bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytometry of raft and caveola membrane microdomains: From flow and imaging techniques to high throughput screening assays
Authors: Kiss Endre , Nagy Péter , Balogh Andrea , Szöllősi János , Matkó János
Published: May 2008

The evolutionarily developed microdomain structure of biological membranes has gained more and more attention in the past decade. The caveolin‐free “membrane rafts,” the caveolin‐expressing rafts (caveolae), as well as other membrane microdomains seem to play an essential role in controlling and coordinating cell‐surface molecular recognition, internalization/endocytosis of the bound molecules or pathogenic organisms and in regulation of transmembrane signal transduction processes. Therefore, in many research fields (e.g. neurobiology and immunology), there is an ongoing need to understand the nature of these microdomains and to quantitatively characterize their lipid and protein composition under various physiological and pathological conditions. Flow and image cytometry offer many sophisticated and routine tools to study these questions. In this review, we give an overview of the past efforts to detect and characterize these membrane microdomains by the use of classical cytometric technologies, and finally we will discuss the results and perspectives of a new line of raft cytometry, the “high throughput screening assays of membrane microdomains,” based on “lipidomic” and “proteomic” approaches. © 2008 International Society for Advancement of Cytometry
Timing and prediction of relapse in a transdiagnostic eating disorder sample
Authors: McFarlane Traci , Olmsted Marion P. , Trottier Kathryn
Published: May 2008

Objective:

To identify factors that predict relapse in eating disorders to direct the development of effective relapse prevention interventions.

Method:

Fifty‐eight participants who had partially remitted from their eating disorder after intensive treatment were prospectively followed for up to 24 months. A transdiagnostic sample was included based on current recommendations.

Results:

The 12‐month survival rate was 0.59, indicating that 41% of the sample had relapsed at this time, and four factors emerged as significant predictors of relapse. These factors included more severe pretreatment caloric restriction, higher residual symptoms at discharge, slower response to treatment, and higher weight‐related self‐evaluation.

Conclusion:

Clinical recommendations based on these data include encouraging clients to adopt the recommended behavioral changes immediately at the beginning of treatment, and to make complete symptom control a priority. In addition, addressing weight‐related self‐evaluation and teaching clients to detach from this schema that connects weight/shape with self‐esteem may be an effective and feasible step toward relapse prevention. © 2008 by Wiley Periodicals, Inc. Int J Eat Disord 2008
Periodic local MP2 method for the study of electronic correlation in crystals: Theory and preliminary applications
Authors: Pisani Cesare , Maschio Lorenzo , Casassa Silvia , Halo Migen , Schütz Martin , Usvyat Denis
Published: May 2008

A computational technique for solving the MP2 equations for periodic systems using a local‐correlation approach and implemented in the CRYSCOR code is presented. The Hartree‐Fock solution provided by the CRYSTAL program is used as a reference. The motivations for the implementation of the new code are discussed, and the techniques adopted are briefly recalled. With respect to the original formulation (Pisani et al., J Chem Phys 2005, 122, 094113), many new features have been introduced in CRYSCOR to improve its efficiency and robustness. In particular, an adaptation of the density fitting scheme to translationally periodic systems is described, based on Fourier transformation techniques. Three examples of application are provided, concerning the CO2 crystal, proton transfer in ice XI, and the adsorption of methane on MgO (001). The results obtained with the periodic LMP2 method for these systems appear more reliable than the ones obtained using density functional theory. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Roles of cations, electronegativity difference, and anionic interlayer interactions in the metallic versus nonmetallic character of Zintl phases related to arsenic
Authors: Alemany Pere , Llunell Miquel , Canadell Enric
Published: May 2008

A first‐principles Density Functional Theory study of several layered solids structurally related to rhombohedral arsenic has been carried out. The electronic structures of rhombohedral arsenic, CaSi2, CaAl2Si2, KSnSb, and SrSn2As2 are discussed in detail, emphasizing on the origins of their metallic or nonmetallic behaviours. It is found that all of these systems are metallic except KSnSb. Electronegativity differences between the elements in the anionic sublattice and/or direct interlayer interactions play the main role in controlling the conductivity behavior. CaSi2 exhibits a peculiar feature since the cation directly influences the conductivity but is not essential for its appearance. Cation‐anion interactions are shown to have an important covalent contribution, but despite this fact and the metallic character found for most of these phases, the Zintl approach still provides a valid approximation to their electronic structure. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Photoionization cross sections of H and H2 with complex Gaussian‐type basis functions optimized for the frequency‐dependent polarizabilities
Authors: Morita Masato , Yabushita Satoshi
Published: May 2008

Within the framework of the complex basis function method, the photoionization cross sections of H and H2 were calculated based on the variational principle for the frequency‐dependent polarizabilities. In these calculations, complex orbital exponents of Gaussian‐type basis functions for the final state continuum wavefunctions were fully optimized for each photon energy with the numerical Newton‐Raphson method. In most cases, the use of only one or two complex Gaussian‐type basis functions was enough to obtain excellent agreement with previous high precision calculations and available experimental results. However, there were a few cases, in which the use of complex basis functions having various angular momentum quantum numbers was crucial to obtain the accurate results. The behavior of the complex orbital exponents as a function of photon energy was discussed in relation to the scaling relation and the effective charge for photoelectron. The success of this method implies the effectiveness of the optimization of orbital exponents to reduce the number of basis functions and shows the possibility to calculate photoionization cross sections of general molecules using only Gaussian‐type basis functions. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Re‐examination of structure optimization of off‐lattice protein AB models by conformational space annealing
Authors: Lee Jinwoo , Joo Keehyoung , Kim Seung‐Yeon , Lee Jooyoung
Published: May 2008

