bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunosenescence of ageing
Authors: Gruver AL , Hudson LL , Sempowski GD 
Published: January 2007

AbstractAgeing is a complex process that negatively impacts the development of the immune system and its ability to function. The mechanisms that underlie these age‐related defects are broad and range from defects in the haematopoietic bone marrow to defects in peripheral lymphocyte migration, maturation and function. The thymus is a central lymphoid organ responsible for production of naïve T cells, which play a vital role in mediating both cellular and humoral immunity. Chronic involution of the thymus gland is thought to be one of the major contributing factors to loss of immune function with increasing age. It has recently been demonstrated that thymic atrophy is mediated by a shift from a stimulatory to a suppressive cytokine microenvironment. In this review we present an overview of the morphological, cellular and biochemical changes that have been implicated in the decline of thymic and peripheral immune function with ageing. We conclude with the clinical implications of age‐associated immunosenescence to vaccine development for tumours and infectious disease. A fundamental understanding of the complex mechanisms by which ageing attenuates immune function will enable translational research teams to develop new therapies and vaccines specifically aimed at overcoming these defects in immunological function in the aged. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Evaluation of density functional theory methods for the electronic interactions between indole and substituted benzene: Applications to horseradish peroxidase
Authors: Van Sickle Karina , Culberson Lori Marie , Holzmacher Jeremy Levin , Cafiero Mauricio 
Published: January 2007

AbstractIn an effort to evaluate and design fast, accurate density functional theory (DFT) methods for calculating electrostatic and dispersion interactions between proteins and ligands, we have set up a model system examining interactions between mono‐substituted benzene and indole in seven different stable conformations. We first optimized the geometries of the monomers at the B3LYP/6‐31G level, and then scanned the potential curves with MP2, HF, B3LYP, SVWN, and HCTH407 [all at the 6‐311++G(d,p) level] to find the optimum separation. We used the approximate counterpoise method to calculate the basis set superposition error‐corrected interaction energies at the optimum geometries. We then applied these methods to the interactions between aromatic active site residues of horseradish peroxidase C with indole‐3‐propionic acid at two different binding sites. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Zum Reaktionsverhalten des polycyclischen Oligoalumosiloxans [Ph2SiO]8[AlO(OH)]4 gegenüber Hexamethyldisilazan
Authors: Veith Michael , Rammo Andreas , Huch Volker , Biegler Julia 
Published: January 2007

AbstractThe Reaction Behaviour of the Polycylic Oligoalumosiloxane [Ph2SiO]8[AlO(OH)]4 towards HexamethyldisilazaneThe reaction of the oligoalumosiloxane [Ph2SiO]8[AlO(OH)]4 (1) with hexamethyldisilazane leads to the triple ionic [Ph2SiO]8[AlO2]2[AlO(O‐SiMe3)]2[NH4·THF]2·2 THF (2) and in the presence of pyridine to [Ph2SiO]8[AlO1.5]4·2py·1.5 C7H8 (3). Apart from the usual characterization techniques (NMR and IR spectroscopy) the molecular structures of 2 and 3 have been determined by single‐X‐ray diffraction analyses. Both alumosiloxanes 2 and 3 present new types of molecular structures with a central four membered Al2O2‐ring, on which the further aluminium atoms are attached via oxygen atoms. This leads to an Al4‐lozenge, which is centered in subtriangles by oxygen atoms.
In vitro migration and adhesion of fibroblasts from different phases of palatal wound healing
Authors: Van Beurden Hugo E. , Snoek Patricia A. M. , Von den Hoff Johannes W. , Torensma Ruurd , Maltha Jaap C. , Kuijpers‐Jagtman Anne M. 
Published: January 2007

