bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate prediction of protonation state as a prerequisite for reliable MM‐PB(GB)SA binding free energy calculations of HIV‐1 protease inhibitors
Authors: Wittayanarakul Kitiyaporn , Hannongbua Supot , Feig Michael 
Published: September 2007

AbstractBinding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV‐1 protease. An MMPB/SA‐type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme‐inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV‐1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Theoretical elucidation of the rhodium‐catalyzed [4 + 2] annulation reactions
Authors: Geng Cai‐Yun , Li Ji‐Lai , Huang Xu‐Ri , Liu Hui‐Ling , Li Zhuo , Sun Chia‐Chung 
Published: September 2007

AbstractThe reaction mechanism of the Rh‐catalyzed [4 + 2] annulation of 4‐alkynals with isocyanates is unraveled using density functional calculations. The reaction mechanisms of the model system and the real substituted system have been investigated and the results are compared. From our theoretical results based on the model and real substituted system, it is shown that (a) the rate‐determining step is the Rh‐H addition to the alkyne, (b) the formation of the cyclopentenone G and glutarimide K represents a severe competition, and (c) the product selectivity should be controlled by the amount of the isocyanates. In addition, it is demonstrated that there exist steric effects in the real substituted system, but missed in model system. Our calculations also show that although the results obtained on the model system could explain the mechanism in principle, the real substituted system could reflect the mechanism more exactly and make the reaction proceed with regioselectivity. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Effects of long‐range electrostatic forces on simulated protein folding kinetics
Authors: Robertson Alex , Luttmann Edgar , Pande Vijay S. 
Published: September 2007

AbstractMolecular dynamics simulations are a useful tool for characterizing protein folding pathways. There are several methods of treating electrostatic forces in these simulations with varying degrees of physical fidelity and computational efficiency. In this article, we compare the reaction field (RF) algorithm, particle‐mesh Ewald (PME), and tapered cutoffs with increasing cutoff radii to address the impact of the electrostatics method employed on the folding kinetics. We quantitatively compare different methods by a correlation of quantitative measures of protein folding kinetics. The results of these comparisons show that for protein folding kinetics, the RF algorithm can quantitatively reproduce the kinetics of the more costly PME algorithm. These results not only assist the selection of appropriate algorithms for future simulations, but also give insight on the role that long‐range electrostatic forces have in protein folding. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
High‐spin versus broken symmetry—Effect of DFT spin density representation on the geometries of three diiron (III) model compounds
Authors: Binning R. C. , Bacelo Daniel E. 
Published: September 2007

AbstractUnrestricted density functional theory calculations have been conducted on three diiron(III) synthetic model compounds containing antiferromagnetically coupled high‐spin (HS) irons for which crystallographic structures and Raman spectral data are available. Three density functionals have been employed: BPW91, PWC, and BOP. The study compares the effects on optimized geometries and harmonic vibrational frequencies of spin‐paired (SP) low‐spin, HS, and broken symmetry antiferromagnetically coupled singlet representations of the spin density distribution. The geometries around the diiron centers in the HS and broken symmetry (BS) representations are found to be similar, both markedly different from those arising from the SP representation. Small differences between the HS and BS results are seen in bond lengths, angles, Raman frequencies, and spin densities associated with oxo and peroxo bridges between the irons. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
Understanding ion channel biology using epitope tags: Progress, pitfalls, and promise
Authors: Maue Robert A. 
Published: September 2007

AbstractEpitope tags have been increasingly used to understand ion channel subunit assembly and interaction, trafficking, subcellular localization, and function in living cells. In particular, epitope tags have proven extremely useful for analyses of closely related, highly homologous channel subunits in endogenous cell contexts in vitro and in vivo, where multiple channel isoforms may be expressed. However, as the variety of epitope tags that have been used has expanded, and the use of tagged channel subunits has become increasingly sophisticated and widespread, there has also been an increase in the number of examples highlighting the potential problems associated with the use of epitope tags for ion channel studies. Described here are some of the epitope tags that have been used to study ion channel subunits, including the HA, FLAG, myc, His6, and green fluorescent protein (GFP) epitopes, as well as some of the applications and avenues of research in which they have proven advantageous. Potential pitfalls and caveats associated with the use of these epitope tags are also discussed, with an emphasis on the need to include careful characterization of epitope‐tagged channel subunits as part of their construction. Finally, potential avenues for future investigation and the development of this approach are considered. J. Cell. Physiol. 213:618–625. © 2007 Wiley‐Liss, Inc.
Application of anodized aluminium oxide as a biochip substrate for a Fabry–Perot interferometer
Authors: Lee Jung‐Chul , An Jin Young , Kim Byung‐Woo 
Published: September 2007

