bluuebunny/crossref_metadata_2025 huggingface dataset:
Elevation of serum cerebral injury markers correlates with serum choline decline after coronary artery bypass grafting surgery
Authors: Ilcol Yesim Ozarda , Basagan-Mogol Elif , Cengiz Mete , Ulus Ismail H.
Published: April 2006

The aims of this study were to determine circulating choline status and its relationship to circulating levels of S-100β protein and neuron-specific enolase, biochemical markers of cerebral injury and cognitive decline, after coronary artery bypass grafting (CABG) surgery. Preoperatively, patients scheduled for off-pump or on-pump CABG surgery had serum concentrations of 12.0±0.2 and 11.7±0.4μmol/L free choline and 2640±65 and 2675±115μmol/L phospholipid-bound choline, respectively. Serum free and bound choline levels decreased by 22–37% or 34–47% and 16–36% or 31–38% at 48h after off-pump or on-pump surgery, respectively. Serum S-100β and neuron-specific enolase increased from preoperative values of 0.083±0.009 and 6.3±0.2μg/L to 0.405±0.022 and 11.4±0.8μg/L, respectively, at 0h postoperatively and remained elevated for 48h after off-pump surgery. Serum free and bound choline concentrations were inversely correlated with the concentrations of S-100β (r=−0.798; p<0.001 and r=−0.734; p<0.001) and neuron-specific enolase (r=−0.840; p<0.001 and r=−0.728; p<0.001). In conclusion, CABG surgery induces a decline in serum free and phospholipid-bound choline concentrations. The decreased serum choline concentrations were inversely correlated with the elevated levels of circulating cerebral injury markers. Thus, a decline in circulating choline may be involved in postoperative cognitive decline.
Intermethod calibration of alanine aminotransferase (ALT) and γ-glutamyltransferase (GGT) results: application to Fibrotest® and Actitest® scores
Authors: Férard Georges , Piton Annie , Messous Djamila , Imbert-Bismut Françoise , Frairi Asmaa , Poynard Thierry , Lessinger Jean-Marc
Published: April 2006

Two multi-component scores (Fibrotest
Geographic Origin as a Branding Tool for Agri-Food Producers
Authors: Tregear Angela , Gorton Matthew
Published: April 2006

Origin indication is a well-established means of differentiation in the agri-food sector, and is likely to become even more popular in light of market growth trends. However, agri-food producers face additional problems to other sectors when using origin due to the particular characteristics of agri-food products and systems. Drawing from the branding and country-of-origin (COO) effects literatures, this paper examines the challenges agri-food firms face when using origin, and discusses alternative response strategies. Specifically, the paper addresses problems arising from two characteristics of origin: as a common resource, and as a strong physical and cultural link to product quality. Critical reflections are also made on the strengths and weaknesses of the branding and COO literatures, in light of their application to the agri-food sector.
Zgornjesavinjski Želodec (Upper Savinja Valley Stomach Sausage) - A Slovene PGI Product
Authors: Slokan Polona , Udovc Andrej
Published: April 2006

The first part of the article sets out from underlining the importance of labeling quality agricultural and food products. After a brief overview of the related EU and Slovenian regulation, it introduces Slovenian trademarks. This is followed by listing those 30 products that have already won the label. The second part of the study deals with the presentation of a definite traditional Slovenian meat-based product: Zgornjesavinjski želodec - having been first to receive PGI denomination. The authors also analyse its demand-supply relations and marketing possibilities, pointing out the dilemma of either satisfying expanding market demand or keeping production to quality.
Benchmarking of the United Kingdom's and Hungary's Fresh Produce Import Supply Chain, Focusing on Food Safety and Quality
Authors: Lehota József , Illés Csaba B.
Published: April 2006