ABSTRACTCleft palate patients often show mid‐facial growth impairment after surgical closure of the defect. This is a consequence of palatal wound healing, and more specifically of wound contraction and scar tissue formation. Cells of the fibroblast lineage are responsible for these processes and they display different phenotypes in the course of the wound healing process. The aim of this study was to analyze the in vitro adhesion and migration of wound fibroblasts, isolated during the palatal wound healing process in the rat. Additionally, we analyzed the expression of β1 integrins and vinculin, the key players in adhesion and migration. Palatal fibroblasts from age‐matched controls were analyzed to measure the effects of normal aging. Palatal fibroblasts from unwounded tissue showed a low migratory behavior (<25 μm), a strong capability to adhere (>80%) and a low expression of β1 integrins and vinculin. In contrast, fibroblasts obtained from healing palatal wounds were highly migratory (>200 μm) coupled to a weak capability to adhere (<65%) and a high expression of vinculin and β1 integrins. These data show that the palatal wound healing process induces a change in fibroblast phenotype from “quiescent” to “activated,” which persists in vitro.
Mutual dependence of murine fetal cutaneous regeneration and peripheral nerve regeneration
Authors: Kishi Kazuo , Ohyama Kyoji , Satoh Hiroko , Kubota Yoshiaki , Tanaka Takara , Imanishi Nobuaki , Nakajima Hideo , Kawamura Kohki , Nakajima Tatsuo 
Published: January 2007

ABSTRACTMammalian fetal cutaneous wounds made at certain developmental stages show complete regeneration. It is reported that wound healing in both adult and fetal skin is disrupted by denervation. Furthermore, fetal cutaneous regeneration has unique aspects such as epidermal wrinkle texture regeneration and dermal regeneration that depend on developmental stage. Therefore, we have examined the relationship of fetal cutaneous regeneration with denervation. We made cutaneous wounds on fetal mice at various developmental time points including embryonic days (E)13, E15, and E17, and compared the regenerating patterns of peripheral nerves in the skin. We found that when the fetuses are wounded at an early stage of development, peripheral nerves regenerate quicker than at later stages of development when peripheral nerve regeneration is delayed. Next, we denervated the intercostal nerves and made wounds at the denervated sites on E13 and E15. We found that epidermal wrinkling and dermal regeneration were disrupted by denervation. These findings indicate that components of fetal cutaneous regeneration and peripheral nerve regeneration are mutually dependent.
SELECTION AND PURIFICATION OF LIQUIDS REQUIRING LOW‐LEVEL SUSPENDED PARTICLES
Authors: Connelly Robert F. 
Published: January 2007

SummaryStandards defining clean environments are becoming quite common. There is a need for similar documents setting forth guidelines for producing and handling clean liquids. Clean liquids are needed as cleaning media for sensitive surfaces and as functional fluids.Certain properties of liquids complicate the control of particulate contamination. Whenever possible, liquids meeting the criteria of the Appendix should be selected. When liquids with limited stability must be employed, controls should be established to minimize contamination generation.The design of an adequate filtration system requires the consideration of many more factors than merely the selection of the correct filter medium. Further, the way in which the system is used and serviced has a profound effect upon performance. Present practices for the storage and transfer of clean liquids leave much to be desired. Improved methods for the transfer of clean liquids have been described.
The Kuroshio Onshore Intrusion along the Shelf Break of the East China Sea: The Origin of the Tsushima Warm Current
Authors: Guo Xinyu , Miyazawa Yasumasa , Yamagata Toshio 
Published: January 2007

