bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand‐induced structural changes of giant hemoglobins
Authors: Numoto Nobutaka , Nakagawa Taro , Kita Akiko , Sasayama Yuichi , Fukumori Yoshihiro , Miki Kunio 
Published: April 2008

AbstractRecent crystallographic studies have revealed the structures of some invertebrate extracellular giant hemoglobins of 3,600 kDa or 400 kDa and their common quaternary structure of dodecameric subassembly composed of four kinds of globin subunits (A1, A2, B1, and B2). These results have provided insight into the mechanisms of their unique functional properties of oxygen binding and sulfide binding. All of these structures were solved with oxygenated or CO‐liganded forms at low or moderate resolutions. We have determined the crystal structure of 400 kDa Hb from a polychaete Oligobrachia mashikoi at 1.95 Å resolution. The electron densities at higher resolution confirm the existence of an isoform of the B1 subunit because of the inconsistency with the model that was built from the formerly known amino acid sequence. The brownish color of the crystals used in this study and the absorption spectrum from the dissolved crystals strongly indicated that the obtained structure was a ferric met state, whereas completele absence of electron density around the distal heme pockets were observed at the A2, B1, and B2 subunits. We concluded that the obtained structure was in unliganded met forms at three of four globin subunits in the 24mer assembly and in oxygenated forms at the remaining A1 subunits. The partially unliganded structure showed remarkable structural changes at the AB loop regions causing quaternary rearrangements of the EF‐dimer structure. In contrast, few changes occurred at the interface regions composed of the E and F helices. These results suggest that the ligand‐induced structural changes of Oligobrachia Hb are quite different from those of the well‐studied mollusk Hb having the same EF‐dimer structure. The structural rearrangements make the dodecameric subassembliy form a tighter conformation than those of fully oxygenated or CO‐liganded dodecamer structure. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Comparative molecular dynamics simulations of histone deacetylase‐like protein: Binding modes and free energy analysis to hydroxamic acid inhibitors
Authors: Yan Chunli , Xiu Zhilong , Li Xiaohui , Li Shenmin , Hao Ce , Teng Hu 
Published: April 2008

AbstractHistone deacetylases (HDACs) play an important role in gene transcription, and inhibitors of HDACs can induce cell differentiation and suppress cell proliferation in tumor cells. Histone deacetylase1 (HDAC1) binds suberanilohydroxamic acid (SAHA) and 7‐phenyl‐2, 4, 6‐hepta‐trienoyl hydroxamic acid (CG‐1521) with moderately low affinity (ΔG = −8.6 and −7.8 kcal mol−1). The structurally related (E)‐2‐(3‐(3‐(hydroxyamino)‐3‐oxoprop‐1‐enyl)phenyl)‐N1,N3‐diphenylmalonamide (SK‐683), a Trichostatin A (TSA)‐like HDAC1 inhibitor, and TSA are bound to the HDAC1 with −12.3 and −10.3 kcal mol−1 of ΔG, higher binding free energies than SAHA and CG‐1521. Histone deacetylase‐like protein (HDLP), an HDAC homologue, shows a 35.2% sequence identity of HDLP and human HDAC1. Molecular dynamics simulation and the molecular mechanics/generalized‐Born surface area (MM‐GBSA) free energy calculations were applied to investigate the factors responsible for the relatively activity of these four inhibitors to HDLP. In addition, computational alanine scanning of the binding site residues was carried out to determine the contribution components from van der Waals, electrostatic interaction, nonpolar and polar energy of solvation as well as the effects of backbones and side‐chains with the MM‐GBSA method. MM‐GBSA methods reproduced the experimental relative affinities of the four inhibitors in good agreement (R2 = 0.996) between experimental and computed binding energies. The MM‐GBSA calculations showed that, the number of hydrogen bonds formed between the HDLP and inhibitors, which varied in the system studied, and electrostatic interactions determined the magnitude of the free energies for HDLP‐inhibitor interactions. The MM‐GBSA calculations revealed that the binding of HDLP to these four hydroxamic acid inhibitors is mainly driven by van der Waals/nonpolar interactions. This study can be a guide for the optimization of HDAC inhibitors and future design of new therapeutic agents for the treatment of cancer. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Exciton dynamics in blends of phosphorescent emitters
Authors: Schütz Christoph , Höfer Bianca , Jaiser Frank , Krueger Hartmut , Thesen Manuel , Janietz Silvia , Köhler Anna 
Published: April 2008