The global structural optimization is carried out for off‐lattice protein AB models in two and three dimensions by conformational space annealing. The models consist of hydrophobic and hydrophilic monomers in Fibonacci sequences. To accelerate the convergence, we have introduced a shift operator in the internal coordinate system, and effectively reduced the search space by forming a quotient space. With this, we significantly improve our previous results on AB models, and provide new low energy conformations. This work provides insights on exploring complicated energy landscapes by exploiting the advantages and limitations of CSA. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Spin‐orbit Ab initio investigation of the photodissociation of dibromomethane in the gas and solution phases
Authors: Liu Yajun , Xiao Hongyan , Sun Mengtao , Fang Weihai
Published: May 2008

A clear and reliable theoretical investigation on dibromomethane (CH2Br2) photodissociation is desired. The calculation must consider: (i) relativistic effects; (ii) the potential energy curves (PECs) of spin‐orbit coupling states; (iii) geometry optimization by the method with both static and dynamic electron correlations; (iv) solvent effects on the photodissociation in the solution. All these have been considered in this study by state‐of‐the‐art quantum chemical calculations. The experimentally observed photodissociation in the gas phase with products of spin‐orbit‐coupled states, Br(2P3/2) and Br*(2P1/2), was assigned by multi‐state second order multiconfigurational perturbation theory in conjunction with spin‐orbit interaction through complete active space state interaction (MS‐CASPT2/CASSI‐SO) PECs. The mechanisms of the experimentally observed photodissociation and photoisomerization in solvent were elucidated by the MS‐CASPT2/CASSI‐SO method combined with polarized continuum model of the solvent. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Emotion recognition, emotional awareness and cognitive bias in individuals with bulimia nervosa
Authors: Legenbauer Tanja , Vocks Silja , Rüddel Heinz
Published: May 2008

Difficulties recognizing emotion have been reported for eating disordered individuals in relation to perception of emotions in others and emotional self‐awareness. It remains unclear whether this is a perceptual or cognitive‐affective problem. Clarification is sought and the question of a cognitive bias is addressed when interpreting facially expressed emotions. Twenty participants with bulimia nervosa (BN) and 20 normal controls (NC) were assessed for ability to recognize emotional and neutral expressions. Emotional self‐awareness was also assessed. Significant differences were found for emotional self‐awareness. For emotional faces, only a poorer recognition of the emotion, surprise, for BN was found. Problems with emotional self‐awareness suggest a cognitive‐affective disturbance in emotion recognition. Implications for therapy are discussed. © 2008 Wiley Periodicals, Inc. J Clin Psychol 64:687–702, 2008.
Sequential batch reactor for eucalypt kraft pulp effluent treatment with Trametes versicolor
Authors: Xavier Ana MRB , Tavares Ana Paula M , Agapito Margarida SM , Evtuguin Dmitry V
Published: May 2008

BACKGROUND: A sequential batch reactor (SBR) was used for eucalypt kraft pulp effluent treatment with Trametes versicolor. A 23 full factorial design and response surface methodology were applied to optimise the batch fermentation conditions. Effluent concentration, culture medium and inoculum age were the factors selected for this study in order to optimise the reduction of chemical oxygen demand (COD).

RESULTS: The presence of Trametes Defined Medium (TDM) in the fermentation was required to obtain a significant COD reduction. Experiments in the batch reactor confirmed, in general, the predicted results of optimisation developed from Erlenmeyer batch assays. The T. versicolor culture remained active during 42 days of study in the SBR, providing approximately 80% of COD reduction.

CONCLUSION: Trametes versicolor may be considered as very promising for the biological treatment of effluents from kraft pulp mills in an SBR system instead of the activated sludge mixed cultures traditionally used. Copyright © 2008 Society of Chemical Industry
Sewage sludge treatment using microwave‐enhanced advanced oxidation processes with and without ferrous sulfate addition
Authors: Lo Kwang V , Liao Ping H , Yin Gui Q
Published: May 2008

BACKGROUND: Microwave‐enhanced advanced oxidation processes with and without the addition of ferrous sulfate (MW/H2O2/Fe2+‐AOP and MW/H2O2‐AOP respectively) were studied for reduction of solids and solubilisation of nutrients from secondary sewage sludge.

RESULTS: For the MW/H2O2/Fe2+‐AOP the yields of solubilisation of orthophosphate and ammonia decreased with increasing temperature. The best results (88.1 mg L−1 for orthophosphate and 22.7 mg L−1 for ammonia) were obtained at a treatment temperature of 40 °C. In contrast, the MW/H2O2‐AOP had an advantage when it was operated at higher temperatures of 60 and 80 °C. The highest yields of solubilisation were obtained at 60 °C for orthophosphate (81.1 mg L−1) and at 80 °C for both ammonia (35.0 mg L−1) and soluble chemical oxygen demand (1954 mg L−1). Over the temperature range used in this study, the MW/H2O2‐AOP gave a better performance than the MW/H2O2/Fe2+‐AOP.