Abstract
A 1/18° nested ocean model is used to determine locations, volume transports, and temporal variations of Kuroshio onshore fluxes across the shelf break of the East China Sea (ECS). The Kuroshio onshore flux shows strong seasonality: maximum (∼3 Sv; 1 Sv ≡ 106 m3 s−1) in autumn and minimum (&lt;0.5 Sv) in summer. Another short-term (∼17 days) variation due to Kuroshio meanders introduces large fluctuations in the onshore fluxes but its seasonal average almost vanishes. The Kuroshio onshore fluxes have two major sources, Kuroshio intrusion northeast of Taiwan and Kuroshio separation southwest of Kyushu; the former provides larger onshore flux than the latter. Therefore, in addition to the waters from the Taiwan Strait and the Kuroshio separation region southwest of Kyushu, the water due to the Kuroshio intrusion northeast of Taiwan is also a major source of the Tsushima Warm Current. A vorticity equation is used to separate the contribution of surface Ekman transport to the Kuroshio onshore fluxes in the ECS from that relating to density fields. For the total Kuroshio onshore flux across the entire shelf break, its seasonal variation is primarily controlled by the Ekman transport while the change in density field is secondary. For the Kuroshio onshore flux at a fixed location along the shelf break, its seasonal variation is primarily related to the change in density field and the Ekman transport is secondary. Furthermore, the role of the Taiwan Strait water and the Kuroshio water across the shelf break on material transport in the ECS is examined with passive tracer experiments. In summer, about half of the tracer in the Tsushima Strait originates in the Taiwan Strait, while the other half comes from the Kuroshio. From summer to winter, the ratio changes dramatically; the contribution from the Taiwan Strait decreases to 20% and that from the Kuroshio increases up to 80%. The tracer originating in the Kuroshio water dominates the bottom layer of the continental shelf in the ECS throughout the year.
The Role of Eddies in Determining the Structure and Response of the Wind-Driven Southern Hemisphere Overturning: Results from the Modeling Eddies in the Southern Ocean (MESO) Project
Authors: Hallberg Robert , Gnanadesikan Anand 
Published: January 2007

Abstract
The Modeling Eddies in the Southern Ocean (MESO) project uses numerical sensitivity studies to examine the role played by Southern Ocean winds and eddies in determining the density structure of the global ocean and the magnitude and structure of the global overturning circulation. A hemispheric isopycnal-coordinate ocean model (which avoids numerical diapycnal diffusion) with realistic geometry is run with idealized forcing at a range of resolutions from coarse (2°) to eddy-permitting (1/6°). A comparison of coarse resolutions with fine resolutions indicates that explicit eddies affect both the structure of the overturning and the response of the overturning to wind stress changes. While the presence of resolved eddies does not greatly affect the prevailing qualitative picture of the ocean circulation, it alters the overturning cells involving the Southern Ocean transformation of dense deep waters and light waters of subtropical origin into intermediate waters. With resolved eddies, the surface-to-intermediate water cell extends farther southward by hundreds of kilometers and the deep-to-intermediate cell draws on comparatively lighter deep waters. The overturning response to changes in the winds is also sensitive to the presence of eddies. In noneddying simulations, changing the Ekman transport produces comparable changes in the overturning, much of it involving transformation of deep waters and resembling the mean circulation. In the eddy-permitting simulations, a significant fraction of the Ekman transport changes are compensated by eddy-induced transport drawing from lighter waters than does the mean overturning. This significant difference calls into question the ability of coarse-resolution ocean models to accurately capture the impact of changes in the Southern Ocean on the global ocean circulation.
Comparing sequences without using alignments: application to HIV/SIV subtyping
Authors: Didier Gilles , Debomy Laurent , Pupin Maude , Zhang Ming , Grossmann Alexander , Devauchelle Claudine , Laprevotte Ivan 
Published: January 2007

Abstract

Background
In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment.

Results
In this paper, HIV (Human Immunodeficiency Virus) and SIV (Simian Immunodeficiency Virus) sequence data are used to evaluate this method. The program produces tree topologies that are identical to those obtained by a combination of standard methods detailed in the HIV Sequence Compendium. Manual alignment editing is not necessary at any stage. Furthermore, only one user-specified parameter is needed for constructing trees.

Conclusion
The extensive tests on HIV/SIV subtyping showed that the virus classifications produced by our method are in good agreement with our best taxonomic knowledge, even in non-coding LTR (Long Terminal Repeat) regions that are not tractable by regular alignment methods due to frequent duplications/insertions/deletions. Our method, however, is not limited to the HIV/SIV subtyping. It provides an alternative tree construction without a time-consuming aligning procedure.
Effect of strenuous exercise on urine concentrations of homovanillic acid, cortisol, and vanillylmandelic acid in sled dogs
Authors: Durocher Lawren L. , Hinchcliff Kenneth W. , Williamson Kathy K. , McKenzie Erica C. , Holbrook Todd C. , Willard Michael , Royer Chris M. , Davis Michael S. 
Published: January 2007

