bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viscosity of potassium soap‐potassium silicate mixtures
Authors: Spencer Robert W. 
Published: March 2007

SummaryViscosity measurements at 20°C. have been made on mixtures of three potassium soaps with four potassium silicates and potassium chloride in the range of 0 to 100 poises. It was found that the additives have a considerable effect on the viscosity of the potassium linseed oil and the soya bean oil soap solutions, but almost no effect on the viscosities of potassium coconut oil soap solutions in the concentration ranges studied. The alkaline silicates caused greater increases in viscosities than the siliceous silicates. Soap‐KC1 mixtures have viscosities of the same order of magnitude as equivalent soap‐silicate mixtures in this viscosity range.
Surface tension determinations of some saturated fat acid methyl esters
Authors: Nevin C. S. , Althouse P. M. , Triebold H. O. 
Published: March 2007

SummaryMethyl esters of saturated naturally occurring fat acids from C6 through C18 were prepared and purified by fractional distillation. Refractive indices were used as a measure of their purity. A micro surface tension apparatus was constructed to comply with a modified capillary rise method devised by Ferguson. The surface tensions of water and of benzene were determined at several temperatures. The results obtained compared quite favorably with the values listed in the International Critical Tables. The surface tensions of the methyl esters were determined at 40°C., 60°C., and 80°C. with an accuracy of ±0.15 dynes/cm. Similar to other homologous series the surface tensions of the fat acid methyl esters decrease with increasing temperature, apparently in a linear manner. As the molecular weight of the methyl ester series increases, the surface tension also increases. Close correlation is shown for the methyl esters between the calculated parachors based upon Gibling's system of values and the experimental parachors.
Evaluation of safflowerseed oil in edible fat products
Authors: Soltoft P. , Dollear F. G. 
Published: March 2007

SummaryFour varieties of safflowerseed grown in Nebraska and Colorado were examined with respect to the composition of the seed, hulls, extracted meal, and oil.The oil from one variety (Nebraska 852) was (A) refined, bleached, and deodorized; and (B) refined, bleached, hydrogenated, and deodorized. The liquid oil and the hardened fat were analyzed with respect to their fatty acid compositions and their stabilities to rancidity and flavor reversion were determined.All of the results indicate that safflowerseed oil is not as suitable for edible purposes as other domestically produced edible oils.
Solidification point curves of binary acid mixtures. VII. Undecanoic to pentacosanoic acids
Authors: Schuette H. A. , Christenson R. M. , Stefansson Unnsteinn H. , Fisher Sallie A. , Vogel H. A. , Walker Joseph 
Published: March 2007

SummaryThe clearly defined inflections which characterize the solidification‐point diagrams of binary mixtures of the adjacent, straight‐chain acids of even number carbon atom content in the C8 to C16 area of the homologous series in question are not evident when an “odd” acid enters the picture. Pertinent diagrams for the adjacent odd‐odd acids, C11 to C25, have been constructed.Although these diagrams have probably no known analytical application at the present, they have a potential one in the indirect determination and characterization of the higher alcohols oxidized to the corresponding acids.
Object detection and mapping for service robot tasks
Authors: Ekvall Staffan , Kragic Danica , Jensfelt Patric 
Published: March 2007

SUMMARYThe problem studied in this paper is a mobile robot that autonomously navigates in a domestic environment, builds a map as it moves along and localizes its position in it. In addition, the robot detects predefined objects, estimates their position in the environment and integrates this with the localization module to automatically put the objects in the generated map. Thus, we demonstrate one of the possible strategies for the integration of spatial and semantic knowledge in a service robot scenario where a simultaneous localization and mapping (SLAM) and object detection recognition system work in synergy to provide a richer representation of the environment than it would be possible with either of the methods alone. Most SLAM systems build maps that are only used for localizing the robot. Such maps are typically based on grids or different types of features such as point and lines. The novelty is the augmentation of this process with an object-recognition system that detects objects in the environment and puts them in the map generated by the SLAM system. The metric map is also split into topological entities corresponding to rooms. In this way, the user can command the robot to retrieve a certain object from a certain room. We present the results of map building and an extensive evaluation of the object detection algorithm performed in an indoor setting.
Setpoint regulation of continuum robots using a fixed camera
Authors: Chitrakaran V. K. , Behal A. , Dawson D. M. , Walker I. D. 
Published: March 2007

