability to elicit LTP from non‐surgical patients will provide a human model system allowing the detailed examination of synaptic plasticity in normal subjects and may have future clinical applications in the assessment of cognitive disorders. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

Psychology > Brain Function and Dysfunction
Neuroscience > Plasticity
Adaptability to organic farming of lentil (Lens culinarisMedik.) varieties developed from conventional breeding programmes
Authors: VLACHOSTERGIOS D. N. , LITHOURGIDIS A. S. , ROUPAKIAS D. G. 
Published: July 2010

SUMMARYThe development of organic agriculture has raised the demand for crop varieties well-adapted to organic farming systems. Most of the varieties presently cultivated in organic agriculture were developed from conventional breeding programmes. The objective of the present work was to study the adaptability to organic farming systems of lentil (Lens culinarisMedik.) varieties developed from conventional breeding programmes. Twenty varieties were evaluated over five environments under organic and conventional farming systems from 2005 to 2007. Genotype×system interactions (GSI) for grain yield were significantly different in four out of the five environments and GSI explained 0·03–0·17 of the variance. Spearman's rank correlation index of the 20 varieties between the conventional and organic system ranged from 0·27 to 0·93 in the five environments. Direct selection of the top five varieties in organic systems resulted in significantly higher grain yields than indirect selection in one out of the five environments. However, among the top five varieties, the highest yielding varieties under conventional farming systems were not always the highest yielding varieties under organic farming systems. These results indicate that the demands of organic agriculture for yield performance could be only partially satisfied by varieties developed under conventional breeding programmes.
Quantification of C and N stocks in grassland topsoils in a Dutch region dominated by dairy farming
Authors: SONNEVELD M. P. W. , VAN DEN AKKER J. J. H. 
Published: July 2010

SUMMARYEstimates on soil organic carbon (SOC) and nitrogen (N) stocks in soils cannot be directly calculated from routine soil analyses, since these often lack measurements on soil bulk density (Bd). Hence, flexible pedotransfer functions are required that allow the calculation of SOC stocks from gravimetrically determined SOC contents. The present paper aimed to: (1) quantify SOC and N stocks in grassland topsoils for a Northern Dutch region dominated by dairy farming and (2) analyse the relationships between SOC and bulk density at the field level. As estimates of SOC and N stocks are potentially affected by soil compaction, the combined measurements on soil bulk density and soil organic matter (SOM) were also evaluated with respect to critical limits for soil compaction using soil density (Sd) for sandy soils and packing density (Pd) for clay soils. The SOC andBdmeasurements were done in the upper 0·1–0·2 m of grasslands at 18 dairy farms, distributed across sandy, clay and peat soils. Both farm data and grassland management data were collected. Non-linear regressions were used to analyse relationships betweenBdand SOM. Significant non-linear relationships were found between gravimetric SOC contents and bulk density for the 0–0·1 m layer (R2=0·80) and the 0·1–0·2 m layer (R2=0·86). None of the fields on sandy soils or clay soils indicated signs for limited rooting in the topsoil although some fields appear to approach the critical limit for compaction for the 0·1–0·2 m layer. Stocks of SOC in the top 0·2 m at farm level were highest in the peat soils (21·7 kg/m2) and lowest in the sandy soils (9·0 kg/m2). Similarly, N stocks were highest for farms on peat soil (1·30 kg/m2) and lowest for farms on sandy soil (0·60 kg/m2). For the sandy soils, the mean SOC stock was significantly higher in fields with shallow groundwater tables.
In defence of logical nominalism: reply to Leftow
Authors: SWINBURNE RICHARD 
Published: July 2010

AbstractThis paper defends (especially in response to Brian Leftow's recent attack) logical nominalism, the thesis that logically necessary truth belongs primarily to sentences and depends solely on the conventions of human language. A sentence is logically necessary (that is, a priori metaphysically necessary) iff its negation entails a contradiction. A sentence is a posteriori metaphysically necessary iff it reduces to a logical necessity when we substitute for rigid designators of objects or properties canonical descriptions of the essential properties of those objects or properties. The truth-conditions of necessary sentences are not to be found in any transcendent reality, such as God's thoughts. ‘There is a God’ is neither a priori nor a posteriori metaphysically necessary; God is necessary in the sense that His existence is not causally contingent on anything else.
Effectiveness of village-based marine reserves on reef invertebrates in Emau, Vanuatu
Authors: DUMAS P. , JIMENEZ H. , LÉOPOLD M. , PETRO G. , JIMMY R. 
Published: July 2010

SUMMARYDespite the current expansion of community-based marine conservation initiatives in the Pacific, few studies have specifically addressed their ecological efficiency to restore or enhance reef invertebrate resources. This paper investigated the effects of two very small (< 0.05 km2) recent village-based marine reserves (tabu areas) located along the shallow fringing reef of Emau island, Vanuatu. Surveys focused on heavily harvested species (namely trochus, giant clams and green snails) and involved both experienced scientists and local villagers. Abundance, density and individual size data were collected by snorkelling along random transect belts located inside and outside the tabu areas, using simple PVC measuring tools specifically developed for participative monitoring. Habitat was assessed using a photographic method to quantitatively describe varied reef substrata. Resource recovery varied between the areas as a result of species-specific responses to contrasted reserve characteristics and local management practices. Fast-growing mobile Trochus niloticus exhibited strong positive abundance and size responses only within the older larger tabu area through the combined effects of protection from harvesting and translocation actions by local fishers. Similar trends were observed to a lesser extent for sessile slow-growing giant clams (Tridacna spp.), but these were not significant after four years of closure. Despite historical evidence of their presence in the area, surveys emphasized the severe population collapse of the heavily targeted green snail (Turbo marmoratus). Under certain conditions, very small-scale reserves, such as those implemented by village-based conservation initiatives, can rapidly and efficiently enhance local reef invertebrate resources. It is still unclear whether the changes are sufficient to restore critical levels of spawning biomass at larger scale and reverse the severe depletion of invertebrate resources occurring in Vanuatu.
Using connectivity metrics and niche modelling to explore the occurrence of the northern crested newt Triturus cristatus (Amphibia, Caudata) in a traditionally managed landscape
Authors: HARTEL TIBOR , NEMES SZILÁRD , ÖLLERER KINGA , COGĂLNICEANU DAN , MOGA COSMIN , ARNTZEN JAN W. 
Published: July 2010

SUMMARYSpatial models are increasingly employed to help understand the distribution of organisms and establish conservation priorities. Classic patch-orientated models may have limited power to accurately predict the organisms' distributions. Pond breeding amphibians are appropriate study organisms because of their complex life cycle, low dispersal and sensitivity to environmental conditions. Here connectivity metrics and niche modelling were used to predict the occurrence of the northern crested newt in a rural landscape from central Romania. Pond-related variables, such as macrophyte cover and the presence of predatory fish, were the most important predictors of newt occurrence, followed by one landscape-related variable (urbanization) and a connectivity metric (nearest neighbouring occupied pond). Most of the landscape and connectivity variables were not adequate predictors, presumably because most of the terrestrial habitats in this traditionally used rural landscape are ecologically optimal for amphibians. Conservation measures for the northern crested newt should promote the preservation of traditional extensive agricultural practices and discourage stocking of ponds with predatory fish.