Abstract
Objective—To determine whether prolonged exercise by conditioned sled dogs affects urine concentrations of homovanillic acid (a metabolite of dopamine), vanillylmandelic acid (a metabolite of norepinephrine and epinephrine), and cortisol.
Animals—24 conditioned Alaskan sled dogs (2 to 8.5 years old) that were in training for a multiday endurance race.
Procedures—Voided urine samples were collected from 4 groups of dogs (randomly selected from 54 dogs) after no exercise (control group; n = 6 dogs), completion of a 160km run (group A; 3), completion of a 420-km run (group B; 7), and completion of a 560-km run (group C; 6). Urine cortisol concentrations were determined by use of an immunoassay technique; urine vanillylmandelic acid and homovanillic acid concentrations were measured via high-performance liquid chromatography.
Results—Compared with the control group, urine cortisol concentration in groups A, B, and C was significantly different (5.33 × 10−4 ± 2.62 × 10−4 μg/dL vs 1.04 × 10−4 ± 2.31 × 10−5 μg/dL, 8.88 × 10−4 ± 5.49 × 10−4 μg/dL, and 6.31 × 10−4 ± 5.09 × 10−4 μg/dL, respectively). Urine homovanillic acid concentration did not differ among the 4 groups. Vanillylmandelic acid was not detected in any urine samples.
Conclusions and Clinical Relevance—Results indicated that prolonged exercise by sled dogs did not affect urine homovanillic acid concentration but did increase urinary cortisol secretion, which is indicative of adrenocortical stimulation. The apparent lack of vanillylmandelic acid in voided urine samples requires further investigation.
Vortex tracking and mixing enhancement in stirred processes
Authors: Ducci A. , Yianneskis M. 
Published: January 2007

AbstractThe precession of macroinstability (MI) vortices in stirred vessels has been investigated with vortex tracking methodologies, and utilized to enhance mixing performance. The techniques used are presented and employed to determine the instantaneous and average location, size and vorticity of the MI vortex for Re = 3,200 and 32,000 in 80 and 294 mm dia. vessels stirred by a Rushton impeller. Measurements of mixing time are performed in a 588 mm dia. vessel with surface insertion of a passive scalar tracer either inside or outside the precessing MI vortex. The data indicate that in‐vortex insertion can result in a mixing time reduction of 20%, and even possibly 30%. © 2007 American Institute of Chemical Engineers AIChE J 2007
Testing alternative explanations of phantom decoy effects
Authors: Pettibone Jonathan C. , Wedell Douglas H. 
Published: January 2007

AbstractPhantom decoys are alternatives that asymmetrically dominate a targeted alternative and yet lead to increased selection of the target when the decoy is declared to be unavailable. This effect is difficult to explain within most standard theoretical accounts of decoy effects. The current experiments tested between three explanations of this effect: (1) the relative advantage model based on loss aversion, (2) similarity substitution, and (3) range weighting. In Experiment 1, participants were presented trinary choice sets, with half of the sets containing a phantom decoy in one of five possible locations within the attribute space. Phantom decoy effects were robust across all decoy locations but one, and the pattern of effects most closely corresponded to predictions of the relative advantage model. Experiment 2 used a within‐subjects manipulation of the five phantom decoy locations. The overall pattern of effects most closely corresponded to predictions from the relative advantage model, as did the pattern for the group of participants who exhibited the strongest phantom decoy effects. Copyright © 2007 John Wiley & Sons, Ltd.
On a Possible Growth Mechanism for Polycyclic Aromatic Hydrocarbon Dications: C7H62++C2H2
Authors: Roithová Jana , Schröder Detlef 
Published: January 2007

AbstractThe mechanism of the bond‐forming reaction between C7H62+ and C2H2 to yield C9 entities has been investigated by density functional theory calculations with close comparison with experimental data. It is shown that the reaction produces the C9H62+ and C9H72+ dications with geometries most probably derived from the indene skeleton. In comparison, the formation of linear structures of dications is much more energy‐demanding and therefore appears improbable.
A Combined Computational and Experimental Approach for the Analysis of the Enantioselective Potential of a New Macrocyclic Receptor for N‐Protected α‐Amino Acids
Authors: Ragusa Andrea , Hayes Joseph M. , Light Mark E. , Kilburn Jeremy D. 
Published: January 2007