AbstractCascading energy transfer is a usually undesired effect in organic‐host guest systems that are designed for light‐emitting purposes. Here we demonstrate a chemical approach to suppressing undesired energy transfer from the blue to the red emitter in multicomponent polymer blends. We have combined a red, green and blue emitting Ir‐complex each with charge transporting molecules to a side‐chain copolymer. The covalent attachment of the phosphorescent emitter is found to prevent cascading energy transfer through steric shielding. This approach approximately doubles the efficiency and brightness of polymer light emitting diodes. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Characterization and quantitative analysis of surfactants in textile wastewater by liquid chromatography/quadrupole‐time‐of‐flight mass spectrometry
Authors: González Susana , Petrović Mira , Radetic Maja , Jovancic Petar , Ilic Vesna , Barceló Damià 
Published: April 2008

AbstractA method based on the application of ultra‐performance liquid chromatography (UPLC) coupled to hybrid quadrupole‐time‐of‐flight mass spectrometry (QqTOF‐MS) with an electrospray (ESI) interface has been developed for the screening and confirmation of several anionic and non‐ionic surfactants: linear alkylbenzenesulfonates (LAS), alkylsulfate (AS), alkylethersulfate (AES), dihexyl sulfosuccinate (DHSS), alcohol ethoxylates (AEOs), coconut diethanolamide (CDEA), nonylphenol ethoxylates (NPEOs), and their degradation products (nonylphenol carboxylate (NPEC), octylphenol carboxylate (OPEC), 4‐nonylphenol (NP), 4‐octylphenol (OP) and NPEO sulfate (NPEO‐SO4)). The developed methodology permits reliable quantification combined with a high accuracy confirmation based on the accurate mass of the (de)protonated molecules in the TOFMS mode. For further confirmation of the identity of the detected compounds the QqTOF mode was used. Accurate masses of product ions obtained by performing collision‐induced dissociation (CID) of the (de)protonated molecules of parent compounds were matched with the ions obtained for a standard solution. The method was applied for the quantitative analysis and high accuracy confirmation of surfactants in complex mixtures in effluents from the textile industry. Positive identification of the target compounds was based on accurate mass measurement of the base peak, at least one product ion and the LC retention time of the analyte compared with that of a standard. The most frequently surfactants found in these textile effluents were NPEO and NPEO‐SO4 in concentrations ranging from 0.93 to 5.68 mg/L for NPEO and 0.06 to 4.30 mg/L for NPEO‐SO4. AEOs were also identified. Copyright © 2008 John Wiley & Sons, Ltd.
Quantification of acetylcholine in microdialysate of subcutaneous tissue by hydrophilic interaction chromatography/tandem mass spectrometry
Authors: Fu Boqiang , Gao Xinyan , Zhang Shi Ping , Cai Zongwei , Shen Jincan 
Published: April 2008

AbstractIt has recently been suggested that acetylcholine plays an important role in the modulation of tissue inflammation. In order to further understand the newly discovered cholinergic anti‐inflammatory pathway, tracking the concentration changes of acetylcholine in tissue is required. This paper describes the development of a method coupling hydrophilic interaction chromatography with electrospray ionization tandem mass spectrometry (HILIC/ESI‐MS/MS) for the separation and quantification of acetylcholine in microdialysis samples of normal rats and of rats with local inflammation. The separation of acetylcholine from interferential endogenous compounds and inorganic cations was achieved with a zwitterionic stationary phase column using isocratic elution. Low‐energy collision‐induced dissociation tandem mass spectrometric (CID‐MS/MS) analysis was carried out in the positive ion mode using multiple reaction monitoring (MRM) of the following mass transitions: m/z 146 → 87 for acetylcholine and m/z 155 → 87 for the internal standard acetylcholine‐D9. The limit of detection for acetylcholine was found to be 0.075 fmol on‐column with a signal‐to‐noise ratio of 3:1. The lower limit of quantification was 0.25 fmol on‐column. The calibration curves obtained for acetylcholine in blank microdialysates were linear in the ranges of 0.025–50 nM and 0.025–0.5 nM, with correlation coefficients equal to or greater than 0.9994 and 0.9969, respectively. The recoveries of acetylcholine for high (2 nM) and low (0.5 nM) concentrations were in the ranges of 90–96% and 95–109%, respectively. The coefficients of variation for intra‐day and inter‐day reproducibility were equal to or less than 7.3% and 10.4%, respectively. The method has been successfully applied in the measurement of acetylcholine in microdialysates from normal and inflamed rat tissue. Copyright © 2008 John Wiley & Sons, Ltd.
A numerical model for roof detailing of cold‐formed purlin‐sheeting systems
Authors: Braham Marc , Ruggerini Antonio , Ubertini Francesco 
Published: April 2008