AbstractBACKGROUND: Non‐uniform distribution of pore size and depth of porous Si chip for a Fabry–Perot interferometer, in a previous study, led to relatively low sensitivity with poor reproducibility when its surface was immobilized with calyx crown derivative (Prolinker A). In this study, porous anodized aluminium oxide (AAO) was used as an alternative biochip substrate for detecting β‐galactosidase, and chip fabrication and surface functionalization methods were optimized.RESULTS: According to structural and spectral analysis of the AAO surface, an optimal operating voltage for anodization was determined as 40 V, which gave the best uniformity in pore size (about 30 nm) and fringe pattern. The ΔEOT (difference in effective optical thickness) showed a linear relationship (R2 = 0.9932) with β‐galactosidase concentration in the range 0.05–5 units enzyme mL−1, corresponding to 0.07–7.0 µg protein mL−1.CONCLUSIONS: With uniformly porous AAO immobilized with Prolinker A, sensitivity was enhanced about 200 times compared with the lowest detection concentration of 10 units mL−1 with the porous Si chip used in the previous study. Copyright © 2007 Society of Chemical Industry
Differences among cell types in NAD+ compartmentalization: A comparison of neurons, astrocytes, and cardiac myocytes
Authors: Alano Conrad C. , Tran Alexandra , Tao Rong , Ying Weihai , Karliner Joel S. , Swanson Raymond A. 
Published: September 2007

AbstractActivation of the nuclear enzyme poly(ADP‐ribose)‐1 leads to the death of neurons and other types of cells by a mechanism involving NAD+ depletion and mitochondrial permeability transition. It has been proposed that the mitochondrial permeability transition (MPT) is required for NAD+ to be released from mitochondria and subsequently consumed by PARP‐1. In the present study we used the MPT inhibitor cyclosporine‐A (CsA) to preserve mitochondrial NAD+ pools during PARP‐1 activation and thereby provide an estimate of mitochondrial NAD+ pool size in different cell types. Rat cardiac myocytes, mouse cardiac myocytes, mouse cortical neurons, and mouse cortical astrocytes were incubated with the genotoxin N‐methyl‐N′‐nitro‐N‐nitrosoguanidine (MNNG) in order to activate PARP‐1. In all four cell types MNNG caused a reduction in total NAD+ content that was blocked by the PARP inhibitor 3,4‐dihydro‐5‐[4‐(1‐piperidinyl)butoxy]‐1(2H)‐isoquinolinone. Inhibition of the mitochondrial permeability transition with cyclosporine‐A (CsA) prevented PARP‐1‐induced NAD+ depletion to a varying degree in the four cell types tested. CsA preserved 83.5% ± 5.2% of total cellular NAD+ in rat cardiac myocytes, 85.7% ± 8.9% in mouse cardiac myocytes, 55.9% ± 12.9% in mouse neurons, and 22.4% ± 7.3% in mouse astrocytes. CsA preserved nearly 100% of NAD+ content in mitochondria isolated from these cells. These results confirm that it is the cytosolic NAD+ pool that is consumed by PARP‐1 and that the mitochondrial NAD+ pool is consumed only after MPT permits mitochondrial NAD+ to exit into the cytosol. These results also suggest large differences in the mitochondrial and cytosolic compartmentalization of NAD+ in these cell types. © 2007 Wiley‐Liss, Inc.
Driving physical mechanisms of flow and dispersion in urban canopies
Authors: Klein P. , Leitl B. , Schatzmann M. 
Published: September 2007