SUMMARYIn this paper, we investigate the problem of measuring the shape of a continuum robot manipulator using visual information from a fixed camera. Specifically, we capture the motion of a set of fictitious planes, each formed by four or more feature points, defined at various strategic locations along the body of the robot. Then, utilizing expressions for the robot forward kinematics as well as the decomposition of a homography relating a reference image of the robot to the actual robot image, we obtain the three-dimensional shape information continuously. We then use this information to demonstrate the development of a kinematic controller to regulate the manipulator end-effector to a constant desired position and orientation.
Olive oil and haemostasis: a review on its healthy effects
Authors: Pérez-Jiménez Francisco , Lista Javier Delgado , Pérez-Martínez Pablo , López-Segura Fernando , Fuentes Francisco , Cortés Begoña , Lozano Aquiles , López-Miranda José 
Published: March 2007

AbstractInterest in the Mediterranean diet (MD) has grown worldwide. Despite the high complexity of its nutrients composition, olive oil emerges as its principal food, since it provides the higher percentage of energy and a lot of bioactive compounds.ObjectiveIn this review, we will discuss the benefits of diets enriched in virgin olive oil, whose effects are probably due not only to its oleic acid content but also to its other potentially health-promoting components.MethodsTraditionally, the benefits of MD were linked to its effect on lipoprotein metabolism, but today we realise that there exists a whole sheaf of other benefits, including the components of haemostasis: platelet function, thrombogenesis and fibrinolysis.ResultsA diet enriched in virgin olive oil can reduce the sensitivity of platelets to aggregation, decreasing von Willebrand and thromboxane B2 plasma levels. Moreover, a particular interest has aroused about its capacity to decrease fasting factor VII plasma levels and to avoid or modulate its postprandial activation. In addition, tissue factor expression in mononuclear cells could be reduced with the chronic intake of virgin olive oil, and finally, studies performed in different experimental situation have shown that it could also increase fibrinolytic activity, reducing plasma concentration of plasma activator inhibitor type-1 (PAI-1).ConclusionThe MD is an alimentary model with a high content of monounsaturated fats that is capable of inducing a wide range of biological effects on the cardiovascular system. The application of modern focuses of study will dilucidate in the future the biological and clinical interest of these findings.
Mediterranean diet and depression
Authors: Sánchez-Villegas A , Henríquez P , Bes-Rastrollo M , Doreste J 
Published: March 2007

AbstractObjectiveThe adherence to a Mediterranean Dietary Pattern ensures an adequate intake of B vitamins and w-3 fatty acids. A protective role on depression has been suggested for both nutrients.DesignCross-sectional analysis from the SUN (Seguimiento Universidad de Navarra) prospective cohort study. Data from 9670 participants (4211 men and 5459 women) were analised. Logistic regression analyses were fitted to assess the association between B-vitamins and w-3 fatty acids intake (quintiles) and the prevalence of depression.ResultsFolate intake was inversely associated with depression prevalence among men, especially smokers. Among women, B12 vitamin intake was inversely associated with depression, especially among smokers and physically active women. No significant associations were observed for w-3 fatty acids intake.ConclusionsThe adherence to a Mediterranean Dietary Pattern ensures an adequate intake of fruits, nuts, vegetables, cereals, legumes or fish, important sources of nutrients linked to depression prevention.
Maximum number of habitable planets at the time of Earth’s origin: new hints for panspermia and the mediocrity principle
Authors: Franck Siegfried , von Bloh Werner , Bounama Christine 
Published: March 2007

