bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating the compatibility of three colorimetric protein assays for two‐dimensional electrophoresis experiments
Authors: Kao Shao‐Hsuan , Wong Hin‐Kwan , Chiang Chia‐Ying , Chen Han‐Min
Published: May 2008

To evaluate compatibility of commonly used colorimetric protein assays for 2‐DE experiments, we investigated the interfering mechanisms of major 2‐DE component(s) in the Lowry‐based assay, the Bradford assay and the bicinchoninic acid (BCA) assay. It was found that some 2‐DE components did not directly interfere with the assays' color development reaction, but possibly influenced the quantitation results by interacting with proteins. Generally, simultaneous presence of 2‐DE components in the samples demonstrated a cooperative rather than additive interference. Interference by reductants in the Lowry‐based assay and the BCA assay were too prominent and could not be completely eliminated by either the reported alkylation procedure or the water dilution procedure. The Bradford assay however, presented a more suitable method for quantitating 2‐DE samples because it was less interfered by most 2‐DE components. Furthermore, despite slightly compromising protein solubility, utilization of reductant free 2‐DE sample buffers conferred application of the Lowry‐based and BCA assays in the 2‐DE experiments.
Proteomic and transcriptomic analysis for streptozotocin‐induced diabetic rat pancreas in response to fungal polysaccharide treatments
Authors: Kim Sang Woo , Hwang Hye Jin , Baek Yu Mi , Lee Sung Hak , Hwang Hee Sun , Yun Jong Won
Published: May 2008

In an attempt to search for novel biomarkers for monitoring diabetes prognosis, we examined the influence of the hypoglycemic fungal extracellular polysaccharides (EPS) on the differential change in pancreatic proteome and transcriptome in streptozotocin (STZ)‐induced diabetic rats using 2‐DE‐based protein mapping and oligonucleotide microarray analysis. The 2‐DE system separated more than 2000 individual spots, demonstrating that 34 proteins out of about 500 matched spots were differentially expressed. A total of 22 overexpressed and 12 underexpressed proteins in 2‐DE map were observed (p<0.05) between the healthy and diabetic rats, of which 26 spots were identified by PMF analysis. Of these, significant down regulation of carbonyl reductase (Cbr), hydroxymethylglutaryl‐CoA synthase (HMGCS), and putative human mitogen‐activated protein kinase activator with WD repeats‐binding protein (MAWDBP) in diabetic pancreas were reported for the first time in this study. When treated with EPS, all these four proteins were reverted to normal levels. The microarray analysis revealed that 96 out of 1272 genes were down‐ or up‐regulated in the diabetic rats and the altered transcript levels of many of these genes were reversed after EPS treatment. In particular, ROS generation in rat islets was significantly increased after STZ treatment, thereafter EPS treatment was likely to play a preventive role in β‐cell destruction mediated by STZ. Taken together, EPS may act as a potent regulator of gene expression for a wide variety of genes in diabetic rats, particularly in antioxidative stress, insulin biosynthesis, and cell proliferation.
Immobilization strategies for single‐chain antibody microarrays
Authors: Seurynck‐Servoss Shannon L. , Baird Cheryl L. , Miller Keith D. , Pefaur Noah B. , Gonzalez Rachel M. , Apiyo David O. , Engelmann Heather E. , Srivastava Sudhir , Kagan Jacob , Rodland Karin D. , Zangar Richard C.
Published: May 2008

Sandwich ELISA microarrays have great potential for validating disease biomarkers. Each ELISA relies on robust‐affinity reagents that retain activity when immobilized on a solid surface or when labeled for detection. Single‐chain antibodies (scFv) are affinity reagents that have greater potential for high‐throughput production than traditional IgG. Unfortunately, scFv are typically less active than IgG following immobilization on a solid surface and not always suitable for use in sandwich ELISAs. We therefore investigated different immobilization strategies and scFv constructs to determine a more robust strategy for using scFv as ELISA reagents. Two promising strategies emerged from these studies: (i) the precapture of epitope‐tagged scFv using an antiepitope antibody and (ii) the direct printing of a thioredoxin (TRX)/scFv fusion protein on glass slides. Both strategies improved the stability of immobilized scFv and increased the sensitivity of the scFv ELISA microarray assays, although the antiepitope precapture method introduced a risk of reagent transfer. Using the direct printing method, we show that scFv against prostate‐specific antigen (PSA) are highly specific when tested against 21 different IgG‐based assays. In addition, the scFv microarray PSA assay gave comparable quantitative results (R2 = 0.95) to a commercial 96‐well ELISA when tested using human serum samples. In addition, we find that TRX‐scFv fusions against epidermal growth factor and toxin X have good LOD. Overall, these results suggest that minor modifications of the scFv construct are sufficient to produce reagents that are suitable for use in multiplex assay systems.
Proteomic analysis of the chicken egg vitelline membrane
Authors: Mann Karlheinz
Published: May 2008