AbstractThe paper summarizes results from recent full‐scale and wind‐tunnel studies and discusses the complexity of urban canopy layer (UCL) flow and related challenges for urban modeling. Wind‐tunnel data for idealized street‐canyon intersections demonstrate that street‐level flow and dispersion patterns are significantly altered for configurations with non‐uniform building heights. For most wind directions, concentration maxima were upto a factor of 2 higher for cases with taller buildings near the intersection. Enhanced vertical downward mixing in the wakes of the taller buildings apparently causes higher street‐level winds close by, but simultaneously, other regions become sheltered from active mixing and poor ventilation. The analysis of Joint Urban 2003 (JU2003) full‐scale data also pointed out that high‐momentum fluid can be effectively mixed down in the wakes of high‐rise buildings, and that UCL flow is predominantly dynamically driven by roof‐level winds. Building‐height variability is thus, a key factor for UCL dynamics and mixing.Additionally, a linear model, which assumes that the along‐ and across‐canyon velocity components are directly proportional to their above roof‐level counterparts, has then been tested. The complexity of UCL flow patterns cannot be captured by such a simple model, but it may be useful for estimating street‐level winds. For the along‐canyon component, more than 70% of the calculated values were within a factor of 2 of the measured values, while for the across‐canyon component less than 50% of the predictions agreed within a factor of 2. The practical applicability of the model was further assessed using JU2003 wind‐tunnel data and a comparison between JU2003 wind‐tunnel and full‐scale flow profiles is also presented. It becomes obvious that UCL flow patterns are significantly altered by changes in upwind wind direction of less than 10° . While the field and laboratory results are qualitatively in good agreement, noticeable differences exist at certain sites. Copyright © 2007 Royal Meteorological Society
A novel injectable scaffold for cartilage tissue engineering using adipose‐derived adult stem cells
Authors: Wei Yiyong , Hu Yunyu , Hao Wei , Han Yisheng , Meng Guolin , Zhang Dezhi , Wu Zixiang , Wang Haiqiang 
Published: September 2007

AbstractArticular cartilage has a limited self‐regenerative capacity. Thus, treatment of cartilage lesions is a major challenge. Tissue engineering using a variety of biomaterials is a promising solution to the problem of cartilage damage. In this in vitro study, we investigated the effect of the presence of cartilage‐tissue chondroitin‐sulfate (CS) in a fibrin scaffold on the differentiation of adipose‐derived adult stem cells (ADAS cells) into chondrocytes. Isolated rabbit ADAS cells were cultured in fibrin matrices with and without CS for up to 14 days. ADAS cells differentiated into chondrocytes in both matrices, but cell proliferation, glycoaminoglycans content, and type II collagen expression were significantly higher in the fibrin–CS matrices than those in the fibrin matrices alone. Histological examination and scanning electronic microscopy revealed the fibrin–CS matrices exceeded in inducing differentiation of ADAS cells into chondrocytes in terms of tissue morphological characteristics. We concluded that the fibrin–CS matrices mimicking native cartilage extracellular matrix could act as a three‐dimensional scaffold for cartilage tissue engineering and have the potential for promoting ADAS cells differentiation into chondrocytes. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:27–33, 2008
Chemical composition, antioxidant capacity and functionality of raw and processed Phaseolus lunatus
Authors: Granito Marisela , Brito Yannellis , Torres Alexia 
Published: September 2007

AbstractThe nutrients, non‐nutritional components and bioactive compounds, as well as the antioxidant capacity of raw, cooked, tray and drum‐dried Phaseolus lunatus have been quantified. Likewise, the minerals, soluble carbohydrates, total polyphenols and tannins in the soaking and cooking waters were quantified. In addition, the functional properties such as the water and oil absorption indexes and the emulsifying and the foaming capacities were studied. The protein content of the raw beans was 24.98% and decreased, like calcium, magnesium and potassium, with the soaking and cooking processes; these losses are found in the soaking and cooking waters. Drum drying decreased anti‐nutritional factors like trypsin inhibitors (66.09%) and cyanhydric acid (50.36%). Similarly, soluble fiber, available starch, total starch, and soluble sugars diminished, while total and insoluble fiber and resistant starch increased. The content of total polyphenols, tannins and antioxidant capacity decreased with thermal processing, being drum drying the process that least diminished antioxidant capacity. Likewise, the water absorption index was increased by 85% and 161.5% with processing. It was shown that P. lunatus is an important source of nutrients and can be consumed in whole bean form or used as a functional ingredient to be added in the development of new products. Copyright © 2007 Society of Chemical Industry
The influence of different single dietary sources on moult induction in laying hens
Authors: Mansoori Behzad , Modirsanei Mehrdad , Farkhoy Mohsen , Kiaei Mohammad‐Mehdi , Honarzad Jila 
Published: September 2007