AbstractVarious methods are suggested in the available codes to design roof detailing in cold formed screwed‐down roof systems made of cold‐formed purlins covered with metal sheeting. The evaluation of the global anchorage force of the roof and the local forces in fasteners is pursued aiming at designing support detailing and purlin‐sheeting connection, respectively. Two factors, “R” and “r”, are here employed to synthetically describe the stabilization forces that are required at the supports and along the span. It is shown that these two factors are implicitly provided by some codes for steel structures, but they can be even directly calculated by a simplified finite element model of the whole roof system, here presented. A comparison with the other available approaches is carried out, revealing that the proposed model is an extremely useful tool both for the design and the verification of the structural elements. The described procedure for calculation is shown to be extremely general and easily adaptable to new roof systems, with structural details even not foreseen in the actual codes. For example it can be used to solve the lack of Eurocode 3, Part 1‐3, Chapter 10, because, as opposed to the assumption of Eurocode, elastic lateral support can here be envisaged, instead of full lateral support.
Design rules for lateral torsional buckling of channel sections subject to web loading
Authors: Snijder H.H. (Bert) , Hoenderkamp J.C.D. (Hans) , Bakker M.C.M. (Monique) , Steenbergen H.M.G.M. (Henri) , de Louw C.H.M. (Karin) 
Published: April 2008

AbstractChannel sections are widely used in practice as beams. However, design rules for eccentrically loaded (not through shear centre) beams with channel cross‐sections are not available in Eurocode 3. In this paper five proposed design rules are summarised, explained and their validity is checked by Finite Element analyses. The design rules yield ultimate loads that are compared to ultimate loads from geometrical and material nonlinear analyses of imperfect (GMNIA) beams with channel cross‐sections. A parameter study is performed by varying the dimensions of the cross‐section, the span length to section height ratio of the beams, the type of loading and the point of load application but is limited to load application through the web of the channels. Based on one of the proposed design rules, this study has led to a new design rule which conforms to Eurocode 3.
Verbundbauten für das neue Berlin
Authors: Aschinger Rainer , Rusch Andreas 
Published: April 2008

AbstractSeit der Wiedervereinigung ist Berlin zu einem Ort reger Bautätigkeit geworden. Standorte, die durch den Mauerbau eher ins Abseits gedrängt worden waren, sind nun wieder eine 1‐A‐Lage und wurden entsprechend hochwertig neu bebaut oder saniert. Dem Berliner Leitbild der Kritischen Rekonstruktion verpflichtet, zeigen die Gebäude oft nach außen nicht, welche großen Ingenieurbauwerke sich hinter den Fassaden verbergen. Im Folgenden soll an ausgewählten Beispielen die als Verbundtragwerk ausgeführte Konstruktion dahinter vorgestellt werden.
Teaching science as a language: A “content‐first” approach to science teaching
Authors: Brown Bryan A. , Ryoo Kihyun 
Published: April 2008

AbstractOur research project was guided by the assumption that students who learn to understand phenomena in everyday terms prior to being taught scientific language will develop improved understanding of new concepts. We used web‐based software to teach students using a “content‐first” approach that allowed students to transition from everyday understanding of phenomena to the use of scientific language. This study involved 49 minority students who were randomly assigned into two groups for analysis: a treatment group (taught with everyday language prior to using scientific language) and a control group (taught with scientific language). Using a pre–post‐test control group design, we assessed students' conceptual and linguistic understanding of photosynthesis. The results of this study indicated that students taught with the “content‐first” approach developed significantly improved understanding when compared to students taught in traditional ways. © 2008 Wiley Periodicals, Inc. J Res Sci Teach 45: 529–553, 2008
Effects of habitat configuration on host–parasitoid food web structure
Authors: Murakami Masashi , Hirao Toshihide , Kasei Akiko 
Published: April 2008