The avian vitelline membrane (VM) is a multilayered proteinaceous structure separating egg white from yolk. The innermost layer of the VM, deposited onto the oocyte plasma membrane in the ovary, corresponds to the mammalian zona pellucida (ZP). The outer layer is produced in the infundibulum, the first section of the oviduct. Using high‐throughput, high‐end LC‐MSn 137 proteins were identified, only 13 of which were known previously to be components of the VM. Depending on the washing protocol, two largely overlapping, but not identical, sets of identified proteins were produced from water‐washed and salt‐washed VMs. Most of the components of the VM were known previously from other egg compartments, such as, for instance, the egg white proteins lysozyme C, ovalbumin, ovotransferrin, and ovomucin. Specific components of the VM not identified previously in other egg compartments included eight ZP proteins, oviductin protease, and two ATPases. The vitelline outer membrane protein (VMO) VMO II was identified as β‐defensin‐11. The list of VM proteins presented in this report is by far the most comprehensive dataset available at present and complements proteomic analyses of chicken egg compartments published previously.
IPOS Sutherland Memorial Lecture: psycho‐oncology and health care research
Authors: Koch Uwe
Published: May 2008

Remarkable changes of health‐care systems, increasing costs of health care and of social inequality in modern societies, an aging population and the increase of chronic illnesses such as cancer implicate various future challenges for the provision of health care. Health‐care research aims to improve the effectiveness and efficiency of patient‐oriented services involving the evaluation of innovative treatment approaches and settings. It deals with the patients' path through different areas of health‐care systems in order to identify significant factors for the provision of quality assurance of structures and resources concerning treatments, processes and health outcomes. Health‐care research focusses on three main topics that play an important role for quality management: (1) the admission to health‐care services and assessment strategies including indication, utilization and specificity of settings and target groups; (2) the treatment process including the implementation, standardization and flexibility of services and dose‐effect relationship of interventions; (3) health‐care outcome including effectiveness and efficiency of interventions and services, the cost‐benefit relationship and the transfer from research to health‐care practice. Given the objectives of health‐care research, the topics of health‐care research in psychosocial care for cancer patients include the study of structural conditions of psycho‐oncological services, the epidemiology of distress and mental disorders and the subjective need of psycho‐oncological support in cancer patients, the improvement of psycho‐oncological measures and assessment strategies in daily treatment, the study of psycho‐oncological interventions under routine conditions, and quality assurance. Requirements of future health‐care research and developments of psycho‐oncology including aspects of orientation, strategies, health‐care equity, and resources are discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Nanostructured ceria: a comparative study from X‐ray diffraction, Raman spectroscopy and BET specific surface measurements
Authors: Saitzek S. , Blach J.‐F. , Villain S. , Gavarri J.‐R.
Published: May 2008

We present a comparative study of nanostructured materials, based on three experimental analyses allowing determination of crystallite sizes or specific surfaces: each of these analyses, X‐ray diffraction profile analyses (XRD), Raman spectroscopy and Brunauer–Emmett–Teller (BET) gas adsorption technique, should deliver nanoparticle size determination from a specific modelling approach. These three experimental techniques were used to correlate specific surfaces to grain sizes, in the case of nanostructured powders of cerium dioxide, CeO2. Ceria powders were first elaborated by a sol–gel method and then subjected to various heat treatments: the resulting sizes calculated from these XRD, Raman and BET techniques were compared and discussed. Nanocrystal sizes were finally correlated to crystal lattice parameters and Raman frequency. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Novel nanocomposites based on poly(p‐dioxanone) and organically modified clays
Authors: Zubitur M. , Fernández A. , Mugica A. , Cortázar M.
Published: May 2008

Novel composites based on poly(p‐dioxanone) (PPDO) and organically modified cationic and anionic clays have been prepared using the technique of melt‐extrusion. The intercalation of the organic modifier in the clays and the dispersion degree of the organically modified clays in the PPDO composites have been analyzed by wide‐angle X‐ray scattering (WAXS) and Atomic Force Microscopy (AFM). An inmiscible system was obtained for PPDO/cationic clays, whereas in the case of PPDO/anionic clays exfoliated nanocomposites were succesfully obtained. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Adhesion hysteresis in dynamic atomic force microscopy
Authors: Köber Mariana , Sahagún Enrique , Fuss Martina , Briones Fernando , Luna Mónica , Sáenz Juan José
Published: May 2008

The effects of adhesion hysteresis in the dynamic‐dissipation curves measured in amplitude‐modulation atomic force microscopy are discussed. Hysteresis in the interaction forces is shown to modify the dynamics of the cantilever leading to different power dissipation curves in the repulsive and attractive regimes. Experimental results together with numerical simulations show that power dissipation, as measured in force microscopy, is not always proportional to the energy dissipated in the tip–sample interaction process. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A motor oil soil for detergency testing
Authors: Matheson K. L. , Smith G. D.
Published: May 2008

Bright Stock/Pale Oil (BS/PO) soil represents a typical motor oil soil, but it is more constant in composition than clean or dirty commercial motor oil. It does not require the addition of any dye, as is the case with mineral oil or cooking oil, and when applied to cloth, it produces very uniform soilings. The statistical reproducibility of detergency tests run with BS/PO is better than mineral oil and about as good as sebum.
Properties of aqueous solution of a fluorocarbon surfactant and a nonionic surfactant, and their mixtures
Authors: Suzuki T. , Ueno M. , Meguro K.
Published: May 2008