AbstractAn investigation was carried out to assess the possibility of using single dietary sources as alternatives to feed deprivation for the induction of moult in commercial laying hens. The study involved six dietary groups of 29 laying hens: unmoulted, dried tomato pomace, alfalfa meal, rice bran, cumin seed meal and feed withdrawal. The birds received the above diets during the moulting period (11 days), and body weight loss and ovary weight regression were measured. Post‐moult production parameters (number of eggs produced per hen per day, egg weight, shell weight, yolk colour and Haugh unit) were measured for 12 weeks. Results showed that all dietary sources were as effective as feed withdrawal in causing ovary weight regression in birds. Birds provided with tomato pomace or alfalfa showed lower weight losses than feed‐deprived birds at the end of the moulting period. Hens moulted by tomato pomace or alfalfa exhibited post‐moult levels of egg production over a 12 week period that were superior to those of hens moulted by feed withdrawal. Post‐moult eggs laid by hens moulted by all dietary sources were of comparable quality to eggs from feed‐deprived hens and superior to those from unmoulted hens. As fibrous feeds with low metabolisable energy and an appreciable amount of protein, dried tomato pomace and alfalfa meal may be fed to hens on an ad libitum basis for effective moult induction while reducing the stress of severe starvation and retaining comparable egg quality and production. Copyright © 2007 Society of Chemical Industry
Chemical composition and in vitro antioxidant studies on Syzygium cumini fruit
Authors: Benherlal Palayyan Saraswathy , Arumughan Chami 
Published: September 2007

AbstractSyzygium cumini, widely known as Jamun, is a tropical tree that yields purple ovoid fleshy fruit. Its seed has traditionally been used in India for the treatment of diabetes. Based on the available ethno‐pharmacological knowledge, further studies were extended to understand the chemical composition and antioxidant activities of three anatomically distinct parts of fruit: the pulp, kernel and seed coat. Fruit parts, their corresponding ethanol extracts and residues were evaluated for chemical composition. The alcoholic extract was evaluated for its antioxidant potential against DPPH•, OH•, O2•− and lipid peroxidation. The whole fruit consisted of 666.0 ± 111.0 g kg−1 pulp, 290.0 ± 40.0 g kg−1 kernel and 50.0 ± 15.0 g kg−1 seed coat. Fresh pulp was rich in carbohydrates, protein and minerals. Total fatty matter was not significant in all three parts of fruit. Detailed mineral analysis showed calcium was abundant in all fruit parts and extracts. Total phenolics, anthocyanins and flavonoid contents of pulp were 3.9 ± 0.5, 1.34 ± 0.2 and 0.07 ± 0.04 g kg−1, respectively. Kernel and seed coat contained 9.0 ± 0.7 and 8.1 ± 0.8 g kg−1 total phenolics respectively. Jamun pulp ethanol extract (PEE), kernel ethanol extract (KEE) and seed coat ethanol extract (SCEE) showed a high degree of phenolic enrichment. DPPH radical scavenging activity of the samples and standards in descending order was: gallic acid > quercetin > Trolox > KEE > BHT > SCEE > PEE. Superoxide radical scavenging activity (IC50) of KEE was six times higher (85.0 ± 5.0 µg mL−1) compared to Trolox (540.0 ± 5.0 µg mL−1) and three times compared to catechin (296.0 ± 11.0 µg mL−1). Hydroxyl radical scavenging activity (IC50) of KEE was 151.0 ± 5.0 µg mL−1 which was comparable with catechin (188.0 ± 6.0 µg mL−1). Inhibition of lipid peroxidation of the extracts was also studied and their activity against peroxide radicals were lower than that of standard compounds (BHT, 79.0 ± 4.0 µg mL−1; quercetin, 166.0 ± 13.0 µg mL−1; Trolox, 175.0 ± 4.0 µg mL−1; PEE, 342.0 ± 17.0 µg mL−1; KEE, 202.0 ± 13.0 µg mL−1 and SCEE, 268.0 ± 13.0 µg mL−1. Copyright © 2007 Society of Chemical Industry
Animal welfare in organic farming systems
Authors: Spoolder Hans AM 
Published: September 2007