CONCLUSION: For sewage sludge treatment the MW/H2O2‐AOP is more effective than the MW/H2O2/Fe2+‐AOP in terms of solid reduction and nutrient solubilisation. It will also be more cost‐effective, as it does not require iron addition in the process. Copyright © 2008 Society of Chemical Industry
Lactic acid production from dining‐hall food waste by Lactobacillus plantarum using response surface methodology
Authors: Ye Zhi‐Long , Lu Min , Zheng Yan , Li Ya‐Hong , Cai Wei‐Min
Published: May 2008

BACKGROUND: Food waste generally has a high starch content and is rich in nutritional compounds, including lipids and proteins. It therefore represents a potential renewable resource. In this study, dining‐hall food waste was used as a substrate for lactic acid production, and response surface methodology was employed to optimise the fermentation conditions.

RESULTS: Lactic acid biosynthesis was significantly affected by the interaction of protease and temperature. Protease, temperature and CaCO3 had significant linear effects on lactic acid production, while α‐amylase and yeast extract had insignificant effects. The optimal conditions were found to be an α‐amylase activity of 13.86 U g−1 dried food waste, a protease activity of 2.12 U g−1 dried food waste, a temperature of 29.31 °C and a CaCO3 concentration of 62.67 g L−1, which resulted in a maximum lactic acid concentration of 98.51 g L−1 (88.75% yield). An increase in inoculum size would be appropriate for accelerating the depletion of initial soluble carbohydrate to enhance the efficiency of α‐amylase in dining‐hall food waste fermentation.

CONCLUSION: A suitable regression model for lactic acid production was developed based on the experimental results. Dining‐hall food waste was found to be a good substrate for lactic acid fermentation with high product yield and without nutrient supplementation. Copyright © 2008 Society of Chemical Industry
Exploring gene‐deleted adenoviral vectors for delivery of short hairpin RNAs and reduction of hepatitis B virus infection in mice
Authors: Rauschhuber Christina , Xu Hui , Salazar Felix H. , Marion Patricia L. , Ehrhardt Anja
Published: May 2008

Background

RNA interference based therapeutic approaches hold promise for the treatment of patients chronically infected with hepatitis B virus (HBV). To conquer HBV infection, long‐term suppression of target transcripts in all hepatocytes without toxic effects may be required. The present study explored gene‐deleted adenoviral vectors (GD‐AdV) lacking all viral coding sequences for delivery of the previously described short hairpin RNA (shRNA) HBVU6no.2, which was demonstrated to result in post‐transcriptional knock‐down of HBV transcripts.

Methods

We established conditions for shRNA delivery expressed from GD‐AdV in vitro and in vivo and observed up to 96% shRNA‐mediated knockdown of luciferase expressed in mouse liver. To investigate in vivo efficacy of HBVU6no.2 expressed from a GD‐AdV, we explored a transient and a transgenic mouse model for HBV infection.

Results

We observed an up to 68% drop in serum HBV surface antigen (HBsAg) levels in the transient and the transgenic mouse model for HBV infection, respectively. Interestingly, we detected an up to 86% drop in HBsAg levels in both animal models after administration of a control GD‐AdV encoding β‐galactosidase. In concordance with reduced serum HBsAg levels, we observed reduced HBV replication as demonstrated by Southern blot analysis of HBV genomes.

Conclusions

The present study demonstrates that GD‐AdV can be used against HBV infection but the design of DNA sequences including shRNAs contained in the vector and virus–host interactions during superinfection needs to be carefully considered. Copyright © 2008 John Wiley & Sons, Ltd.
Functional morphology of the feeding apparatus, feeding constraints, and suction performance in the nurse shark Ginglymostoma cirratum
Authors: Motta Philip J. , Hueter Robert E. , Tricas Timothy C. , Summers Adam P. , Huber Daniel R. , Lowry Dayv , Mara Kyle R. , Matott Michael P. , Whitenack, Lisa B. , Wintzer Alpa P.
Published: May 2008

The nurse shark, Ginglymostoma cirratum, is an obligate suction feeder that preys on benthic invertebrates and fish. Its cranial morphology exhibits a suite of structural and functional modifications that facilitate this mode of prey capture. During suction‐feeding, subambient pressure is generated by the ventral expansion of the hyoid apparatus and the floor of its buccopharyngeal cavity. As in suction‐feeding bony fishes, the nurse shark exhibits expansive, compressive, and recovery kinematic phases that produce posterior‐directed water flow through the buccopharyngeal cavity. However, there is generally neither a preparatory phase nor cranial elevation. Suction is generated by the rapid depression of the buccopharyngeal floor by the coracoarcualis, coracohyoideus, and coracobranchiales muscles. Because the hyoid arch of G. cirratum is loosely connected to the mandible, contraction of the rectus cervicis muscle group can greatly depress the floor of the buccopharyngeal cavity below the depressed mandible, resulting in large volumetric expansion. Suction pressures in the nurse shark vary greatly, but include the greatest subambient pressures reported for an aquatic‐feeding vertebrate. Maximum suction pressure does not appear to be related to shark size, but is correlated with the rate of buccopharyngeal expansion. As in suction‐feeding bony fishes, suction in the nurse shark is only effective within approximately 3 cm in front of the mouth. The foraging behavior of this shark is most likely constrained to ambushing or stalking due to the exponential decay of effective suction in front of the mouth. Prey capture may be facilitated by foraging within reef confines and close to the substrate, which can enhance the effective suction distance, or by foraging at night when it can more closely approach prey. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.
Morphological and biomechanical changes of the feeding apparatus in developing southern flounder, Paralichthys lethostigma
Authors: Francis Austin W. , Turingan Ralph G.
Published: May 2008