AbstractIn this paper we estimate the number of habitable planets in our Galaxy over cosmological time scales. This number can be derived from the planet formation rate (PFR) of Earth-like planets and the convolution of this value with the probability of being habitable. The PFR is calculated from the star formation rate (SFR) with the help of a so-called Goldilocks problem. The probability that an Earth-like planet is in the habitable zone (HZ) is estimated with the help of our Earth system model. In order to calculate the HZ an integrated system approach is used, taking into account a variety of climatological, biogeochemical, and geodynamical processes. Habitability is linked to the photosynthetic activity on the planetary surface. We find that habitability strongly depends on the age of the stellar system and the characteristics of a virtual Earth-like planet. There was a maximum number of habitable planets around the time of the Earth’s origin and interstellar panspermia was most probable at that time. Furthermore, we discuss our results in the framework of the so-called principle of mediocrity.
Domain-enhanced analysis of microarray data using GO annotations
Authors: Liu Jiajun , Hughes-Oliver Jacqueline M. , Menius J. Alan 
Published: March 2007

AbstractMotivation: New biological systems technologies give scientists the ability to measure thousands of bio-molecules including genes, proteins, lipids and metabolites. We use domain knowledge, e.g. the Gene Ontology, to guide analysis of such data. By focusing on domain-aggregated results at, say the molecular function level, increased interpretability is available to biological scientists beyond what is possible if results are presented at the gene level.Results: We use a ‘top–down’ approach to perform domain aggregation by first combining gene expressions before testing for differentially expressed patterns. This is in contrast to the more standard ‘bottom–up’ approach, where genes are first tested individually then aggregated by domain knowledge. The benefits are greater sensitivity for detecting signals. Our method, domain-enhanced analysis (DEA) is assessed and compared to other methods using simulation studies and analysis of two publicly available leukemia data sets.Availability: Our DEA method uses functions available in R (http://www.r-project.org/) and SAS (http://www.sas.com/). The two experimental data sets used in our analysis are available in R as Bioconductor packages, ‘ALL’ and ‘golubEsets’ (http://www.bioconductor.org/).Contact: jliu6@stat.ncsu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
The impact of function perturbations in Boolean networks
Authors: Xiao Yufei , Dougherty Edward R. 
Published: March 2007

AbstractMotivation: A network is said to be robust relative to a certain network characteristic if a small change in network structure does not significantly affect the characteristic. From the perspective of network stability, robustness is desirable; however, from the perspective of intervention to exert influence on network behavior, it is undesirable. For Boolean networks, there are two fundamental types of robustness. One type pertains to perturbing the state of the network and the other to perturbing the rule-based structure.Results: This article explores the impact of function perturbations in Boolean networks from two aspects: (1) analysis: predict the impact on network state transitions and attractors via analytical approaches or identify a perturbation by observing its consequences; (2) synthesis: preserve or modify the network characteristics, especially attractors, by introducing a judicious change to the functions. The results are applied to achieve intervention that structurally alters the network to achieve a more favorable steady-state distribution and to identify the function perturbation that has led to altered observed behavior. The intervention procedure is applied to a WNT5A network to reduce the risk of metastasis in melanoma, and the identification procedure is applied to a Drosophila melanogaster segmentation polarity gene network to identify regulatory function perturbation.Contact: edward@ece.tamu.edu
UniRef: comprehensive and non-redundant UniProt reference clusters
Authors: Suzek Baris E. , Huang Hongzhan , McGarvey Peter , Mazumder Raja , Wu Cathy H. 
Published: March 2007

AbstractMotivation: Redundant protein sequences in biological databases hinder sequence similarity searches and make interpretation of search results difficult. Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences.Results: The UniRef (UniProt Reference Clusters) provide clustered sets of sequences from the UniProt Knowledgebase (UniProtKB) and selected UniProt Archive records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences. Currently covering &gt;4 million source sequences, the UniRef100 database combines identical sequences and subfragments from any source organism into a single UniRef entry. UniRef90 and UniRef50 are built by clustering UniRef100 sequences at the 90 or 50% sequence identity levels. UniRef100, UniRef90 and UniRef50 yield a database size reduction of ∼10, 40 and 70%, respectively, from the source sequence set. The reduced redundancy increases the speed of similarity searches and improves detection of distant relationships. UniRef entries contain summary cluster and membership information, including the sequence of a representative protein, member count and common taxonomy of the cluster, the accession numbers of all the merged entries and links to rich functional annotation in UniProtKB to facilitate biological discovery. UniRef has already been applied to broad research areas ranging from genome annotation to proteomics data analysis.Availability: UniRef is updated biweekly and is available for online search and retrieval at http://www.uniprot.org, as well as for download at ftp://ftp.uniprot.org/pub/databases/uniprot/unirefContact: bes23@georgetown.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Inherent chaperone‐like activity of aspartic proteases reveals a distant evolutionary relation to double‐ψ barrel domains of AAA‐ATPases
Authors: Hulko Michael , Lupas Andrei N. , Martin Jörg 
Published: March 2007

