bluuebunny/crossref_metadata_2025_split huggingface dataset:
Backbone Amide Linker Strategy for the Synthesis of 1,4‐Triazole‐Containing Cyclic Tetra‐ and Pentapeptides
Authors: Springer Jasper , de Cuba Kimberly R. , Calvet‐Vitale Sandrine , Geenevasen Jan A. J. , Hermkens Pedro H. H. , Hiemstra Henk , van Maarseveen Jan H. 
Published: April 2008

AbstractA backbone amide linker strategy was chosen for the solid‐phase synthesis of triazole‐containing cyclic tetra‐ and pentapeptides. An alkyne‐substituted linker derived from 4‐hydroxy‐2‐methoxybenzaldehyde was elongated by using standard “Fmoc‐based” solid phase chemistry and terminated by coupling of an azido acid. In solution, the peptides were cyclized by a CuI‐catalyzed azide‐alkyne cycloaddition reaction. The solid‐supported synthesized linear peptides had to be cleaved prior to cyclization. As an example of cyclic tetrapeptides, a triazole analog of cyclo‐[Pro‐Val‐Pro‐Tyr] (2) was prepared by the solid‐phase/solution‐phase method. For the cyclic pentapeptides, segetalin B (3) was chosen as a model compound to show the applicability of this method.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
A distributed shear and flexural flexibility model with shear–flexure interaction for R/C members subjected to seismic loading
Authors: Mergos P. E. , Kappos A. J. 
Published: April 2008

AbstractA beam–column‐type finite element for seismic assessment of reinforced concrete (R/C) frame structures is presented. This finite element consists of two interacting, distributed flexibility sub‐elements representing inelastic flexural and shear response. Following this formulation, the proposed model is able to capture spread of flexural yielding, as well as spread of shear cracking, in R/C members. The model accounts for shear strength degradation with inelastic curvature demand, as well as coupling between inelastic flexural and shear deformations after flexural yielding, observed in many experimental studies. An empirical relationship is proposed for evaluating the average shear distortion of R/C columns at the onset of stirrup yielding. The proposed numerical model is validated against experimental results involving R/C columns subjected to cyclic loading. It is shown that the model can predict well the hysteretic response of R/C columns with different failure modes, i.e. flexure‐critical elements, elements failing in shear after flexural yielding, and shear‐critical R/C members. Copyright © 2008 John Wiley & Sons, Ltd.
Gold‐silver and silver‐silver nanoparticle constructs based on DNA hybridization of thiol‐ and amino‐functionalized oligonucleotides
Authors: Steinbrück A. , Csaki A. , Ritter K. , Leich M. , Köhler J. M. , Fritzsche W. 
Published: April 2008

AbstractMetal nanoparticle constructs of particles of different sizes and materials were prepared, using DNA as connecting element. Therefore, gold and silver nanoparticles were functionalized with complementary DNA sequences that enabled a controlled coupling. The well‐established system based on thiolated DNA was thereby complemented with amino‐functionalized DNA. The realization of specific DNA‐DNA bonds due to hybridization was controlled by the ionic strength. The results demonstrate the potential of the combination of different particle sizes, composition as well as coupling chemistry in order to realize controlled conjugates of nanoparticles. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Where shall we meet? A role for genome organisation and nuclear sub‐compartments in mediating interchromosomal interactions
Authors: Osborne Cameron S. , Eskiw Christopher H. 
Published: April 2008

AbstractA recent spate of examples of specific interactions between loci on separate chromosomes in mammalian nuclei has illuminated another layer of complexity in gene regulation. As the specifics of the cross‐talk between interacting loci are worked out, it is also important to consider exactly how, when and where loci can ever reliably find each other within such an intricate environment. Answers may lie in how the genome is organised in relation to itself and to specialised nuclear sub‐compartments. Here, we discuss how such specialised nuclear bodies may have the potential to specifically sequester loci and provide a context where interchromosomal communications can occur. J. Cell. Biochem. 104: 1553–1561, 2008. © 2008 Wiley‐Liss, Inc.
Associative versus dissociative binding of CO to 4d transition metal trimers: A density functional study
Authors: Addicoat Matthew A. , Buntine Mark A. , Yates Brian , Metha Gregory F. 
Published: April 2008