Countries that are candidates for EU accession face a complex and urgent task to adopt and implement the acquis communautaireon food safety. For the food industries in Candidate Countries, this implies that EU standards of food production and processing, quality and safety have to be met in order to ensure a high level of consumer protection and satisfaction. The purpose of this paper is to assess progress towards new levels of food safety performance in one Candidate Country, Hungary, in one food sector (fresh produce), and evaluate the capacity of the system to demonstrate quality assurance to the satisfaction of private customers and public regulators. The analysis of food safety performance has been undertaken using a novel application of the benchmarking methodology taking the UK fresh produce importing chain as the benchmark.
Genetic, Age and Light Mediated Effects on Crystallin Protein Expression in the Retina
Authors: Organisciak Daniel , Darrow Ruth , Gu Xiaorong , Barsalou Linda , Crabb John W.
Published: April 2006

To probe for possible relationships between retinal crystallins and retinal degenerations, protein expression was compared in normal Sprague‐Dawley rats, treated or not with intense light, Royal College of Surgeons (RCS) rats and transgenic rats expressing rhodopsin mutations. Rats were reared in dim cyclic light for 21–75 days. Photoreceptor cell DNA levels were determined at various ages to assess the rates of visual cell loss. 1D‐ and 2D‐gel electrophoresis was used to profile retinal protein expression. Crystallins were identified by western analysis and by tandem mass spectrometry. In normal rat retinas, α, β and γ crystallins were present, although αA‐ and γ‐crystallins exhibited some increase with age. As measured by DNA levels, the rate of genetically induced photoreceptor cell loss was greater in rats with faster degenerating retinas (RCS, S334‐ter Line 4, P23H Line 3) than in rats with slower degenerating retinas (S334‐ter Line 9, P23H Line 2). In genetic models of retinal degeneration increased levels of immunore‐activity for all crystallins, especially αA‐insert, correlated with the different rates of photoreceptor loss. In the light induced degeneration model αA‐insert was unchanged, truncated αB‐crystallin levels were increased and γ‐crystallins were greatly reduced. In the RCS rat retina 16 different crystallins were identified. Our data suggests that an increase in crystallin expression occurs during various retinal degenerations and that the increases may be related to the severity, type and onset of retinal degeneration.
Lateral Bone Condensing and Expansion for Placement of Endosseous Dental Implants: A New Technique
Authors: Siddiqui Azfar A. , Sosovicka Mark
Published: April 2006

Placement of endosseous dental implants can be a problem due to bone resorption if the patient has been missing teeth for a considerable period of time. In the literature, bone-grafting techniques have shown variable results. Additionally, bone grafting requires a longer treatment time and a need for a second surgery, and it adds significant cost to the treatment. These factors often discourage patients from having dental-implant treatment. Another technique for placement of dental implants in narrow bone ridges is repositioning and remodeling of alveolar bone by condensing and expansion with the help of bone osteotomes. This article presents 2 cases, 1 in the maxilla and 1 in the mandible, for placement of endosseous dental implants with the use of a new bone-expansion osteotome kit that utilizes a screw-type configuration for bone condensing and expansion.
Robust Portfolio Selection with and without Relative Entropy
Authors: Taboga Marco
Published: April 2006

We analyze two robust portfolio selection models, where a mean-variance investor considers possible deviations from a reference distribution of asset returns, adopting a maxmin criterion. The two models differ in the metric used to measure the distance between the reference distribution of asset returns and the alternative probability distributions. In the first model, where relative entropy is used as a measure of distance between distributions, an observational equivalence result obtains, whereby introducing robustness is equivalent to increasing risk aversion and, therefore, the percentage composition of the optimal portfolio of risky assets is equal to that of the optimal portfolio held by an investor without concerns for robustness. In the second model, introducing an alternative measure of distance between distributions, we show that observational equivalence ceases to hold and the proportions between risky assets are altered. We exploit the natural game-theoretic interpretation of the maxmin setting to illustrate the differences between the two models.
Resources as an Input of Production in a Two-Sector Economy
Authors: Xie Jia
Published: April 2006