The feeding biomechanics of premetamorphic, metamorphic, and postmetamorphic southern flounder, Paralichthys lethostigma, were investigated to better understand the origin and design of adult pleuronectiform feeding mechanisms. Larval P. lethostigma were sampled from culture tanks every day from first feeding through metamorphosis. Fish were then fixed, cleared, and double stained for cartilage and bone. Postmetamorphic juvenile and adult fish were obtained from aquaculture facilities, fixed, and the muscles and bones of the head dissected. All fish were digitally photographed from both sides of the head. Measurements from digital images included head depth, head length, and quadratal angle (a measure of articular‐quadrate position). Measurements were also made of closing in‐lever, opening in‐lever, and out‐lever moment arm lengths for the determination of lower jaw opening and closing mechanical advantage. In premetamorphic larvae, quadratal angle increased from 40° to 80°, opening lever ratio increased from 0.10 to 0.37, and closing lever ratio increased from 0.06 to 0.40. From these measurements and observations of cleared and double‐stained specimens, it was determined that lower jaw depression and elevation changed from a hyoid‐based to an opercular‐based mechanism prior to the onset of metamorphosis. With migration of the right eye to the left side of the head, quadratal angle remained relatively unchanged at 72° to 84°, opening lever ratio decreased from a high of 0.32 to a low of 0.14, and closing lever ratio decreased to as low as 0.17. Postmetamorphic fish exhibited little change with a quadratal angle of 83° to 84°, an opening lever ratio of 0.19, and a closing lever ratio of 0.17 to 0.19. Paired measurements made on the left (ocular) and right (blind) sides of the head indicated that quadratal angle was asymmetrical during metamorphosis (P = 0.003, α = 0.017). Mechanical advantage for lower jaw elevation was also bilaterally asymmetrical following metamorphosis (P = 0.002, α = 0.013). Because mechanical advantage for lower jaw depression was not directionally asymmetrical in metamorphic or postmetamorphic P. lethostigma, functional asymmetry (lateral jaw flexion) is not predicted for jaw opening. These results suggest differences in the design and function of feeding mechanisms for premetamorphic, metamorphic, and postmetamorphic P. lethostigma. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.
Tumor interstitial fluid pressure may regulate angiogenic factors in osteosarcoma
Authors: Nathan Saminathan S. , Huvos Andrew G. , Casas‐Ganem Jorge E. , Yang Rui , Linkov Irina , Sowers Rebecca , DiResta Gene R. , Gorlick Richard , Healey John H.
Published: May 2008

We have previously shown that osteosarcomas (OS) have states of increased interstitial fluid pressure (IFP), which correlate with increased proliferation and chemosensitivity. In this study, we hypothesized that constitutively raised IFP in OS regulates angiogenesis. Sixteen patients with the clinical diagnosis of OS underwent blood flow and IFP readings by the wick‐in‐needle method at the time and location of open biopsy. Vascularity was determined by capillary density in the biopsy specimens. We performed digital image analysis of immunohistochemical staining for CD31, VEGF‐A, VEGF‐C, and TPA on paraffin‐embedded tissue blocks of the biopsy samples. Clinical results were validated in a pressurized cell culture system. Interstitial fluid pressures in the tumors (mean 33.5 ± SD 17.2 mmHg) were significantly higher (p = 0.00001) than that in normal tissue (2.9 ± 5.7 mmHg). Pressure readings were significantly higher in low vascularity tumors compared to high vascularity tumors (p < 0.001). In the OS cell lines, growth in a pressurized environment was associated with VEGF‐A downregulation, VEGF‐C upregulation, and TPA upregulation. The reverse was seen in the OB cell line. Growth in the HUVEC cell line was not significantly inhibited in a pressurized environment. Immunohistochemical assessment for VEGF‐A (p = 0.01), VEGF‐C (p = 0.008), and TPA (p = 0.0001) translation were consistent with the findings on PCR. Our data suggests that some molecules in angiogenesis are regulated by changes in IFP. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1520–1525, 2008
Muscle strength quantification in small animals: A new transcutaneous technique in rabbits
Authors: Meffert Rainer H. , Frey Sönke P. , Jansen Hendrik , Ochman Sabine , Raschke Michael J. , Langer Martin
Published: May 2008

The objective of this study was to develop a new, simple, and noninvasive technique to measure the force produced by dorsi‐flexion of the foot in small animals. In addition, this study aimed to quantitatively describe changes in muscle and soft tissue structures using histomorphometry. The recovery of the dorsi‐flexing muscles in the tibialis anterior compartment in New Zealand White rabbits was evaluated after musculoskeletal trauma by measuring isometric contractions after submaximal transcutaneous electrical stimulation of the peroneal nerve. The trauma included muscle and bone trauma that was treated with limb shortening followed by distraction osteogenesis. Muscle contractions were initiated at an amplitude of 5.1 mA for a duration of 2.56 ms at intervals of 50 ms. Based on consecutive measurements of the force on days 5, 10, 15, 20, 25, and 30 postsurgery, a positive trend in recovery of the stimulated force produced by dorsi‐flexion of the foot was observed. The muscle strength at 30 days postsurgery was compared to that measured presurgery (baseline): 55% of the animals had dorsi‐flexion strength that was 60% below that of the presurgery baseline muscle strength; 36% of the animals had dorsi‐flexion strength that was greater than 60% of the baseline measure, indicating that there was a significant decrease in force produced by dorsi‐flexion of the foot after trauma on all testing days (p < 0.01) and that a severe muscular injury was set with limited recovery. This technique provides a new option for examining muscle regeneration and rehabilitation in small animals. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1526–1532, 2008
Non‐enzymatic glycation of chondrocyte‐seeded collagen gels for cartilage tissue engineering
Authors: Roy Rani , Boskey Adele L. , Bonassar Lawrence J.
Published: May 2008