AbstractDensity functional calculations were performed to determine equilibrium geometrical structures, transition states and relative energies for M3 clusters (M = Nb, Mo, Tc, Ru, Rh, Pd, Ag) reacting with CO, leading to proposed reaction pathways. For the Nb3, Mo3, and Tc3 clusters, the lowest energy structure correlates to dissociated CO, with the C and O atoms bound on opposite sides of the metal triangle. For all other trimers, the lowest energy structures maintain the CO moiety. In the case of Pd3 and Ag3 the dissociated geometries lie higher in energy than the sum of the separated reactants. In most cases, several multiplicities were found to be similar in energy and for Mo3CO and Pd3CO singlet‐triplet minimum energy crossing points were identified. In the case of Rh3CO, minimum energy crossing points for the doublet, quartet, and sextet reaction pathways were determined and compared. The electron densities of pertinent M3CO species were investigated using Natural Bond Order calculations. It was found that the effect of the metal trimer on the energy of the pure p‐type π* antibonding orbital of carbon monoxide directly correlates with the occurrence of CO dissociation. © 2008 Wiley Periodicals, Inc.J Comput Chem, 2008.
Inflammatory responses of endothelial cells experiencing reduction in flow after conditioning by shear stress
Authors: Matharu Nick M. , McGettrick Helen M. , Salmon Mike , Kissane Steve , Vohra Rajiv K. , Rainger G.Ed. , Nash Gerard B. 
Published: April 2008

AbstractExposure of endothelial cells (EC) to shear stress reduces their response to tumour necrosis factor‐α (TNF). We tested how shear‐conditioned EC responded to reduction in flow, either by spontaneously binding leukocytes, or by increasing sensitivity to TNF. Human umbilical vein EC were exposed to shear stress of 2.0 Pa (20 dyn/cm2) for 24 h. Shear was then reduced to stasis (30 sec perfusion each hour to exchange medium) or 0.003 Pa (creeping flow). At chosen times, neutrophils were perfused over the EC at 0.1 Pa (effective reperfusion). EC developed an ability to capture flowing neutrophils that lasted from 1 to 3 h after flow reduction, which was reduced by antibody against P‐selectin or pre‐treatment of EC with an inhibitor of NADPH‐oxidase. Adhesion of neutrophils to TNF‐treated EC was greatly suppressed by shear‐conditioning, remained suppressed immediately after cessation of flow and then took 48 h to approach the level in static cultures. Interestingly, the response to TNF remained suppressed in cultures switched to creeping flow. Gene array analysis confirmed that differently recovered cells had separate phenotypes. Thus, an acute response of EC to reduction in shear may contribute to leukocyte recruitment, along with hypoxia, in ischaemia and reperfusion. Prolonged cessation of flow may increase the sensitivity of EC to inflammatory stimuli, but this effect may be suppressed by residual flow. J. Cell. Physiol. 216: 732–741, 2008, © 2008 Wiley‐Liss, Inc.
Solubilization at high pH results in improved recovery of proteins from inclusion bodies of E. coli
Authors: Singh Surinder M. , Upadhyay Arun K. , Panda Amulya K. 
Published: April 2008

AbstractBACKGROUND: Solubilization of inclusion bodies using high concentration of chaotropes followed by suboptimal refolding results in lower recovery of bioactive proteins from E. coli. Growing evidence indicates that aggregation of expressed proteins into inclusion bodies is molecular specific in nature and proteins in inclusion bodies have native‐like secondary structure. Protecting these pre‐existing native‐like secondary structures of proteins using mild solubilization conditions is one of the key steps in improved recovery of bioactive protein from inclusion bodies of E. coli.RESULTS: Inclusion bodies of seven proteins (hGH, oGH, Pyk, PKS, aldolase, enolase and superoxide dismutase) were solubilized at pH 12 in the presence of 2 mol L−1 urea and were subsequently refolded and purified. Enrichment of inclusion bodies after cell lysis, mild solubilization at alkaline pH and pulsatile refolding resulted in lower aggregation of protein during refolding and improved the final recovery of protein from inclusion bodies of E. coli. The efficiency of protein recovery from inclusion bodies was 30–40% for most of the proteins. This was almost two times higher than that achieved when inclusion bodies were solubilized in 8 mol L−1 urea and subsequently refolded. Purified hGH and Pyk were functionally active in respective in vitro assays.CONCLUSION: Non‐denaturing solubilization of inclusion body proteins at alkaline pH is a viable alternative to the use of high molar concentration chaotropes for efficient recovery of inclusion body proteins. Mild solubilization and pulsatile refolding contribute synergistically to reduce the extent of aggregation during refolding and result in high throughput recovery of bioactive proteins from inclusion bodies of E. coli. Copyright © 2008 Society of Chemical Industry
Nondestructive optical determination of fiber organization in intact myocardial wall
Authors: Smith Rebecca M. , Matiukas Arvydas , Zemlin Christian W. , Pertsov Arkady M. 
Published: April 2008