AbstractChaperones and proteases share the ability to interact with unfolded proteins. Here we show that enzymatically inactive forms of the aspartic proteases HIV‐1 protease and pepsin have inherent chaperone‐like activity and can prevent the aggregation of denatured substrate proteins. In contrast to proteolysis, which requires dimeric enzymes, chaperone‐like activity could be observed also with monomeric domains. The involvement of the active site cleft in the chaperone‐like function was demonstrated by the inhibitory effect of peptide substrate inhibitors. The high structural similarity between aspartic proteases and the N‐terminal double‐ψ barrels of Cdc48‐like proteins, which are involved in the unfolding and dissociation of proteins, suggests that they share a common ancestor. The latent chaperone‐like activity in aspartic proteases can be seen as a relic that has further evolved to serve substrate binding in the context of proteolytic activity.
A combined structural dynamics approach identifies a putative switch in factor VIIa employed by tissue factor to initiate blood coagulation
Authors: Olsen Ole H. , Rand Kasper D. , Østergaard Henrik , Persson Egon 
Published: March 2007

AbstractCoagulation factor VIIa (FVIIa) requires tissue factor (TF) to attain full catalytic competency and to initiate blood coagulation. In this study, the mechanism by which TF allosterically activates FVIIa is investigated by a structural dynamics approach that combines molecular dynamics (MD) simulations and hydrogen/deuterium exchange (HX) mass spectrometry on free and TF‐bound FVIIa. The differences in conformational dynamics from MD simulations are shown to be confined to regions of FVIIa observed to undergo structural stabilization as judged by HX experiments, especially implicating activation loop 3 (residues 365–374{216–225}) of the so‐called activation domain and the 170‐loop (residues 313–322{170A–175}) succeeding the TF‐binding helix. The latter finding is corroborated by experiments demonstrating rapid deglycosylation of Asn322 in free FVIIa by PNGase F but almost complete protection in the presence of TF or an active‐site inhibitor. Based on MD simulations, a key switch of the TF‐induced structural changes is identified as the interacting pair Leu305{163} and Phe374{225} in FVIIa, whose mutual conformations are guided by the presence of TF and observed to be closely linked to the structural stability of activation loop 3. Altogether, our findings strongly support an allosteric activation mechanism initiated by the stabilization of the Leu305{163}/Phe374{225} pair, which, in turn, stabilizes activation loop 3 and the S1 and S3 substrate pockets, the activation pocket, and N‐terminal insertion.
A filamentous molecular chaperone of the prefoldin family from the deep‐sea hyperthermophile Methanocaldococcus jannaschii
Authors: Whitehead Timothy A. , Boonyaratanakornkit Boonchai B. , Höllrigl Volker , Clark Douglas S. 
Published: March 2007

AbstractPrefoldin is a molecular chaperone found in the domains eukarya and archaea that acts in conjunction with Group II chaperonin to correctly fold other nascent proteins. Previously, our group identified a putative single subunit of prefoldin, γ PFD, that was up‐regulated in response to heat stress in the hyperthermophilic archaeon Methanocaldococcus jannaschii. In order to characterize this protein, we subcloned and expressed it and the other two prefoldin subunits from M. jannaschii, α and β PFD, into Eschericia coli and characterized the proteins. Whereas α and β PFD readily assembled into the expected hexamer, γ PFD would not assemble with either protein. Instead, γ PFD forms long filaments of defined dimensions measuring 8.5 nm × 1.7–3.5 nm and lengths exceeding 1 μm. Filamentous γ PFD acts as a molecular chaperone through in vitro assays, in a manner comparable to PFD. A possible molecular model for filament assembly is discussed.
Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications
Authors: Choi Eun Jung , Mao Jessica , Mayo Stephen L. 
Published: March 2007