Collagen glycated with ribose (250 mM) in solution (pre‐glycation) and as a gel (post‐glycation) was seeded with chondrocytes and the effects of glycation on chondrocyte matrix assembly in culture were determined. Pre‐glycation enhanced GAG accumulation significantly over controls at both 2 and 4 weeks (p < 0.05), although at both time points there were no statistical differences in cell number between pre‐glycated and control gels. The increased proteoglycan accumulation was shown to be in part due to significantly increased GAG retention by the pre‐glycated constructs (p < 0.05). Total collagen content in these pre‐glycated gels was also significantly higher than unglycated gels at 4 weeks (p < 0.05). With post‐glycation of collagen gels, chondrocyte number and GAG accumulation were all significantly lower than controls (p < 0.05). Post‐glycation also inhibited GAG retention by the constructs (p < 0.05). Given these results, pre‐glycation may be an improved processing method for collagen gels for tissue engineering techniques. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1434–1439, 2008
The canine bilateral groove model of osteoarthritis
Authors: Intema Femke , DeGroot Jeroen , Elshof Bram , Vianen Marieke E. , Yocum Sue , Zuurmond Annemarie , Mastbergen Simon C. , Lafeber Floris P.
Published: May 2008

In studies aimed at local treatment of experimental osteoarthritis (OA) it is optimal to have an internal (untreated) OA control. Such an approach excludes interanimal variation, and allows paired statistical evaluation of treatment efficacy. For this purpose, we developed and characterized a bilateral version of the canine Groove model. We hypothesized that the bilateral version of the canine Groove model would show consistent and clear development of features of OA similar to those found in the unilateral version. In six Beagle dogs, grooves were surgically made in the articular cartilage of the femoral condyles of both knee joints. Six additional dogs underwent bilateral sham surgery. The degree of OA was quantified 20 weeks after surgery and was compared in retrospect to 23 animals that undergone the same procedure in a single knee joint with the contralateral knee serving as a non‐OA control. Bilateral groove surgery resulted in OA. This was based on the observed ineffective repair response in which an increase in proteoglycan synthesis, a diminished retention of these newly formed proteoglycans, and an enhanced loss of resident proteoglycans resulted in a decreased cartilage proteoglycan content. These biochemical effects were corroborated by clear histological features of OA. All these effects were found in femor as well as in the (surgically untouched) tibia. Interestingly, features of OA were slightly more severe in the bilateral model than in the unilateral variant. The bilateral canine Groove model showed consistent and clear development of features of OA, comparable to the unilateral model. © 2008 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:1471–1477, 2008
Densitometric determination of zinc bacitracin and nystatin in animal feed
Authors: Injac Rade , Strukelj Borut , Djordjevic‐Milic Vukosava , Karljikovic‐Rajic Katarina , Lingeman Henk
Published: May 2008

BACKGROUND: The European Union has forbidden the use of antibiotics as additives in animal feed. Zn‐bacitracin (Zn‐BC) and nystatin (NYS) were frequently used for their growth‐promoting effects and for feed conversion in poultry, pigs and cattle. An HPTLC method has been developed for separating Zn‐BC and NYS in the mixture, for routine quality control.

RESULTS: The separation was obtained using RP‐18 F254S coated HPTLC plates with acetonitrile/methanol (equal volumes):toluene:KH2PO4/KOH (buffer, pH 6.8) = 57:3:40 (v/v/v), adjusted with HCl to pH 8.2, as a mobile phase. The densitograms were monitored at 192, 215 and 305 nm and both antibiotics were assayed at 215 nm. The method was shown to be specific, accurate (recoveries were 98.7 ± 0.5% and 104.8 ± 0.7% for Zn‐BC and NYS, respectively), linear over the tested range (correlation coefficients, 0.9982 and 0.9884), and precise (intermediate precision RSD below 2.2% for both analytes) with efficient separation (Rs = 3.5).

CONCLUSION: The method was applied for determining Zn‐BC and NYS as additives in spiked matrices of commercial animal feedstuffs. According to LOD values for each antibiotic, the minimum detectable amount in feed is 4.5 and 5.5 ppm of Zn‐BC and NYS, respectively. Copyright © 2008 Society of Chemical Industry
Architectures and performance evaluation of bandwidth brokers
Authors: Bouras Christos , Primpas Dimitris
Published: May 2008