The surface tensions of aqueous solutions of lithium perfluorooctane sulfonate (LiFOS) and hexaethyleneglycoln‐dodecylether (6ED), and of their mixtures, were measured. The effect of each surfactant additives on the adsorption and the micelle formation was discussed on the basis of the surface tension values using the Langmuir adsorption equation for the mixture of both surfactants and the modified Szyszkowski equation. From these results, in the range of low concentrations of 6ED or LiFOS, some of the 6ED molecules which had already adsorbed on the solution surface were found to be replaced by LiFOS molecules in an addition of LiFOS surfactant and vice‐versa. In the ranges of higher concentration above critical micelle concentration (CMC) of each surfactant, it was concluded that the mixed micelle could be formed in the mixed system of both surfactants as well as in the mixed system of two kinds of ordinary hydrocarbon surfactants.
Ricinoleic acid inPhyllanthus niruri seed oil
Authors: Ahmad M. U. , Husain S. K. , Osman S. M.
Published: May 2008

Seed oil ofPhyllanthus niruri (Euphorbiaceae) contains 1.2% ricinoleic (12‐hydroxy‐cis‐9‐octadecenoic) acid, previously unknown in the genusPhyllanthus. Identification is based on thin layer and gas liquid chromatography, infrared, nuclear magnetic resonance, and mass spectrometry analysis as well as chemical methods. Other major components of the oil are linoleic acid (21%) and linolenic acid (51.4%).
Selective hydrogenation of soybean oil: XI. Trialkyl silane‐activated copper catalysts
Authors: Koritala S.
Published: May 2008

Addition of triethyl silane to copper stearate resulted in an active heterogenous catalyst for the hydrogenation of soybean oil. The linolenate selectivity of this catalyst (KLe/KLo=2.4 to 3.9) was much lower than that obtained with copper chromite (8.4). Unlike copper‐chromite catalyst, triethyl silane‐activated copper formed stearate during hydrogenation. Both silica and alumina increased catalyst activity. Linolenate selectivity improved slightly in the presence of alumina.
Race and Prosecution Expenditures
Authors: Cameron Samuel
Published: May 2008

There has been a steady accumulation of literature on racial differentials in crime and the response of the criminal justice system. A neglected component of societal response to crime has been the volume of prosecution expenditures. This article seeks to repair this neglect by examining state level difference in per capita prosecution expenditures in 1980 using a multiple regression equation. The results show that, holding other factors constant, lower prosecution expenditures are associated with higher percentages of blacks in a state's population. The relationship of this to discrimination is discussed in terms of England.
A Sociological Analysis of Minority Business
Authors: Fratoe Frank A.
Published: May 2008

This sociological analysis contends that minority business is foremost a group-level phenomenon and is highly dependent upon social group resources for its development. This approach has its origins in the fact that other interpretations of minority business do not adequately account for the large proportional differences of owners across ethnic/racial groups. Census data on specific groups are examined to demonstrate those differences, both in regard to business participation rates and self-employment income. To help explain the differences, major functions performed by self-help networks supporting minority business are reviewed from the sociological research literature. The final section contains several policy implications.
Financing Black Politics: A Study of Congressional Elections
Authors: Smith Robert C.
Published: May 2008

This article investigates the financing of the campaigns of black candidates for the U.S. House of Representatives. Although incumbent black candidates receive lower levels of campaign contributions than their white counterparts, analysis of expenditure data shows that their campaigns are adequately funded, with most of them winning by large margins and retaining modest surpluses. Black challengers, however, are substantially underfunded and are rarely able to conduct competitive campaigns. The implications of this incumbent-challenger financial disparity for the accountability and responsiveness of members of Congress representing black constituencies are discussed.
Incentive Schemes and Racial Wage Discrimination
Authors: Belman Dale , Heywood John S.
Published: May 2008

We use a major micro data set to investigate the influence of incentive schemes on wage discrimination against blacks. Incentive schemes which directly link earnings and productivity appear to generally raise earnings, but they increase wages of blacks proportionately more than those of whites. This reduces the residual attributable to discrimination and suggests it is easier to discriminate when earnings are based on perceptions of input (evaluations of effort) rather than on measures of output.
A Longitudinal Analysis of Racial Wage Differentials for Young Nonfarm Rural Workers
Authors: Reid Clifford E.
Published: May 2008

A longitudinal data base is used to estimate racial wage differentials for young nonfarm rural workers for 1968, 1973, and 1978. The empirical results indicate the existence of large wage differentials between young white and young black nonfarm rural workers of both sexes. The results also indicate that the wage differential for young men has increased over time while the differential for young women has decreased slightly over time.
The Economic Interests of Black and White Women: Are They Similar?
Authors: Malveaux Julianne
Published: May 2008

Are the economic interests of black and white women similar? This article explores this question by reviewing data on the “feminization of poverty,” data on changes in the economic status of blacks, and differences in the occupational status of black and white women. The article reviews several policy questions, discusses ways in which the interests of black and white women differ in the policy arena, and concludes that although there are some similarities in the interests of black and white women, the racial interests of black women suggest that the interests of black and white women may frequently differ.
Black Banks: A Survey and Analysis of the Literature
Authors: Cole John A. , Edwards Alfred L. , Hamilton Earl G. , Reuben Lucy J.
Published: May 2008