AbstractThe dispersal of organisms among patches affects community structure in spatially heterogeneous habitats. The enhancement of dispersal frequency among patches can be expected to increase potential interaction between organisms in food webs. However, it has been difficult to fairly evaluate the effects of dispersal on the food web structure because the quantification of actual dispersal is difficult. In this study, in order to manipulate the dispersal frequency, two oak plantations (each with 100 oak trees) were established as high‐patch connectivity (1‐m interval) and low‐patch connectivity (3‐m interval) plots. Quantitative food webs of herbivores and their parasitoids were constructed for the high‐ and low‐connectivity plots, and quantitative measures of food web metrics as indices of structure were calculated for both webs to examine dispersal effects on food web complexity. In the entire web, 86 herbivore species (Lepidoptera and Coleoptera) were attacked by 50 parasitoid species (Hymenoptera and Diptera). As a result, although we found no significant difference in herbivore abundance between high‐ and low‐connectivity plots, a higher parasitism rate and greater complexity in web structure were observed in many food web metrics for the high‐connectivity plot. Furthermore, the parasitoid overlap diagram showed a higher potential for indirect interactions among herbivore species in the high‐connectivity plot. These results imply that the increase in dispersal frequency among habitat patches facilitates food web complexity, and the role of dispersal as a determinant of food web structure should be considered in food web ecology.
The effect of pharmacological stress on intraventricular dyssynchrony in left ventricular systolic dysfunction
Authors: Chattopadhyay Sudipta , Alamgir Mohammed F. , Nikitin Nikolay P. , Fraser Alan G. , Clark Andrew L. , Cleland John G.F. 
Published: April 2008

AbstractBackground:Cardiac resynchronisation therapy (CRT) improves symptoms and exercise capacity in many patients with heart failure (HF) who have left ventricular systolic dysfunction (LVSD) and markers of dyssynchrony. LV dyssynchrony is conventionally measured at rest but the symptoms of heart failure occur predominantly on exercise. Induction or exacerbation of dyssynchrony during stress might identify additional patients who could benefit from CRT.Methods and results:Seventy‐seven patients (47 with QRSd<120 ms and 30 with QRSd>120 ms) with heart failure due to left ventricular systolic dysfunction and 22 normal subjects underwent dobutamine stress echocardiography using colour tissue Doppler imaging. Left intraventricular dyssynchrony was measured as the standard deviation of the time to peak velocity from the onset of the QRS (Ts‐SD) and the difference between the maximum and minimum time to peak velocity (Tscor‐diff) in the 12 non‐apical segments at rest and during peak stress. Timings were corrected for heart rate. The mean values of these indices increased with stress in both groups of patients but not in control subjects (p < 0.001). The prevalence of conventionally‐defined dyssynchrony also increased with stress.Conclusion:In patients with heart failure, the severity and the prevalence of intraventricular dyssynchrony increase with stress. Whether stress‐induced dyssynchrony will identify patients who might benefit from CRT awaits further research.
Rapeseed protein inhibits the initiation of insulin resistance by a high-saturated fat, high-sucrose diet in rats
Authors: Mariotti François , Hermier Dominique , Sarrat Charlotte , Magné Joëlle , Fénart Evelyne , Evrard Jacques , Tomé Daniel , Huneau Jean François 
Published: April 2008

In contrast to the quality of carbohydrates and lipids, little is known on the influence of the type of dietary protein on the development of the metabolic or insulin resistance syndrome. Cysteine intake has been recently documented to impact insulin sensitivity. The aim of this study was to determine whether rapeseed protein, an emergent cysteine-rich protein, could inhibit the onset of the metabolic syndrome. For 9 weeks, rats were fed a diet rich in saturated fats and sucrose, which also included 20 % protein either as milk protein (‘Induction’ diet I) or rapeseed protein (diet R). A third, control group received an isoenergetic diet containing milk protein but polyunsaturated fats and starch (‘Prudent’ diet P). Plasma glucose, insulin, TAG and cholesterol, and blood pressure were monitored during the study, glucose tolerance was tested at week 7 and body composition determined at week 9. Plasma glucose, insulin and TAG increased during the experiment and, at week 9, plasma insulin was significantly 34 % lower in the R group and 56 % lower in P group as compared with the I group. The insulin peak after the glucose load was significantly 28–30 % lower in R and P than in I and the insulin sensitivity index was significantly higher in R than in I. Unexpectedly, peripheral fat deposition was slightly higher in R than in I. In this model, substituting rapeseed protein for milk protein had preventive effects on the early onset of insulin resistance, similar to those achieved by manipulating the types of dietary fat and carbohydrates.
The effect of Anonchocephalus chilensis Riggenbach (Eucestoda: Bothriocephalidea) on infracommunity patterns in Genypterus maculatus Tschudi (Osteichthyes: Ophidiidae)
Authors: Muñoz S.A. , George-Nascimento M. 
Published: April 2008