DiffServ is the basis of contemporary QoS‐enabled networks. Setting up DiffServ QoS requires extensive engineering effort in dimensioning and provisioning, especially for adjacent networks under different administrations linked in a ‘federated’ hierarchy. The bandwidth broker is an entity that is responsible for the management of the resources and the QoS service operation in an automated way. In this paper, we present, test and compare two different architectures of bandwidth brokers: a centralized one and a distributed one. We also deal with the inter‐domain operation of the bandwidth broker in order to perform end‐to‐end provisioning. The paper presents the relevant aspects for inter‐domain operation of a bandwidth broker and focuses on pathfinding issues. We discuss two models for inter‐domain routing through bandwidth brokers, analyzing their advantages and comparing them. Copyright © 2008 John Wiley & Sons, Ltd.
Preparation of a variety of fluoroalkyl end‐capped N‐(1,1‐dimethyl‐3‐oxobutyl)acrylamide oligomer/silica nanocomposites possessing no weight loss characteristic at 800°C
Authors: Sawada Hideo , Tashima Tsukasa , Kodama Shun
Published: May 2008

A variety of fluoroalkyl end‐capped N‐(1,1‐dimethyl‐3‐oxobutyl)acrylamide oligomer [RF‐(DOBAA)n‐ RF]/silica nanocomposites, in which the oligomer contents are 18–96%, were prepared by reactions of the corresponding fluorinated oligomer with tetraethoxysilane and silica nanoparticles under alkaline conditions. Each fluorinated oligomer/silica composite thus obtained is nanometer size‐controlled very fine particles (22–68 nm) possessing a good dispersibility and stability in a variety of solvents including water. Interestingly, the weight loss of RF‐(DOBAA)n‐RF/silica nanocomposites, in which the oligomer contents are 18–72%, were not observed at all even at 800°C, as well as the original silica nanoparticles, although the corresponding sub‐micrometer size‐controlled RF‐ (DOBAA)n‐RF/silica composites (particle size: 359 nm) decomposed completely at 800°C to afford the weight loss in proportion to the content of RF‐(DOBAA)n‐RF oligomer in composites. On the other hand, a slight weight loss of RF‐(DOBAA)n‐RF/silica nanocomposites, in which the oligomer contents are 75–94%, was observed at 800°C compared to that of the original silica nanoparticles. Copyright © 2008 John Wiley & Sons, Ltd.
Quantification of seed oil from species with varying oil content using supercritical fluid extraction
Authors: Seal Charlotte E. , Kranner Ilse , Pritchard Hugh W.
Published: May 2008

Introduction: The quantity and composition of seed oil affects seed viability and storability and hence the value of a species as a resource for nutrition and plant conservation. Supercritical fluid extraction with carbon dioxide (SFE‐CO2) offers a rapid, environmentally friendly alternative to traditional solvent extraction.

Objective: To develop a method using SFE‐CO2 to quantify the seed oil content in a broad range of species with high to low oil contents.

Methodology: Seed oil was extracted using SFE‐CO2 from four crop species representing high, medium and low oil content: Helianthus annuus, Asteraceae, with ca. 55% oil; Brassica napus, Brassicaceae, with ca. 50% oil; Glycine max, Fabaceae, with ca. 20% oil; and Pisum sativum, Fabaceae, with ca. 2% oil. Extraction pressures of 5000, 6000 and 7500 psi and temperatures of 40, 60 and 80°C were examined and a second step using 15% ethanol as a modifier included. Oil yields were compared with that achieved from Smalley Butt extraction. The optimised SFE‐CO2 method was validated on six species from taxonomically distant families and with varying oil contents: Swietenia humilis (Meliaceae), Stenocereus thurberi (Cactaceae), Sinapis alba (Brassicaceae), Robinia pseudoacacia (Fabaceae), Poa pratensis (Poaceae) and Trachycarpus fortunei (Arecaceae).

Results: The two‐step extraction at 6000 psi and 80°C produced oil yields equivalent to or higher than Smalley Butt extraction for all species, including challenging species from the Brassicaceae family.

Conclusion: SFE‐CO2 enables the rapid analysis of seed oils across a broad range of seed oil contents. Copyright © 2008 John Wiley & Sons, Ltd.
Cyclic polypeptides by thermal polymerization of α‐amino acid N‐carboxyanhydrides
Authors: Kricheldorf Hans R. , Lossow Colin V. , Lomadze Nino , Schwarz Gert
Published: May 2008

The NCAs of the following five amino acids were polymerized in bulk at 120 °C without addition of a catalyst or initiator: sarcosine (Sar), L‐alanine (L‐Ala), D,L‐phenylalanine (D,L‐Phe), D,L‐leucine (D,L‐Leu) and D,L‐valine (D,L‐Val). The virgin reaction products were characterized by viscosity measurements 13C NMR spectroscopy and MALDI‐TOF mass spectrometry. In addition to numerous low molar mass byproducts cyclic polypeptides were formed as the main reaction products in the mass range above 800 Da. Two types of cyclic oligo‐ and polypeptides were detected in all cases with exception of sarcosine NCA, which only yielded one class of cyclic polypeptides. The efficient formation of cyclic oligo‐ and polypeptides explains why high molar mass polymers cannot be obtained by thermal polymerizations of α‐amino acid NCAs. Various polymerization mechanisms were discussed. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4012–4020, 2008
Stimuli‐responsive cationic terpolymers by RAFT polymerization: Synthesis, characterization, and protein interaction studies
Authors: Rossi Nicholas A. A. , Jadhav Vaibhav , Lai Benjamin F. L. , Maiti Souvik , Kizhakkedathu Jayachandran N.
Published: May 2008