The analysis of the role of black banks in black economic development began in the early 1970s. At that time the focus was on the profitability of these institutions. Since then both the number of black banks and the research on their performance have increased significantly. This article reviews the recent literature on black banks in order to provide a conceptual framework for policies that will promote their growth and prosperity. The authors conclude that there is a clear need for future research in every area relating to black banks.
Impact of Preferential Procurement Policies on Minority-Owned Businesses
Authors: Bates Timothy
Published: May 2008

Financial data on minority firms that compete for business in government and corporate set-aside programs reveal that these firms lag behind their nonminority counterparts in important respects. They are, relative to nonminorities, (1) less profitable, (2) younger, and (3) much more highly leveraged. Large-scale minority enterprises are no longer the rarity that they were 20 years ago. These firms have not, however, achieved parity with their nonminority cohorts, and their unique traits—especially undercapitalization—continue to reflect the vestiges of discrimination.
Tumor cells can escape DNA‐damaging cisplatin through DNA endoreduplication and reversible polyploidy
Authors: Puig Pierre‐Emmanuel , Guilly Marie‐Noëlle , Bouchot André , Droin Nathalie , Cathelin Dominique , Bouyer Florence , Favier Laure , Ghiringhelli François , Kroemer Guido , Solary Eric , Martin François , Chauffert Bruno
Published: May 2008

Cancer chemotherapy can induce tumor regression followed, in many cases, by relapse in the long‐term. Thus this study was performed to assess the determinants of such phenomenon using an in vivo cancer model and in vitro approaches. When animals bearing an established tumor are treated by cisplatin, the tumor initially undergoes a dramatic shrinkage and is characterized by giant tumor cells that do not proliferate but maintain DNA synthesis. After several weeks of latency, the tumor resumes its progression and consists of small proliferating cells. Similarly, when tumor cells are exposed in vitro to pharmacological concentrations of cisplatin, mitotic activity stops initially but cells maintain DNA duplication. This DNA endoreduplication generates giant polyploid cells that then initiate abortive mitoses and can die through mitotic catastrophe. However, many polyploid cells survive for weeks as non‐proliferating mono‐ or multi‐nucleated giant cells which acquire a senescence phenotype. Prolonged observation of these cells sheds light on the delayed emergence of a limited number of extensive colonies which originate from polyploid cells, as demonstrated by cell sorting analysis. Theses colonies are made of small diploid cells which differ from parental cells by stereotyped chromosomal aberrations and an increased resistance to cytotoxic drugs. These data suggest that a multistep pathway, including DNA endoreduplication, polyploidy, then depolyploidization and generation of clonogenic escape cells can account for tumor relapse after initial efficient chemotherapy.
Clinical use of a haemoglobin-based oxygen carrying solution (Oxyglobin®) in 48 cats (2002–2006)
Authors: Weingart Christiane , Kohn Barbara
Published: May 2008

The objective of this retrospective study was the evaluation of the administration of a haemoglobin (Hb)-based oxygen carrying solution (Oxyglobin®) to cats over a time period of 4 years. Indication, infusion volume/24 h, number of Oxyglobin® infusions/cat, Hb concentration pre- and post-infusion, adverse events, and patient outcome were evaluated. Forty-eight anaemic cats received 65 Oxyglobin® infusions. Prior to administration of Oxyglobin®, Hb concentration ranged from 2 to 7.8 g/dl (median 4.9 g/dl), the volume of Oxyglobin® administered was 4.4–25 ml/kg/24 h (median 9.8 ml/kg/24 h). An increase of Hb was noted after 41 of 49 infusion events. Severe side effects were noted in seven cats with cardiac disease, which developed pulmonary oedema (five), pleural effusion (three), and respiratory distress (one). They received 6.7–19.8 ml/kg/24 h (median 12.3 ml/kg/24 h) of Oxyglobin®. Four of these seven cats received whole blood transfusions on the same day; five cats died and one was euthanased. Overall 24-h survival rate was 77%. Administration of Oxyglobin® efficiently increased the Hb concentration. However, in cats suffering from cardiac disease, there is a high risk of life-threatening circulatory overload at the doses used in this study.
Partial lateral corpectomy for ventral extradural thoracic spinal cord compression in a cat
Authors: Böttcher Peter , Flegel Thomas , Böttcher Irene C. , Grevel Vera , Oechtering Gerhard
Published: May 2008

A 7-year-old, female spayed, domestic shorthair cat was presented for ambulatory paraparesis. No trauma history was reported. Myelography and subsequent computed tomography revealed multiple ventrally located extradural spinal cord compressive lesions possibly due to intervertebral disc disease. Compression at the level of Th3–Th4 intervertebral disc space was considered responsible for the paraparesis. The lesion was approached via a right-sided lateral partial corpectomy as described for dogs. Complete spinal decompression was achieved, as documented intraoperatively by visual inspection and palpation of the spinal canal. No surgery related complications were encountered and the cat improved gradually within 8 weeks after the procedure. At 1 year follow-up only a slight proprioceptive deficit in the right hind limb could be noted. This is the first report of partial lateral corpectomy in a cat and should encourage the use of this technique even in small patients.
2008 American Association of Feline Practitioners' feline retrovirus management guidelines
Authors: Levy Julie , Crawford Cynda , Hartmann Katrin , Hofmann-Lehmann Regina , Little Susan , Sundahl Eliza , Thayer Vicki
Published: May 2008