AbstractMapping the myocardial fiber organization is important for assessing the electrical and mechanical properties of normal and diseased hearts. Current methods to determine the fiber organization have several limitations: histological sectioning mechanically distorts the tissue and is labor‐intensive, while diffusion tensor imaging has low spatial resolution and requires expensive MRI scanners. Here, we utilized optical clearing, a fluorescent dye, and confocal microscopy to create three‐dimensional reconstructions of the myocardial fiber organization of guinea pig and mouse hearts. We have optimized the staining and clearing procedure to allow for the nondestructive imaging of whole hearts with a thickness up to 3.5 mm. Myocardial fibers could clearly be identified at all depths in all preparations. We determined the change of fiber orientation across strips of guinea pig left ventricular wall. Our study confirms the qualitative result that there is a steady counterclockwise fiber rotation across the ventricular wall. Quantitatively, we found a total fiber rotation of 105.7 ± 14.9° (mean ± standard error of the mean); this value lies within the range reported by previous studies. These results show that optical clearing, in combination with a fluorescent dye and confocal microscopy, is a practical and accurate method for determining myocardial fiber organization. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
AFM characterization of rabbit spermatozoa
Authors: Ierardi Vincenzo , Niccolini Alberto , Alderighi Michele , Gazzano Angelo , Martelli Franco , Solaro Roberto 
Published: April 2008

AbstractAtomic force microscopy (AFM) has been applied for determining the topological and structural features of rabbit spermatozoa. Fresh ejaculated spermatozoa were adsorbed passively onto a silicon slide or by motility from suspension onto a poly(L‐lysine)‐coated glass coverslip and then imaged in air and in buffer saline, respectively. AFM images clearly highlighted many details of spermatozoa head, neck, and tail. Distinct features were observed in the plasmatic membrane of spermatozoa. In particular, head topography easily recognized the acrosome, equatorial segment, equatorial subsegment, and postacrosome regions. Moreover, AFM images revealed the presence of double belt of invaginations around the spermatozoa head, at the boundary between equatorial subsegment and postacrosome regions. All together, the collected AFM images clearly defined a detailed map of spermatozoa morphology while giving some hints on the internal structure. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
Angiofil®‐mediated visualization of the vascular system by microcomputed tomography: A feasibility study
Authors: Grabherr Silke , Hess Andreas , Karolczak Marek , Thali Michael J. , Friess Sebastian D. , Kalender Willi A. , Dirnhofer Richard , Djonov Valentin 
Published: April 2008

AbstractVisualization of the vascular systems of organs or of small animals is important for an assessment of basic physiological conditions, especially in studies that involve genetically manipulated mice. For a detailed morphological analysis of the vascular tree, it is necessary to demonstrate the system in its entirety. In this study, we present a new lipophilic contrast agent, Angiofil®, for performing postmortem microangiography by using microcomputed tomography. The new contrast agent was tested in 10 wild‐type mice. Imaging of the vascular system revealed vessels down to the caliber of capillaries, and the digital three‐dimensional data obtained from the scans allowed for virtual cutting, amplification, and scaling without destroying the sample. By use of computer software, parameters such as vessel length and caliber could be quantified and remapped by color coding onto the surface of the vascular system. The liquid Angiofil® is easy to handle and highly radio‐opaque. Because of its lipophilic abilities, it is retained intravascularly, hence it facilitates virtual vessel segmentation, and yields an enduring signal which is advantageous during repetitive investigations, or if samples need to be transported from the site of preparation to the place of actual analysis, respectively. These characteristics make Angiofil® a promising novel contrast agent; when combined with microcomputed tomography, it has the potential to turn into a powerful method for rapid vascular phenotyping. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
Spatial heterogeneity of soil properties and its mapping with apparent electrical conductivity
Authors: Michael Mertens Franz , Pätzold Stefan , Welp Gerhard 
Published: April 2008