This paper extends models of renewable resources to an economy with two sectors, resource extraction and production. In contrast to one sector models, we show that the optimal strategies in the single-firm model are essentially different from those in the two-player model. In the single-player model, the optimal strategy is to keep the resource extraction a constant multiple of production labor. In the two-player model, the optimal strategy for each player is to keep extracting labor a constant multiple of production labor. It is also shown that the extraction-to-production labor ratio is increasing with the wage and the interest rate and is decreasing with the production TFP, the extraction TFP, and the stock level in the single-player model, but not in the two-player model. Finally, I show that another way for each firm to maximize profit is to raise its zero-profit stock level by maximizing its geometric average TFP.
The Value of Broadband and the Deadweight Loss of Taxing New Technology
Authors: Goolsbee Austan
Published: April 2006

With fixed costs of developing technology, taxes can generate large efficiency costs by slowing the rate of diffusion and these costs are not accounted for in conventional analyses. This paper illustrates the potential importance of this idea in the context of taxes on broadband Internet access at an early stage of its existence by combining data on individual demand by area with data on supplier entry into those markets. Applying a tax to broadband in 1998 would have reduced the quantity and generated a large deadweight loss in the conventional model but when the analysis accounts for the fixed costs of entering new markets, taxes lead to delayed entry in several markets. In these places, the lost consumer surplus is additional deadweight loss and it more than doubles the true efficiency costs from taxation. The conventional model also dramatically understates the share of the tax burden borne by consumers.
Credit Constraints and Contract Enforcement
Authors: Powers Dennis
Published: April 2006

This paper demonstrates that credit constraints can lead to the inability to enforce contracts, thereby creating inefficiency. If time elapses between the contract period and the enforcement period, a credit constrained agent that uses the proceeds of trade to fund consumption faces a greater cost to enforce a contract than an unconstrained agent. This allows the other party to a contract to hold up the credit constrained agent, thereby creating inefficiency. This is demonstrated for two types of enforcement mechanisms; enforcement of a one-time trade via the courts, and enforcement of a long-term trade via a punishment strategy.
Malaysian Registered Nurses' Professional Learning
Authors: Chiu Lee H
Published: April 2006

Findings of a study of the impact of professional learning on Malaysian registered nurses are reported. The offshore delivery post-registration nursing degree programme is a formal aspect of professional learning, which enables Malaysian registered nurses to upgrade their hospital-based training or diploma of nursing qualification to a degree. Using a qualitative case study approach, data were collected from twelve programme graduates, through individual and focus group interviews. The programme promoted their personal professional growth and enhanced their professional development. It increased self-confidence, knowledge, self-fulfillment, critical thinking ability, interpersonal skills, interest in research and research utilisation, and life-long learning. There was evidence of career mobility and a raised awareness of their professional role and responsibility.
Genetic Algorithm and Fuzzy Logic Based Optimal Location of Facts Device in a Power System Network
Authors: Jeevarathinam Baskaran
Published: April 2006

The flexible AC transmission system (FACTS) in a power system improves the stability, reduces the losses, reduces the cost of generation and also improves the loadability of the system. In the proposed work, a non-traditional optimization technique, a Genetic Algorithm (GA) is conjunction with Fuzzy logic (FL) is used to optimize the various process parameters involved in introduction of FACTS devices in a power system. The various parameters taken into consideration were the location of the device, their type, and their rated value of the devices. The simulation was performed on a 30-bus power system with various types of FACTS controllers, modeled for steady state studies. The optimization results are compared to the solution given by another search method. This comparison confirms the efficiency of the proposed method which makes it promising to solve combinorial problem of FACTS device location in a power system network.
Design of a Series Compensator for Enhancing Power Quality during the Starting of an Induction Motor
Authors: Li Jian Duo , Choi San Shing , Vilathgamuwa Don Mahinda
Published: April 2006

Mitigation of voltage-sag effects on loads due to the starting of an induction motor is considered. If a series compensator is connected upstream of the motor, the large transient current caused by the switching event could damage the compensator or deplete the energy stored in it. Maximum motor-starting current and the required energy during the starting process are derived from which the ratings of the compensator can be determined. Simulation verifies the analysis is effective and the compensator is shown to be able to maintain good supply quality during the motor- start event.
Fluidization Characteristics of Moist Food Particles
Authors: Senadeera Wijitha , Wijesinghe Bandu , Young Gordon , Bhandari Bhesh
Published: April 2006