Feline leukemia virus (FeLV) and feline immunodeficiency virus (FIV) are among the most common infectious diseases of cats. Although vaccines are available for both viruses, identification and segregation of infected cats form the cornerstone for preventing new infections. Guidelines in this report have been developed for diagnosis, prevention, treatment, and management of FeLV and FIV infections. All cats should be tested for FeLV and FIV infections at appropriate intervals based on individual risk assessments. This includes testing at the time of acquisition, following exposure to an infected cat or a cat of unknown infection status, prior to vaccination against FeLV or FIV, prior to entering group housing, and when cats become sick. No test is 100% accurate at all times under all conditions; results should be interpreted along with the patient's health and risk factors. Retroviral tests can diagnose only infection, not clinical disease, and cats infected with FeLV or FIV may live for many years. A decision for euthanasia should never be based solely on whether or not the cat is infected. Vaccination against FeLV is highly recommended in kittens. In adult cats, antiretroviral vaccines are considered non-core and should be administered only if a risk assessment indicates they are appropriate. Few large controlled studies have been performed using antiviral or immunomodulating drugs for the treatment of naturally infected cats. More research is needed to identify best practices to improve long-term outcomes following retroviral infections in cats.
Miracles: metaphysics, physics, and physicalism
Authors: MCDERMID KIRK
Published: May 2008

Debates about the metaphysical compatibility between miracles and natural laws often appear to prejudge the issue by either adopting or rejecting a strong physicalist thesis (the idea that the physical is all that exists). The operative component of physicalism is a causal closure principle: that every caused event is a physically caused event. If physicalism and this strong causal closure principle are accepted, then supernatural interventions are ruled outtout court, while rejecting physicalism gives miracles metaphysical carte blanche. This paper argues for a more moderate version of physicalism that respects important physicalist intuitions about causal closure while allowing for miracles' logical possibility. A recent proposal for a specific mechanism for the production of miracles (Larmer (1996d)) is criticized and rejected. In its place, two separate mechanisms (suitable for deterministic and indeterministic worlds, respectively) are proposed that do conform to a more moderate physicalism, and their potential and limitations are explored.
Enzymatic Production of Epigallocatechin by Using an Epigallocatechin Gallate Hydrolase Induced from Aspergillus oryzae
Authors: Zhong Kun , Shao Zhiyu , Hong Feng
Published: May 2008

Catechins are a group of polyphenolic compounds that are antioxidants having beneficial biological activities. There are four main catechins in green tea, and each has its own biological features. In order to fully exploit prominent biological activities of specific catechins and to develop new medicine from catechins, it is necessary to obtain pure catechin preparations by isolation from natural sources, by chemical synthesis, or by biotransformation reactions with high yield and specificity. In this study epigallocatechin gallate (EGCG) can be hydrolyzed to epigallocatechin (EGC) by a hydrolase from Aspergillus oryzae after induction by addition of EGCG to the cultures. However, cultures without EGCG induction did not show any EGCG hydrolysis activity. The yield of EGC could reach at least 70%. Thin layer chromatography and high performance liquid chromatography were applied to separate and quantify EGCG and EGC.
Molecular Dynamic Investigation of the Interaction of Supported Affinity Ligands with Monoclonal Antibodies
Authors: Zamolo Laura , Busini Valentina , Moiani Davide , Moscatelli Davide , Cavallotti Carlo
Published: May 2008

Diagnostics and therapeutic treatments based on monoclonal antibodies have been attaining an increasing importance in the past decades, but their large scale employment requires the optimization of purification processes. To obtain this goal, research is focusing on affinity chromatography techniques and the development of new synthetic ligands. In this work we present a computational investigation aimed at obtaining some guidelines for the rational design of affinity ligands, through the study of their interactions with both monoclonal antibodies (modeled as the FC domain of human IgG) and a model support material (agarose). The study was carried out performing molecular dynamics simulations of the support‐spacer‐ligand‐IgG complex in explicit water. Binding energies between IgG and two supported ligands, a disubstituted derivative of trichlorotriazine and a tetrameric peptide, were determined with the linear interaction energy and MM‐GBSA approaches. A detailed study of the possible binding sites of the considered ligands was performed exploiting docking protocols and MD simulations. It was found that both ligands bind IgG in the same site as protein A, which is the hinge region between the CH2 and CH3 domains of IgG. However this site is not easily accessible and requires a high mobility of the ligands. The energetic analysis revealed that van der Waals and electrostatic energies of interaction of the triazine ligand with the support are significant and comparable to those with the protein, so that they limit its capability to reach the protein binding site. A similar result was found also for the tetrameric peptide, which is however able to circumvent the problem; for steric reasons only two of its arms can interact at the same time with the agarose support, thus leaving the remaining two available to bind the protein. These results indicate that the interaction between ligand and support material is an important parameter, which should be considered in the computational and experimental design of ligands for affinity chromatography.
A three‐dimensional variational data assimilation scheme for the Regional Ocean Modeling System: Implementation and basic experiments
Authors: Li Zhijin , Chao Yi , McWilliams James C. , Ide Kayo
Published: May 2008