AbstractLipid transfer proteins (LTPs) are a family of proteins that bind and transfer lipids. Utilizing the maize LTP, we have successfully engineered fluorescent reagentless biosensors for the natural ligand of LTPs; this was achieved by using computational protein design to remove a disulfide bridge and attaching a thio‐reactive fluorophore. Conformational change induced by ligand titration is thought to affect the fluorescence of the fluorophore, allowing detection of ligand binding. Fluorescence measurements show that our LTP variants have affinity to palmitate that is consistent with wild‐type LTP. These molecules have the potential to be utilized as scaffolds to design hydrophobic ligand biosensors or to serve as drug carriers.
The S2 subsites of cathepsins K and L and their contribution to collagen degradation
Authors: Lecaille Fabien , Chowdhury Shafinaz , Purisima Enrico , Brömme Dieter , Lalmanach Gilles 
Published: March 2007

AbstractThe exchange of residues 67 and 205 of the S2 pocket of human cysteine cathepsins K and L induces a permutation of their substrate specificity toward fluorogenic peptide substrates. While the cathepsin L‐like cathepsin K (Tyr67Leu/Leu205Ala) mutant has a marked preference for Phe, the Leu67Tyr/Ala205Leu cathepsin L variant shows an effective cathepsin K‐like preference for Leu and Pro. A similar turnaround of inhibition was observed by using specific inhibitors of cathepsin K [1‐(N‐Benzyloxycarbonyl‐leucyl)‐5‐(N‐Boc‐phenylalanyl‐leucyl)carbohydrazide] and cathepsin L [N‐(4‐biphenylacetyl)‐S‐methylcysteine‐(D)‐Arg‐Phe‐β‐phenethylamide]. Molecular modeling studies indicated that mutations alter the character of both S2 and S3 subsites, while docking calculations were consistent with kinetics data. The cathepsin K‐like cathepsin L was unable to mimic the collagen‐degrading activity of cathepsin K against collagens I and II, DQ‐collagens I and IV, and elastin‐Congo Red. In summary, double mutations of the S2 pocket of cathepsins K (Y67L/L205A) and L (L67Y/A205L) induce a switch of their enzymatic specificity toward small selective inhibitors and peptidyl substrates, confirming the key role of residues 67 and 205. However, mutations in the S2 subsite pocket of cathepsin L alone without engineering of binding sites to chondroitin sulfate are not sufficient to generate a cathepsin K‐like collagenase, emphasizing the pivotal role of the complex formation between glycosaminoglycans and cathepsin K for its unique collagenolytic activity.
Structure‐based mutagenesis of the substrate‐recognition domain of Nrdp1/FLRF identifies the binding site for the receptor tyrosine kinase ErbB3
Authors: Bouyain Samuel , Leahy Daniel J. 
Published: March 2007

AbstractThe E3 ubiquitin ligase neuregulin receptor degrading protein 1 (Nrdp1) mediates the ligand‐independent degradation of the epidermal growth factor receptor family member ErbB3/HER3. By regulating cellular levels of ErbB3, Nrdp1 influences ErbB3‐mediated signaling, which is essential for normal vertebrate development. Nrdp1 belongs to the tripartite or RBCC (RING, B‐box, coiled‐coil) family of ubiquitin ligases in which the RING domain is responsible for ubiquitin ligation and a variable C‐terminal region mediates substrate recognition. We report here the 1.95 Å crystal structure of the C‐terminal domain of Nrdp1 and show that this domain is sufficient to mediate ErbB3 binding. Furthermore, we have used site‐directed mutagenesis to map regions of the Nrdp1 surface that are important for interacting with ErbB3 and mediating its degradation in transfected cells. The ErbB3‐binding site localizes to a region of Nrdp1 that is conserved from invertebrates to vertebrates, in contrast to ErbB3, which is only found in vertebrates. This observation suggests that Nrdp1 uses a common binding site to recognize its targets in different species.