Changes in fluidization behaviour of green peas particulates with change in moisture content during drying were investigated using a fluidized bed dryer. All drying experiments were conducted at 50 + 2 0C and 13 + 2 % RH using a heat pump dehumidifier system. Fluidization experiments were undertaken for the bedheights of 100, 80, 60 and 40 mm and at 10 moisture content levels.Fluidization behaviour was best fitted to the linear model of Umf = A + B m. A generalized model was also formulated using the height variation. Also generalized equation and Ergun equation was used to compare minimum fluidization velocity.
Regional Inequality in Medicare Spending: The Key to Medicare Reform?
Authors: Skinner Jonathan , Wennberg John E.
Published: April 2006

Medicare expenditures per capita vary widely across different parts of the country. Average fee-for-service per capita expenditures in 1995/96 were $3,420 in Eugene, Oregon, $3,663 in Minneapolis, $7,847 in Miami, and $8,861 in McAllen, Texas. These measures are adjusted for differences across regions in the age, sex, and racial composition of the population, as well as differences in the underlying cost of healthcare. In this paper, we focus on these geographical variations in the Medicare program and argue that they are central to any proposed reform of the Medicare system. The first question that must be addressed is, are these expenditures higher in high-cost areas because the elderly population there is sicker? The answer is, largely no. Many of the areas with the highest levels of spending have similar underlying disease burdens to regions with low levels of spending. Nor does quality of care or patient satisfaction appear to be better in the high-expenditure areas. These disparities bring up a number of issues related to equity across regions, efficiency of Medicare spending, and the potential for funding Medicare reform. Reducing the intensity of care in high-expenditure regions can fund prescription drug benefits for the entire Medicare population, or extend the solvency of the Medicare trust funds by ten years, without obvious adverse implications for the health or satisfaction of the elderly population.
What Does HMO Market Share Measure? Examining Provider Choice Restrictions
Authors: Baker Laurence
Published: April 2006

Many discussions of managed care, as well as policy making and research efforts, treat managed care with a broad brush, forcing a wide variety of organizations into a single framework that facilitates discussion but abstracts from a number of key issues. Although it may be instructive to conduct broad discussions about managed care, a more detailed understanding of the specific activities that managed care plans undertake and their likely effects is required to support comprehensive policy efforts. Frequently, however, efforts to be more detailed are hampered by shortcomings in the measurement of managed care.This paper lays out a framework of the various activities undertaken by managed care organizations that may be helpful in developing further efforts to understand and measure specific plan activities. The paper also discusses and evaluates some common measures. Detailed data on the exact activities of health insurers and managed care plans are not widely available. One commonly used, but less detailed, measure is the percent of the population enrolled in health maintenance organizations (HMOs). Another places markets on a continuum based on the estimated stage of managed care development in the market. Using data from a new survey, this article compares available measures with more detailed data, suggesting that available data on HMO market share seems to accurately reflect HMO activity, but may not capture the prevalence of some underlying activities of plans like having strong restrictions on enrollee choice of providers, and may also not capture the prevalence of other forms of managed care plans (e.g. Preferred Provider Organizations).These results suggest the importance of distinguishing between the many activities of managed care plans when considering policies that would influence the development of managed care, and when evaluating results from research studies that primarily rely on measures of HMO activity. Results from studies of HMOs may not apply to other types of managed care plans. Policies that target HMOs, or other managed care plans broadly, may be less effective than policies that target specific activities of plans.
Trends in the Use of Intensive Procedures at the End of Life
Authors: Barnato Amber E. , Garber Alan M. , Kagay Christopher R. , McClellan Mark C.
Published: April 2006