A three‐dimensional variational data assimilation scheme for the Regional Ocean Modeling System (ROMS), named ROMS3DVAR, has been described in the work of Li et al. (2008). In this paper, ROMS3DVAR is applied to the central California coastal region, an area characterized by inhomogeneity and anisotropy, as well as by dynamically unbalanced flows. A method for estimating the model error variances from limited observations is presented, and the construction of the inhomogeneous and anisotropic error correlations based on the Kronecker product is demonstrated. A set of single observation experiments illustrates the inhomogeneous and anisotropic error correlations and weak dynamic constraints used. Results are presented from the assimilation of data gathered during the Autonomous Ocean Sampling Network (AOSN) experiment during August 2003. The results show that ROMS3DVAR is capable of reproducing complex flows associated with upwelling and relaxation, as well as the rapid transitions between them. Some difficulties encountered during the experiment are also discussed.
A new method for deducing the effective collision frequency profile in the D‐region
Authors: Beharrell M. , Honary F.
Published: May 2008

A method based on linear regularization is presented for the deduction of the effective collision frequency profile in the D‐region using an incoherent scatter radar and a colocated riometer. The deduced collision frequency above EISCAT, Tromsø, for the period 09 November 2004 to 13 November 2004 matches very well with that calculated using neutral densities and temperatures from the NRLMSISe‐00 atmospheric model between 68 km and 95 km during active (ap > 50) and quiet (ap < 50) conditions. We also confirm the validity of using the Appleton‐Hartree equation with effective collision frequencies when calculating the ionospheric absorption at high frequencies.
Modeling of the mesoscale structure of coupled upwelling/downwelling events and the related input of nutrients to the upper mixed layer in the Gulf of Finland, Baltic Sea
Authors: Zhurbas Victor , Laanemets Jaan , Vahtera Emil
Published: May 2008

A high resolution numerical study is undertaken to simulate an upwelling event along the northern coast of the Gulf of Finland, 21–29 July 1999, which was documented well by in situ and remote measurements. The simulated sequence of SST maps shows a reasonably good resemblance to that of satellite infrared imagery, including both mesoscale coherent structures (filaments or squirts) and the whole process of post‐upwelling relaxation of the temperature field. Upwelling along the northern coast of the Gulf is accompanied by downwelling along the southern coast so that two longshore baroclinic jets and related fronts are developed simultaneously. When the strong westerly winds producing the upwelling/downwelling weaken, the longshore jets become unstable and produce transverse jets, cold/warm water squirts. Using pseudo‐random simulated fields of temperature and velocity of currents, the apparent lateral diffusivity due to squirts is directly estimated at 500 m2 s−1. The model is also applied to estimate nutrient transport. Simulated phosphate concentration in the surface layer at the cold side of upwelling front is found to be about 0.3 mmol m−3 which is consistent with observations. The total content of phosphorus and nitrogen in the upper 10 m layer of the Gulf introduced by the upwelling event is estimated to be 387 and 36 tons, respectively. It follows, that the upwelling event transports nutrients into the upper layer with clear excess of phosphorus (N:P = 36:387 = 0.093) compared to the Redfield ratio of 7.2. Therefore phosphorus input caused by upwelling during summer most likely promotes nitrogen‐fixing cyanobacteria blooms.
Numerical modeling of frontal and basal accretion at collisional margins
Authors: Selzer Cornelia , Buiter Susanne J. H. , Pfiffner O. Adrian
Published: May 2008

We investigate the deformation of orogenic wedges that form in the early stages of continent‐continent collisions using a two‐dimensional numerical model limited to the upper lithosphere. Our models show that deformation at the plate margins is influenced by rheology, surface processes, and the balance between inward mass flux and outward subduction flux, as controlled by the subduction load (which represents the effects of slab pull and resistive forces) and flexural downbending. We find three characteristic deformation modes: (1) near‐pure subduction with little or no accretion; (2) frontal accretion with development of an accretionary wedge built up by offscraping of the sediment layer at shallow depth; and (3) independent frontal and basal accretion where a retrothrust allows stacking of basement nappes at crustal to mantle depths. Near‐pure subduction is enabled for “ordinary‐rheology” materials, characterized by brittle and viscous material behavior (approximating a “Christmas tree‐type” depth profile), and almost zero friction along the subduction shear zone. Frontal accretion occurs when slightly increased friction along the subduction shear zone allows offscraping of the sediment layer from the subducting plate. Independent frontal and basal accretion develops in strong‐rheology models with an almost fully brittle material behavior. Major surface erosion or a reduction of the subduction load promote the development of large basement nappes. Frontal accretion is favored by major sedimentation during convergence, a large backstop, and in the case of a lateral transition from a “strong‐rheology” to an “ordinary‐rheology” subducting plate. Our numerical models develop first‐order characteristics as observed in natural orogenic wedges, for example upper crustal nappe stacks, frontal and basal accretion, or extension in the core of an orogen. Frontal and basal accretion are interdependent, and tend to stabilize the subduction system.
Fish oil fatty acids improve postprandial vascular reactivity in healthy men
Authors: Armah Christopher K. , Jackson Kim G. , Doman Izzy , James Lewis , Cheghani Farah , Minihane Anne M.
Published: May 2008