The controlled synthesis and characterization of a range of stimuli responsive cationic terpolymers containing varying amounts of N‐isopropylacrylamide (NIPAM), 3‐(methylacryloylamino)propyl trimethylammonium chloride (MAPTAC), and poly(ethylene glycol)monomethyl methacrylate (PEGMA) is presented. The terpolymers were synthesized using reversible addition‐fragmentation chain transfer (RAFT) polymerization. Compositions of the terpolymers determined using 1H NMR were in close agreement to the theoretical values determined from the monomer feed ratios. GPC‐MALLS was used to analyze the molecular weight characteristics of the polymers, which were found to have low polydispersities (Mw/Mn 1.1–1.4). The phase transitions were studied as a function of PEGMA and NIPAM content using temperature controlled 1H NMR and turbidity measurements (UV‐Vis). The relationship between thermal stability and the comonomer ratio of the polymers was measured using thermogravimetric analysis (TGA). Protein interaction studies were performed to determine the suitability of the polymers for biological applications. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4021–4029, 2008
Ring‐opening copolymerization of ethylene carbonate and ε‐caprolactone catalyzed by neodymium tris(2,6‐di‐tert‐butyl‐4‐methylphenolate): Synthesis, characterization, and dynamic mechanic analysis
Authors: Chen Feng , Zhu Weipu , Xu Ning , Shen Zhiquan
Published: May 2008

The ring‐opening copolymerization of ethylene carbonate (EC) with ε‐caprolactone (CL) was carried out using neodymium tris(2,6‐di‐tert‐butyl‐4‐methylphenolate) as a single‐component catalyst. Copolymers containing up to 22.0% EC contents with high molecular weights (up to 23.97 × 104) and moderate molecular weight distributions (between 1.66 and 2.03) were synthesized at room temperature. Compared with homopoly(ε‐caprolactone), the copolymers with EC units exhibited increased glass transition temperatures (−35.6 °C), reduced melting temperatures (44.5 °C), and greatly enhanced elongation percentage at break (2383%) based on dynamic mechanic analysis. The crystallinities of the copolymers decreased with the increasing EC molar percentage in the products. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4050–4055, 2008
Interactions of ionic liquids with polysaccharides. VI. Pure cellulose nanoparticles from trimethylsilyl cellulose synthesized in ionic liquids
Authors: Köhler Sarah , Liebert Tim , Heinze Thomas
Published: May 2008

Trimethylsilyl cellulose (TMSC) can be efficiently synthesized with 1,1,1,3,3,3‐hexamethyldisilazane (HMDS) by applying the ionic liquids (ILs) 1‐ethyl‐3‐methylimidazolium acetate, 1‐ethyl‐3‐methylimidazolium chloride, and 1‐butyl‐3‐methylimidazolium chloride as reaction medium, yielding pure biopolymer derivatives with degrees of substitution (DS) up to 2.89. Cosolvents, for example, chloroform, could be used to adjust the viscosity of the system and to achieve the miscibility of the components. During the synthesis of highly functionalized derivatives precipitation of the TMSC occurred, which simplifies the recycling of the IL. The high tendency of TMSC toward the formation of supermolecular structures was exploited for the formation of nanoparticles studying a simple dialysis process. Amazingly, pure cellulose nanoparticles can be obtained by dissolving TMSC in tetrahydrofurane or N,N‐dimethyl acetamide and dialysis against water. FTIR spectroscopy confirmed the complete removal of the TMS functions during this process. Scanning electron microscopy, dynamic light scattering, atomic force microscopy, and particle size distribution analysis showed that cellulose particles down to a size of 170 nm are accessible in this simple manner. The nanoparticle suspensions exhibit viscosities in the range of water. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4070–4080, 2008
In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
Authors: Bolstad Erin S. D. , Anderson Amy C.
Published: May 2008

Accurate ranking during in silico lead optimization is critical to drive the generation of new ligands with higher affinity, yet it is especially difficult because of the subtle changes between analogs. In order to assess the role of the structure of the receptor in delivering accurate lead ranking results, we docked a set of forty related inhibitors to structures of one species of dihydrofolate reductase (DHFR) derived from crystallographic, NMR solution data, and homology models. In this study, the crystal structures yielded the superior results: the compounds were placed in the active site in the conserved orientation and the docking scores for 80% percent of the compounds clustered into the same bins as the measured affinity. Single receptor structures derived from NMR data or homology models did not serve as accurate docking receptors. To our knowledge, these are the first experiments that assess ranking of homologous lead compounds using a variety of receptor structures. We then extended the study to investigate whether ensembles, either computationally or experimentally derived, of all of the single starting structures aid, hinder or have no effect on the performance of the starting template. Impressively, when ensembles of receptor structures derived from NMR data or homology models were employed, docking accuracy improved to a level equal to that of the high resolution crystal structures. The same experiments using a second species of DHFR and set of ligands confirm the results. A comparison of the structures of the individual ensemble members to the starting structures shows that the effect of the ensembles can be ascribed to protein flexibility in addition to absorption of computational error. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Threading without optimizing weighting factors for scoring function
Authors: Yang Yifeng David , Park Changsoon , Kihara Daisuke
Published: May 2008