Despite widely publicized changes in attitudes toward the care of the dying and rapid growth in hospice care and other services targeted toward the dying, a remarkably stable 30 percent of total Medicare expenditures is spent on the 5 percent of Medicare bene
Creating Price Indexes for Measuring Productivity in Mental Health Care
Authors: Busch Susan H. , Berndt Ernst R. , Frank Richard G.
Published: April 2006

Economists have long suggested that to be reliable, a preferred medical care price index should employ time-varying weights to measure outcomes-adjusted changes in the price of treating an episode of illness. In this article, we report on several years of research developing alternative indexes for the treatment of the acute phase of major depression, for the period 19911996. The introduction of new treatment technologies in the past two decades suggests well-known measurement issues may be prominent in constructing such a price index.We report on the results of four successively re
Effects of Competition Under Prospective Payment on Hospital Costs Among High- and Low-Cost Admissions: Evidence from California, 1983 and 1993
Authors: Meltzer David , Chung Jeanette
Published: April 2006

Competition and prospective payment systems have been widely used to attempt to control health care costs. Although much of the increase in medical costs over the past half-century has been concentrated among a few high-cost users of health care, prospective payment systems may provide incentives to reduce expenditures selectively on high-cost users relative to low-cost users, and this pressure may be increased by competition. We use data on hospital charges and cost-to-charge ratios from California in 1983 and 1993 to examine the effects of competition on costs for high- and low-cost admissions before and after the establishment of the Medicare Prospective Payment System (PPS). Comparing persons above and below age 65 before and after the establishment of PPS, we find that competition is associated with increased costs before PPS in both age groups, but decreased costs afterwards, especially among those above age 65 with the highest costs. We conclude that the combination of competition and prospective payment systems may result in incentives to reduce spending selectively among the most expensive patients. This conclusion raises important issues relevant to the use of competition and prospective payment to control costs. It also implies that, at minimum, there is a need to carefully monitor outcomes for the sickest patients under prospective payment systems in competitive environments.
Tax Credits, the Distribution of Subsidized Health Insurance Premiums, and the Uninsured
Authors: Pauly Mark V. , Herring Bradley , Song David
Published: April 2006

This paper investigates the impact of a$1,000 refundable tax credit for self-only coverage on net premiums and insurance purchases for a representative sample of potential buyers in the individual insurance market. Two methods are used to estimate the distribution of premiums: predicted premiums based on a sample of actual purchasers, and premium quotations drawn from an e-insurance website. In most of the simulations, the net premiums for half or more of the prospective buyers are reduced to zero or low levels. The number of uninsured is reduced by 21 to 85 percent, depending on the size of the deductible in the benchmark plan. However, the results are sensitive to assumptions about insurer underwriting practices.
Geographic structure of human genetic variation: medical and evolutionary implications
Authors: Bertorelle Giorgio , Barbujani Guido
Published: April 2006

The geographic structure of human populations can be summarized by two numbers: 85 and 15, and two keywords:
Continuous Genetic Change
(CGC), and
outliers
. Eighty‐five and fifteen percent of the global variation represent, on the average, the genetic differences within and between populations, respectively. CGC characterizes most of the differences between groups at different geographic scales; and outlier populations, or genetic isolates, generated by different types of barriers to gene flow, punctuate with peaks the clinal landscape. The presence of this patterning, probably consistent across the genome with some exceptions, has several biomedical and evolutionary implications. However, its origin and evolution is only partially understood, and the geographic distribution of genetic variation at selectively important genes is still poorly investigated. Major efforts in these directions, as well as in the study of potential population outliers, will be of great importance to better define and predict the implications and future evolution of our geographic structure.
Genomics of
Rickettsia
Authors: Ogata Hiroyuki , Raoult Didier
Published: April 2006

Rickettsia
are obligate intracellular bacteria associated with arthropods. Many
Rickettsia
species are the agents of human diseases. During the last years, genome sequence analysis has substantially advanced our understanding of the parasitic lifestyle and the virulence mechanisms of the microorganisms. Comparative genome analysis provided insights into the evolutionary mechanisms through which
Rickettsia
have adapted to their intracellular life.
MAGE
‐
OM
: An object model for the communication of microarray data
Authors: Ball Catherine A. , Spellman Paul T. , Miller Michael
Published: April 2006