Chronic fish oil intervention had been shown to have a positive impact on endothelial function. Although high-fat meals have often been associated with a loss of postprandial vascular reactivity, studies examining the effects of fish oil fatty acids on vascular function in the postprandial phase are limited. The aim of the present study was to examine the impact of the addition of fish oil fatty acids to a standard test meal on postprandial vascular reactivity. A total of 25 men received in a random order either a placebo oil meal (40 g of mixed fat; fatty acid profile representative of the U.K. diet) or a fish oil meal (31 g of mixed fat and 9 g of fish oil) on two occasions. Vascular reactivity was measured at baseline (0 h) and 4 h after the meal by laser Doppler iontophoresis, and blood samples were taken for the measurement of plasma lipids, total nitrite, glucose and insulin. eNOS (endothelial NO synthase) and NADPH oxidase gene expression were determined in endothelial cells after incubation with TRLs (triacylglycerol-rich lipoproteins) isolated from the plasma samples taken at 4 h. Compared with baseline, sodium nitroprusside (an endothelium-independent vasodilator)-induced reactivity (P=0.024) and plasma nitrite levels (P=0.001) were increased after the fish oil meal. In endothelial cells, postprandial TRLs isolated after the fish oil meal increased eNOS and decreased NADPH oxidase gene expression compared with TRLs isolated following the placebo oil meal (P≤0.03). In conclusion, meal fatty acids appear to be an important determinant of vascular reactivity, with fish oils significantly improving postprandial endothelium-independent vasodilation.
Corporate governance in Scandinavia: comparing networks and formal institutions
Authors: Sinani Evis , Stafsudd Anna , Thomsen Steen , Edling Christofer , Randøy Trond
Published: May 2008

Abstract This article addresses the role of formal institutions and informal networks on corporate governance practices. The existing corporate governance literature has mostly examined the formal institutions, such as the effect of legal systems. Our contribution is to consider the effect of informal ‘small world’ characteristics of ownership and board networks. We use the case of Scandinavia (Denmark, Norway and Sweden) to examine these effects. Our empirical results reveal large differences in formal board and ownership structures between the Scandinavian countries, but strong similarities in terms of law enforcement, political stability, government effectiveness, rule of law, control of corruption as well as voice and accountability. We find that all three countries can be characterized as ‘small worlds' in which trust, information diffusion and reputation mechanisms are active governance mechanisms.
The Social Science Research Center Berlin: organizational learning as a research and institutional project
Authors: Antal Ariane Berthoin , Kocka Jürgen
Published: May 2008

Abstract This article describes an academic institution that is committed to conducting problem‐oriented basic research, a combination that is unusual in Europe, if not the world. After sketching the history of the Social Science Research Center Berlin (WZB) and the development of its diverse research areas, a large empirical project is presented to illustrate the kinds of studies undertaken there by scholars working across disciplinary and national boundaries. We describe and reflect on how the team explored organizational learning in the People's Republic of China, the Federal Republic of Germany and Israel, and summarize some key findings. We conclude by looking at how the WZB itself engages in organizational learning to respond to or stay ahead of changes in its socio‐political as well as its academic environment.
Parallel proton transfer pathways in aqueous acid-base reactions
Authors: Cox M. J. , Bakker H. J.
Published: May 2008

We study the mechanism of proton transfer (PT) between the photoacid 8-hydroxy-1,3, 6-pyrenetrisulfonic acid (HPTS) and the base chloroacetate in aqueous solution. We investigate both proton and deuteron transfer reactions in solutions with base concentrations ranging from 0.25M to 4M. Using femtosecond midinfrared spectroscopy, we probe the vibrational responses of HPTS, its conjugate photobase, the hydrated proton/deuteron, and chloroacetate. The measurement of these four resonances allows us to follow the sequence of proton departure from the acid, its uptake by the water solvent, and its arrival at the base. In recent studies it was shown that proton transfer to carboxylate bases proceeds via Grotthuss conduction through a water wire connecting the acid and the base [Mohammed et al., Science 310, 83 (2005);Agnew. Chem. Int. Ed. 46, 1458 (2007);Siwick and Bakker, J. Am. Chem. Soc. 129, 13412 (2007); J. Phys. Chem. B 112, 378 (2008)]. Here we show that, for the weaker base chloroacetate, an alternative channel for proton transfer arises. In this channel the proton is first transferred to the water solvent and only later taken up from the water by the base. We study the base concentration dependence of the two competing channels.
Refractive index calculation using the structural properties of La4Ti9O24 glass
Authors: Arai Yasutomo , Itoh Keiji , Kohara Shinji , Yu Jianding
Published: May 2008