AbstractThe use of parasite body size (i.e. body mass) is a promising proxy to improve the study of patterns in parasite infracommunities, which are usually analysed using only numerical descriptors. This study deals with the importance and effect of the presence of a large endoparasite species, the cestode Anonchocephalus chilensis in a marine fish species, Genypterus maculatus, on the structure of the parasite infracommunities. Numerical and volumetric measures of aggregated properties of parasite infracommunities were compared and their correlation examined. The highly dominant presence of A. chilensis by volume causes a dramatic change in the patterns observed, including a smaller total volume of the remaining species when this volumetrically dominant species is present. However, C-scores and V-ratios, both indices based on null models of species occurrence, do not support the idea of communities structured by interspecific competition. Analyses reveal that numerical and volumetric community descriptors are complementary ways to search for patterns and to reveal processes within these systems.
Host specificity is linked to intraspecific variability in the genusLamellodiscus(Monogenea)
Authors: KACI-CHAOUCH T. , VERNEAU O. , DESDEVISES Y. 
Published: April 2008

SUMMARYWe investigated whether host specificity is linked to variability within species ofLamellodiscusmonogeneans, which are gill ectoparasites of the Sparidae. We sampled fish parasites in the northeastern part of the Mediterranean Sea: 4 specialist species, using 1 single host species, and 3 generalist species, using 2 distinct host species. Intraspecific variability was assessed from 2 different datasets. Morphometric variability of the attachment organ, called the haptor, was estimated first from measurements of several sclerified haptoral parts on 102 individuals. Genetic variability was calculated based on comparisons of sequences derived from the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA of 62 individuals. Morphometric variances in the specialistversusgeneralist species were comparedviaprincipal component analysis andF-tests, and uncorrected genetic distances (p-distances) were estimated within each species. We showed that the inter-individual variance of morphometric characters, as well as p-distances, are clearly greater within generalist species than specialist ones. These findings suggest that a relative increase in morphological and molecular variability enhances the possibility to colonize new host species in monogeneans, and supports the hypothesis that intraspecific variability could be a potential determinant of host specificity.
Imitation as a conjunction
Authors: Heyes Cecilia 
Published: April 2008

AbstractThe conjunctive conception takes imitation to be a combination of observational learning and copying. In the target article, and elsewhere, this conception generates problems in (1) explaining the copying of intransitive actions, (2) elucidating the potential functions of imitation, and (3) recognising when the correspondence problem has been avoided rather than solved. Hurley's careful use of subpersonal and personal levels of explanation shows us how to tackle these and other questions about imitation.
Flexibility and development of mirroring mechanisms
Authors: Longo Matthew R. , Bertenthal Bennett I. 
Published: April 2008

AbstractThe empirical support for the shared circuits model (SCM) is mixed. We review recent results from our own lab and others supporting a central claim of SCM that mirroring occurs at multiple levels of representation. By contrast, the model is silent as to why human infants are capable of showing imitative behaviours mediated by a mirror system. This limitation is a problem with formal models that address neither the neural correlates nor the behavioural evidence directly.
Failure, instead of inhibition, should be monitored for the distinction of self/other and actual/possible actions
Authors: Makino Takaki 
Published: April 2008

AbstractI suggest that layer 4 of the shared circuits model (SCM) should monitor the failure of performing an action, instead of output inhibition, to obtain actual/possible and self/other distinctions. The target article's assumption of selective inhibition leaves some questions unanswered, such as the criteria for the selection. Monitoring failure can answer these questions because failure does not require selection. It also provides a basis for more likely explanation for the phylogenetic and ontogenetic origin of both monitoring and output inhibition.