Meaningful exchange of many high‐throughput biological data is difficult without sufficient information depth and without well‐accepted data formats. Microarray data can be exchanged with the Microarray Gene Expression Markup Language (MAGE‐ML), which is based on a conceptualization of microarray experiments modeled using the unified modeling language (UML) named MAGE‐OM (Microarray Gene Expression Object Model). MAGE was (and continues to be) developed in a collaborative and cooperative manner by many members of the grass‐roots Microarray Gene Expression Data Society (MGED). The MAGE‐ OM was developed with the express intent to provide enough depth and breadth to fully capture data required to meet the standards for the minimum information annotating a microarray experiment (MIAME). MAGE developers and adopters have contributed to a freely available software tool kit (MAGE‐STK) that eases the integration of MAGE‐ML into end users' systems. Future plans include developing a second version of MAGE‐OM that will reduce ambiguities, completely integrate the MGED Ontology, fully capture higher level analysis steps and will be broad enough to contribute to a greater object model for a superset of large‐scale biomedical technologies, called Functional Genomics (FuGE).
Protein Prenyltransferases
Authors: Zhang Hong
Published: April 2006

Protein prenyltransferases (PPT) are Zn metalloenzymes that catalyze the covalent attachment of farnesyl or geranylgeranyl isoprenoids to the C‐terminal cysteine residue(s) of many cellular proteins involved in signal transduction and intracellular vesicle transport. There are three subfamilies of protein prenyltransferases: protein farnesyltransferase (PFT), protein geranylgeranyltransferase type I (PGGT‐I), and protein geranylgeranyltransferase type II (PGGT‐II) or Rab geranylgeranyltransferase (RabGGT). All members of PPT are heterodimers composed of an α‐ and a β‐subunit. The crystal structures of PFT, RabGGT, and, in particular, the complex structures of PFT with its substrates or product elucidated the active site configuration and substrate‐binding mode of these enzymes. An intrinsically bound Zn ion was found to be coordinated to an aspartate, a cysteine, and a histidine residue from the β‐subunit. This Zn ion has been shown to be directly involved in the catalysis by activating the protein substrate cysteine thiol for the nucleophilic attack on the C1 atom of the farnesyl or geranylgeranyl diphosphate. PFT has been a primary anticancer drug target, and extensive biochemical and structural studies have been conducted on the kinetics and mechanistic aspects of the enzyme. Progress has also been made in the structural and enzymological studies of RabGGT and PGGT‐I.
E. coli Alkaline Phosphatase
Authors: Kantrowitz Evan R
Published: April 2006

Escherichia coli

alkaline phosphatase (AP) is a metalloenzyme that catalyzes the nonspecific hydrolysis of phosphomonoesters. Because of the extensive functional and structural studies available on the AP from

E. coli

, this enzyme has become the model for all APs. The two active sites of dimeric AP each contain binding sites for two Zn
2+
and one Mg
2+
. These metals are critical for dimer formation and catalytic activity. The reaction proceeds via a phosphoseryl intermediate formed by the attack of the hydroxyl oxygen of Ser102 on the phosphorus of the substrate. The substrate is stabilized in the active site by binding to Zn
2+
. In the second step of the double in‐line displacement mechanism, a hydroxyl bound to Zn
2+
hydrolyzes the phosphoseryl intermediate. Under basic conditions, the slow step in the mechanism is the release of phosphate from the noncovalent enzyme–phosphate complex. X‐ray structures of the free enzyme, the phosphoseryl intermediate, an enzyme–vanadate complex that mimics the transition state, and the enzyme–phosphate noncovalent complex have been used to delineate molecular details of the catalytic mechanism. Sequence alignments of APs from various species have been used to provide explanations for the enhanced activity of the mammalian APs as compared to the bacterial APs and why certain APs utilize Co
2+
in place of Zn
2+
. The molecular details of phosphate hydrolysis ascertained from the study of AP has applications to other enzymes that are involved in phosphate ester hydrolysis.
Metallothioneins
Authors: Zangger Klaus , Armitage Ian M
Published: April 2006