AbstractThe site‐specific cultivation as part of the precision‐agriculture concept is more and more introduced into practical farming. However, soil information is often not available in a spatial resolution intrinsically needed for precision farming or other site‐specific soil use and management purposes. One approach to obtain spatially high‐resolution soil data is the non‐invasive measurement of the apparent electrical conductivity (ECa). In this study, we recorded the ECa on three fields with an EM38 (Geonics, Canada). The ECa data were compared with (1) ground truth data obtained by conventional drilling, (2) traditional soil maps (large scale, ≤1:5,000), (3) the growth and yield of corn. The temporal variability of the ECa due to varying soil moisture and temperature was taken into account by repeated measurements of the same fields and subsequent averaging of the ECa values. Significant correlations (r² = 0.76) were found between the mean weighted clay content (0–1.5 m) and the ECa. Furthermore, in soils with differently textured layers, ECa was used to estimate the thickness of the uppermost loess layer. A comparison of ECa and large‐scale soil maps reveals some pros and cons of ECa measurements. The main advantages of ECa recordings are the high spatial resolution in combination with low efforts. Yet, the ECa signal is no direct measure for a soil type or unit. Depending on the variability of substrates and layering, the ECa pattern can be a precise indicator for the spatial distribution of different soils. A strong conformity of the spatial variability of plant growth (derived from orthophotos and yield maps) and ECa patterns within a field indicates that the ECa signal per se—without conversion to traditional soil parameters—integrates the effects of various soil variables that govern soil fertility. Altogether, ECa surveys can be a powerful tool to facilitate and improve conventional soil mapping.
Soil properties and tree growth along an altitudinal transect in Ecuadorian tropical montane forest
Authors: Wilcke Wolfgang , Oelmann Yvonne , Schmitt Andrea , Valarezo Carlos , Zech Wolfgang , Homeier Jürgen 
Published: April 2008

AbstractIn tropical montane forests, soil properties change with increasing altitude, and tree‐growth decreases. In a tropical montane forest in Ecuador, we determined soil and tree properties along an altitudinal transect between 1960 and 2450 m asl. In different vegetation units, all horizons of three replicate profiles at each of eight sites were sampled and height, basal area, and diameter growth of trees were recorded. We determined pH and total concentrations of Al, C, Ca, K, Mg, Mn, N, Na, P, S, Zn, polyphenols, and lignin in all soil horizons and in the mineral soil additionally the effective cation‐exchange capacity (CEC). The soils were Cambisols, Planosols, and Histosols. The concentrations of Mg, Mn, N, P, and S in the O horizons and of Al, C, and all nutrients except Ca in the A horizons correlated significantly negatively with altitude. The C : N, C : P, and C : S ratios increased, and the lignin concentrations decreased in O and A horizons with increasing altitude. Forest stature, tree basal area, and tree growth decreased with altitude. An ANOVA analysis indicated that macronutrients (e.g., N, P, Ca) and micronutrients (e.g., Mn) in the O layer and in the soil mineral A horizon were correlated with tree growth. Furthermore, lignin concentrations in the O layer and the C : N ratio in soil affected tree growth. These effects were consistent, even if the effect of altitude was accounted for in a hierarchical statistical model. This suggests a contribution of nutrient deficiencies to reduced tree growth possibly caused by reduced organic‐matter turnover at higher altitudes.
Nitrous oxide emissions and dynamics of soil nitrogen under 15N‐labeled cow urine and dung patches on a sandy grassland soil
Authors: Wachendorf Christine , Lampe Carola , Taube Friedhelm , Dittert Klaus 
Published: April 2008