Optimizing weighting factors for a linear combination of terms in a scoring function is a crucial step for success in developing a threading algorithm. Usually weighting factors are optimized to yield the highest success rate on a training dataset, and the determined constant values for the weighting factors are used for any target sequence. Here we explore completely different approaches to handle weighting factors for a scoring function of threading. Throughout this study we use a model system of gapless threading using a scoring function with two terms combined by a weighting factor, a main chain angle potential and a residue contact potential. First, we demonstrate that the optimal weighting factor for recognizing the native structure differs from target sequence to target sequence. Then, we present three novel threading methods which circumvent training dataset‐based weighting factor optimization. The basic idea of the three methods is to employ different weighting factor values and finally select a template structure for a target sequence by examining characteristics of the distribution of scores computed by using the different weighting factor values. Interestingly, the success rate of our approaches is comparable to the conventional threading method where the weighting factor is optimized based on a training dataset. Moreover, when the size of the training set available for the conventional threading method is small, our approach often performs better. In addition, we predict a target‐specific weighting factor optimal for a target sequence by an artificial neural network from features of the target sequence. Finally, we show that our novel methods can be used to assess the confidence of prediction of a conventional threading with an optimized constant weighting factor by considering consensus prediction between them. Implication to the underlined energy landscape of protein folding is discussed. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium
Authors: Branco Ricardo J.F. , Seifert Alexander , Budde Michael , Urlacher Vlada B. , Ramos Maria J. , Pleiss Jürgen
Published: May 2008

The molecular basis of regioselectivity of cytochrome P450 monooxygenases from Bacillus megaterium (CYP102A1) with its flexible and widely opened active site is still not well understood. In the present work (−)‐α‐pinene bound complexes with two triple mutants were modeled to elucidate the contribution of the three major factors that mediate selectivity: active site shape, protein flexibility, and chemical reactivity of the substrate. For the triple mutant A74G F87V L188Q (GVQ), one stable, productive conformation of the substrate (conformation I) was identified by multiple molecular dynamics simulations. The model predicts pinene epoxide as a major product (42% pinene oxide, 23% verbenol) which is in agreement with the experimental product profile (70% pinene oxide, 20% verbenol). In contrast, for the triple mutant A74G F87G L188Q (GGQ) two stable productive substrate conformations were identified (conformations IIa and IIb), and verbenol was predicted as major product (81% verbenol, 16% myrtenol), which is in agreement with experimental results (77% verbenol, 10% myrtenol). The effect of chemical reactivity of the substrate was demonstrated by comparison of (−)‐α‐pinene to its regioisomer (−)‐β‐pinene, where the product profile is shifted from 68% pinocarveol and 32% myrtanal in mutant GVQ, to 40% pinocarveol and 60% myrtanal in mutant GGQ. Our results strongly suggest a major role of residue 87 in anchoring (−)‐α‐pinene during substrate binding which provides a simple and elegant rationalization of the dynamic structure of this enzyme‐substrate complex. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural classification of CDR‐H3 revisited: A lesson in antibody modeling
Authors: Kuroda Daisuke , Shirai Hiroki , Kobori Masato , Nakamura Haruki
Published: May 2008

Among the six complementarity‐determining regions (CDRs) in the variable domains of an antibody, the third CDR of the heavy chain (CDR‐H3), which lies in the center of the antigen‐binding site, plays a particularly important role in antigen recognition. CDR‐H3 shows significant variability in its length, sequence, and structure. Although difficult, model building of this segment is the most critical step in antibody modeling. Since our first proposal of the “H3‐rules,” which classify CDR‐H3 structure based on amino acid sequence, the number of experimentally determined antibody structures has increased. Here, we revise these H3‐rules and propose an improved classification scheme for CDR‐H3 structure modeling. In addition, we determine the common features of CDR‐H3 in antibody drugs as well as discuss the concept of “antibody druggability,” which can be applied as an indicator of antibody evaluation during drug discovery. Proteins 2008. © 2008 Wiley‐Liss, Inc.
The environmental fate of diuron under a conventional production regime in a sugarcane farm during the plant cane phase
Authors: Stork Peter R , Bennett Frederick R , Bell Michael J
Published: May 2008

BACKGROUND: Field studies of diuron and its metabolites 3‐(3,4‐dichlorophenyl)‐1‐methylurea (DCPMU), 3,4‐dichlorophenylurea (DCPU) and 3,4‐dichloroaniline (DCA) were conducted in a farm soil and in stream sediments in coastal Queensland, Australia.

RESULTS: During a 38 week period after a 1.6 kg ha−1 diuron application, 70–100% of detected compounds were within 0–15 cm of the farm soil, and 3–10% reached the 30–45 cm depth. First‐order t1/2 degradation averaged 49 ± 0.9 days for the 0–15, 0–30 and 0–45 cm soil depths. Farm runoff was collected in the first 13–50 min of episodes lasting 55–90 min. Average concentrations of diuron, DCPU and DCPMU in runoff were 93, 30 and 83–825 µg L−1 respectively. Their total loading in all runoff was > 0.6% of applied diuron. Diuron and DCPMU concentrations in stream sediments were between 3–22 and 4–31 µg kg−1 soil respectively. The DCPMU/diuron sediment ratio was > 1.

CONCLUSION: Retention of diuron and its metabolites in farm topsoil indicated their negligible potential for groundwater contamination. Minimal amounts of diuron and DCMPU escaped in farm runoff. This may entail a significant loading into the wider environment at annual amounts of application. The concentrations and ratio of diuron and DCPMU in stream sediments indicated that they had prolonged residence times and potential for accumulation in sediments. The higher ecotoxicity of DCPMU compared with diuron and the combined presence of both compounds in stream sediments suggest that together they would have a greater impact on sensitive aquatic species than as currently apportioned by assessments that are based upon diuron alone. Copyright © 2008 Society of Chemical Industry