AbstractThe concept of farm animal welfare can, for practical purposes, be translated into the so‐called Five Freedoms.1 Organic farming aims to meet animal welfare needs and should therefore comply with these Freedoms. The first Freedom, from hunger and thirst, is met in any system properly managed to organic standards. The Freedom from thermal and physical discomfort is challenged as organic husbandry systems face more climatic extremes. However, they also provide more ‘control’ to the animal by offering a choice when seeking warmth or a cool place to lie. The Freedom from pain, injury and disease is the most complicated one. Organic farming virtually bans mutilations (e.g. debeaking, tail docking), although some are still allowed and practised (e.g. castration). Organic animals are more exposed to wildlife and at risk of contracting infectious diseases. However, it is possible (although not proven) that organically managed animals are more resistant to illness. The Freedom to express normal behaviour is met through environmental enrichment and group housing. The Freedom from fear and distress is supported by e.g. extra (social) space. In conclusion, if animal health can be maintained, organic farming is very well placed to provide good animal welfare. Copyright © 2007 Society of Chemical Industry
Lipid processing in ionic liquids
Authors: Lue Bena‐Marie , Guo Zheng , Xu Xuebing 
Published: September 2007

AbstractIonic liquids (ILs) have been touted as ”green” alternatives to traditional molecular solvents and have many unique properties which make them extremely desirable substitutes. Among their most attractive properties are their lack of vapour pressure, broad liquid range, strong solvating power and the ability to tailor properties of individual ILs to meet specific requirements. This article highlights current research as well as the vast potential of ILs for use as media for reactions, separation and processing in the lipid area.
Is the metabolic syndrome a useful concept?
Authors: Stanley John 
Published: September 2007

AbstractNot all obese individuals are insulin resistant while individuals who fail to develop adequate adipose tissue mass, a rare disorder called lipodystrophy, are insulin resistant. These observations suggest that the relationship between body fat and insulin resistance is complex. This relationship can be explained by considering body fat distribution. According to one idea visceral fat is characterised by the overproduction of fatty acids which stimulate glucose production by the liver and inhibit glucose use by skeletal muscle and the underproduction of adipokines such as adiponectin which improve insulin resistance. Hence individuals with excess visceral fat become insulin resistant. According to a second idea excess visceral fat is a marker for dysfunctional adipose tissue. Energy in excess of requirements is normally stored as triacylglycerols in subcutaneous fat. If this is defective then triacylglycerols are stored at other ectopic sites leading to impaired function. Obese individuals without insulin resistance store their triacylglycerols in subcutaneous fat and are protected. Individuals with lipodystrophy have no subcutaneous fat so they develop insulin resistance.
A Comparative Study of Oxygen Permeabilities of Film‐Forming Polymers by Quenching of Platinum Porphyrin Phosphorescence
Authors: Hess Sandra , Becker Alfons , Baluschev Stanislav , Yakutkin Vladimir , Wegner Gerhard 
Published: September 2007

AbstractOxygen permeabilities of different polymers were determined by using two different methods based on quenching of an excited phosphorescent dye by oxygen. In the first method, the phosphorescent dye platinum octaethylporphyrin is directly dissolved in the polymer film of interest whereas in the second method a sensor film is used which is separated from the film of interest by a spacer. The polymers investigated are PMMA, PVC, PVAc, cellulose acetate, PEMA, and PS. The resulting oxygen permeability coefficients are compared with data reported in the literature. It was found that oxygen permeation strongly depends on the protocol of preparation and thermal history of the films.magnified image