A high refractive index of 2.231±0.001 at 1313 nm is achieved in a colorless, transparent spherical La4Ti9O24 glass that was prepared by using an aerodynamic levitation furnace. We also investigate the origin of the high refractive index based on the Lines theory. The physical parameters necessary for the theoretical calculations are the averaged nearest-neighbor Ti–O and La–O distances that are deduced by neutron and synchrotron x-ray diffraction measurement and the partial molar volumes of TiO2 and LaO1.5 in the glass. The sum of the calculated TiO2 and LaO1.5 susceptibilities provides a La4Ti9O24 glass refractive index of 2.244. This is very close to the experimental refractive index of the glass. In addition, the theoretical calculation results suggest that the oxygen fivefold Ti (TiO5) cluster produces greater susceptibilities than the sixfold Ti (TiO6) cluster in the glass.
Universal occurrence of the phase-flip bifurcation in time-delay coupled systems
Authors: Prasad Awadhesh , Dana Syamal Kumar , Karnatak Rajat , Kurths Jürgen , Blasius Bernd , Ramaswamy Ramakrishna
Published: May 2008

Recently, the phase-flip bifurcation has been described as a fundamental transition in time-delay coupled, phase-synchronized nonlinear dynamical systems. The bifurcation is characterized by a change of the synchronized dynamics from being in-phase to antiphase, or vice versa; the phase-difference between the oscillators undergoes a jump of π as a function of the coupling strength or the time delay. This phase-flip is accompanied by discontinuous changes in the frequency of the synchronized oscillators, and in the largest negative Lyapunov exponent or its derivative. Here we illustrate the phenomenology of the bifurcation for several classes of nonlinear oscillators, in the regimes of both periodic and chaotic dynamics. We present extensive numerical simulations and compute the oscillation frequencies and the Lyapunov spectra as a function of the coupling strength. In particular, our simulations provide clear evidence of the phase-flip bifurcation in excitable laser and Fitzhugh–Nagumo neuronal models, and in diffusively coupled predator-prey models with either limit cycle or chaotic dynamics. Our analysis demonstrates marked jumps of the time-delayed and instantaneous fluxes between the two interacting oscillators across the bifurcation; this has strong implications for the performance of the system as well as for practical applications. We further construct an electronic circuit consisting of two coupled Chua oscillators and provide the first formal experimental demonstration of the bifurcation. In totality, our study demonstrates that the phase-flip phenomenon is of broad relevance and importance for a wide range of physical and natural systems.
Energy of eigenmodes in magnetohydrodynamic flows of ideal fluids
Authors: Khalzov I. V. , Smolyakov A. I. , Ilgisonis V. I.
Published: May 2008

Energy of eigenmodes in magnetohydrodynamic (MHD) flows of ideal fluids is studied analytically. It is shown that the energy of unstable modes is zero, while the energy of stable oscillatory modes (waves) can assume both positive and negative values. Negative energy waves always correspond to eigenmodes with a finite component of the wave-vector along the flow. Coupling of negative and positive energy waves is shown to be a universal mechanism of MHD instabilities in flowing media. As an example, the energy of eigenmodes of magnetorotational instability is calculated.
Reflection positivity and monotonicity
Authors: Jaffe Arthur , Ritter Gordon
Published: May 2008

We prove general reflection positivity results on Riemannian manifolds for both scalar fields and Dirac fields, and comment on applications to quantum field theory. As another application, we prove the inequality CD⩽CN between Dirichlet and Neumann covariance operators on a manifold with a reflection.
Comment on “Band gap bowing and electron localization of GaXIn1−XN” [J. Appl. Phys. 100, 093717 (2006)]
Authors: Bagayoko D. , Franklin L. , Zhao G. L. , Jin H.
Published: May 2008

Some previous density functional theory (DFT) calculations of the band gap of wurtzite and cubic InN, before the work of Lee and Wang [J. Appl. Phys. 100, 093717 (2006)], are in agreement with the screened-exchange findings of these authors and with experiment. These previous findings point to an intrinsic capability of DFT, in the local density approximation, to correctly describe the band gap of semiconductors. These comments also discuss some recent results [Phys. Rev. B 76, 037101 (2007)] on an extensive hybridization of the In 4d and N 2s bands that is lost when the d electrons are included in the core. Our discussions in these comments indicate that when the two inherently coupled equations of DFT are both solved self-consistently, the resulting bands, including low-lying conduction ones, appear to have much more physics content than previously believed.
Characterization of plasma etching damage on p-type GaN using Schottky diodes
Authors: Kato M. , Mikamo K. , Ichimura M. , Kanechika M. , Ishiguro O. , Kachi T.
Published: May 2008

The plasma etching damage in p-type GaN has been characterized. From current-voltage and capacitance-voltage characteristics of Schottky diodes, it was revealed that inductively coupled plasma (ICP) etching causes an increase in series resistance of the Schottky diodes and compensation of acceptors in p-type GaN. We investigated deep levels near the valence band of p-type GaN using current deep level transient spectroscopy (DLTS), and no deep level originating from the ICP etching damage was observed. On the other hand, by capacitance DLTS measurements for n-type GaN, we observed an increase in concentration of a donor-type defect with an activation energy of 0.25eV after the ICP etching. The origin of this defect would be due to nitrogen vacancies. We also observed this defect by photocapacitance measurements for ICP-etched p-type GaN. For both n- and p-type GaN, we found that the low bias power ICP etching is effective to reduce the concentration of this defect introduced by the high bias power ICP etching.