AbstractGrazing animals highly influence the nutrient cycle by a direct return of 80% of the consumed N in form of dung and urine. In the autumn‐winter period, N uptake by the sward is low and rates of seepage water in sandy soils are high, hence high mineral‐N contents in soil and in seepage water as well as large losses of N2O are expected after cattle grazing in autumn. The objective of this study was the quanitfication of N loss deriving from urine and dung leaching and by N2O emission. Therefore the deposition of urine and dung patches was simulated in maximum rates excreted by cows by application of 15N‐labeled cow urine and dung (equivalent to 1030 kg N ha–1 and 1052 kg N ha–1, respectively) on a sandy pasture soil in N Germany. Leachate was collected in weekly intervals from free‐draining lysimeters, and 15N‐NO$ _3^- $, 15N‐NH$ _4^+ $, and 15N‐DON (dissolved organic N) were monitored over 171 d. Furthermore, the 15N‐N2O emission rates and the dynamics of inorganic 15N in the upper soil layer were monitored in a field trial, adjacent to the lysimeters. After 10 d following the urine application, the urea was completely hydrolyzed, shown by a 100% recovery of urine‐N in the soil NH$ _4^+ $. The following decrease of 15N‐NH$ _4^+ $ in the soil was higher than the increase of 15N‐NO$ _3^- $, and some N loss was explained by leaching. Amounts of 51% and 2.5% of the applied 15N were found in leachate as inorganic N, 2.4% and 0.7% as DON derived from urine and dung, respectively. Release of N2O from urine and dung patches applied to the pasture was low, with losses of 0.05% and 0.33% of the applied 15N, respectively. Overall loss of dung‐derived N was very low, but as the bulk dung N remained in the soil, N loss after mineralization of the dung needs to be investigated.
Classification schemes for the acidity, base saturation, and acidification status of forest soils in Switzerland
Authors: Blaser Peter , Walthert Lorenz , Zimmermann Stephan , Graf Pannatier Elisabeth , Luster Jörg 
Published: April 2008

AbstractSoil chemical parameters related to soil acidity were determined for 1450 soil samples taken from individual mineral soil horizons in 257 forest soils in Switzerland, 196 developed from carbonate‐containing and 61 from carbonate‐free parent material. The distribution of pH values and exchangeable base cations in corresponding pH ranges were related to the capacity and rate of buffer reactions in the soil. Based on this, five acidity classes for individual soil samples were defined.To describe and classify the status of soil acidity and base saturation (BS) of an entire soil body, the pH and the BS of the total fine earth in the soil were calculated from the pH and BS, respectively, of the individual soil horizons and the estimated volumetric content of fine earth.The status of soil acidification of soil profiles was assessed primarily using the total amount of exchangeable acidic cations in percent of the CEC of the fine earth in the entire soil profile. As a second factor, the gradient between the acidity class of the most acidic soil horizon and the estimated acidity class at the beginning of soil formation was used. The application of these classification schemes to our collection of soil profiles revealed the great influence played by the type of parent material. The acidification status of most soils on carbonate‐containing parent material was classified as very weak to weak, whereas soils on carbonate‐free parent material were found to be strongly to very strongly acidified.In terms of parent rock material, microclimate, and natural vegetation, the results of this study and the proposed classification schemes can be considered appropriate for large parts of Europe.
Do water regimes affect iron‐plaque formation and microbial communities in the rhizosphere of paddy rice?
Authors: Chen Xue‐Ping , Kong Wei‐Dong , He Ji‐Zheng , Liu Wen‐Ju , Smith Sally E. , Smith F. Andrew , Zhu Yong‐Guan 
Published: April 2008

AbstractPot experiments were conducted to investigate the effect of soil water regimes on the formation of iron (Fe) plaque on the root surface of rice seedlings (Oryza sativa L.) and on the microbial functional diversity in a paddy soil. The rice seedlings were subjected to three moisture regimes (submergence, 100%, and 60% water‐holding capacity [WHC]), and were grown for 5 and 11 weeks. Aerobic lithotrophic Fe(II)‐oxidizing (FeOB) and acetate‐utilizing Fe(III)‐reducing bacteria (FeRB) in the rhizosphere and non‐rhizosphere soil were determined at 5 weeks using the most probable number (MPN) method. The carbon substrate use patterns of the microbial communities in the rhizosphere and non‐rhizosphere soil samples were determined at 11 weeks using Biolog‐GN2 plates. The amount of Fe plaque (per unit dry root weight) was much higher under submerged conditions than at lower soil moisture contents and decreased with plant age. There was a positive correlation between the amount of Fe plaque and phosphorus accumulated in the Fe plaque at both sampling times (r = 0.98 and 0.92, respectively, n = 12). Numbers of FeOB and FeRB in the submerged soil were lower than in aerobic soil, but by two orders of magnitude higher in the rhizosphere than in the bulk soil. On the other hand, the functional diversity of the rhizosphere microbial communities was much higher than that of the non‐rhizosphere soil, irrespective of soil water regimes. We conclude that soil flooding results in a decreased number and diversity of Fe‐oxidizing/reducing bacteria, while increasing the Fe‐plaque formation.