AbstractA new macrocyclic receptor incorporating a thiourea moiety has been synthesised. Crystal structures of the macrocycle showed that the receptor has a rigid backbone but the thiourea moiety can orientate itself to bind to a DMSO solvent molecule. Force‐field (MMFFs) calculations were performed to model the macrocycle and its binding properties with respect to N‐protected amino acids, which were measured experimentally by NMR titration. Binding free energies were calculated by using the mode integration algorithm (MINTA) or free‐energy perturbation (FEP). Excellent qualitative agreement with experiment was obtained. To further exploit the accuracy of the free‐energy predictions for this system, the faster free‐energy algorithm MINTA was used as a prediction tool to test the binding affinity of the macrocycle towards a series of several other amino acid derivatives, which speeded up considerably the screening process and reduced laboratory costs.
Microporous Organic Materials from Hydrophobic Dipeptides
Authors: Görbitz Carl Henrik 
Published: January 2007

AbstractIn the last few years dipeptides with two hydrophobic residues (hydrophobic dipeptides) have emerged as an unexpected source of stable microporous organic materials. Supramolecular self‐assembly of the rather small building blocks is dictated by stringent demands on the hydrogen‐bond formation by the peptide main chains and the aggregation of hydrophobic entities in the side chains. A systematic survey of structures derived from single‐crystal X‐ray diffraction studies has revealed the existence of two large classes of structures, differing in the dimensionality of the hydrogen‐bonding patterns in the crystals and the nature of the channels. The present review summarizes the structural properties of the microporous dipeptides and discusses their potential applications.
Automated laser scanning cytometry: A powerful tool for multi‐parameter analysis of drug‐induced apoptosis
Authors: Holme Andrea Lisa , Yadav Sanjiv Kumar , Pervaiz Shazib 
Published: January 2007

AbstractBackground:Simultaneous analysis of multiple intracellular events is critical for assessing the effect of biological response modifiers, including the efficacy of chemotherapy. Here we used the automated laser scanning cytometry (LSC) for multi‐parameter analysis of drug‐induced tumor cell apoptosis.Materials:Using 2‐mercaptopyridine‐N‐oxide‐hydrate sodium salt, or the commonly used chemotherapeutic agents etoposide and camptothecin, we performed simultaneous analyses of apoptosis‐related morphological features as well as fluorescence‐based biochemical changes in a 96‐well format.Results:We demonstrate the scope of LSC as a platform for comparing multiple variables between different cell populations, distinguishing unique events at a single cell level within a sample population, and enabling simultaneous screenings in a single assay at multiple dosages and time‐points.Conclusion:These data underscore the power of LSC for simultaneous multi‐parameter analysis, which could have implications for screening or assessing the efficacy of drug responses in heterogeneous cell populations and at the single cell level. © 2007 International Society for Analytical Cytology.
Seismic performance of electric transmission network under component failures
Authors: Shinozuka M. , Dong X. , Chen T. C. , Jin X. 
Published: January 2007

AbstractDealing with the transmission network of electric power systems, this paper identifies the sequential failures of receiving station components under a severe earthquake. Such failures progressively degrade the power network performance, potentially leading to a network blackout. Hence, in this paper, these components are incorporated into the network systems analysis taking their seismic vulnerability into consideration in the form of fragility curves for the evaluation of the network performance under seismic conditions. Specifically, most critical to the operation of transmission network, transformers, disconnect switches, circuit breakers and buses are integrated into the systems analysis, exploring the possibility of progressive failures of these components. The scenarios of these component failures can make it possible to estimate quantitatively direct cost of damage, emergency repair and restoration, and duration of power interruption and attendant economic losses and societal disruption. Copyright © 2006 John Wiley & Sons, Ltd.