Metallothioneins (MTs) are small cysteine‐rich polypeptides that bind a series of metal ions and have been found in a variety of animals and even some plants. In animals, the different isoforms of MTs occur in tissues ranging from liver and kidney (isoforms 1 and 2) to the brain (isoform 3) and stratified epithelia (isoform 4). Today, the term metallothionein (MT) is used to denote ‘polypeptides resembling equine renal metallothionein in several of their features.’ On the basis of differing amino acid sequences and structural characteristics, MTs have been subdivided into three classes (I, II, and III), the first of which describes proteins with locations of cysteines closely related to those in equine renal metallothionein. Proteins with cysteine locations only distantly related to equine renal metallothionein are described in class II and atypical, nontranslationally synthesized metal‐thiolate polypeptides are contained in class III. Here we will focus on the structurally well‐characterized class I MTs, which bind zinc or its isomorphous metal‐ion substitute, cadmium. Specifically, these are MT2 from rabbit, rat, and human; MT1 from mouse, blue crab, and lobster; mouse MT3 and sea urchin MTA. In addition, the only structurally characterized class II zinc/cadmium‐containing MT, the cyanobacterial Smta will be discussed.

With the exception of the prokaryotic Smta, all these proteins show a dumbbell‐shaped two‐domain structure with six (blue crab and lobster MT1) or seven (all others) divalent metals bound in two separate metal–cysteine clusters. Although the exact physiological function of MTs is still not clear, a number of presumed functions have been put forward. In addition to the originally proposed dual role of MTs in zinc and copper homeostasis and heavy metal detoxification, they are also thought to be involved in the stress response to reactive oxygen species and possibly play a role at inflammatory sites as scavengers of nitric oxide.
5′‐Nucleotidase
Authors: Sträter Norbert
Published: April 2006

Escherichia coli

5′‐nucleotidase (5′‐NT) is a monomeric protein of 525 amino acids (58.1 kDa). The enzyme has a nutritional function in bacteria where it is exported to the periplasmic space to hydrolyze external nucleotides and UDP‐glucose. Related animal 5′‐nucleotidases are attached to the cell membrane via a GPI anchor and hydrolyze nucleotides as extracellular signaling substances.

E. coli

5′‐NT belongs to the calcineurin superfamily of metallophosphatases and contains two divalent metal ions at a distance of about 3.3 Å. One of these metal ions is probably Zn
2+
in vivo
. However, the Zn
2+
–Zn
2+
form is relatively inactive, whereas good activity is seen in the presence of Mg
2+
, Mn
2+
, and Co
2+
. The protein consists of two domains: a larger N‐terminal domain, which is related to the calcineurin superfamily and contains the two catalytic metal ions and its ligands, and the C‐terminal domain, which bears the substrate specificity pocket that binds the nucleoside moiety of the substrates. Thus, the active site is located at the interface between both domains. In the proposed catalytic mechanism, both metal ions are involved in substrate binding, activation of the nucleophile, and transition‐state stabilization. In addition, a catalytic histidine residue (His117 in

E. coli

5′‐NT) is strictly conserved in all enzymes of this superfamily.
EHDomain
Authors: Overduin Michael , Ravi Kiran Mahadev
Published: April 2006

The Eps15 homology (EH) domain is a 100‐residue protein‐interaction module that consists of a pair of helix‐loop‐helix EF hand motifs. The second EF hand typically binds calcium tightly, providing structural stability. The EH domain is either found singly or in a series of two or three tandem repeats in a variety of eukaryotic proteins that are involved in endocytosis, vesicle transport, and signal transduction. Its function is to mediate interactions with Asn‐Pro‐Phe (NPF) sequences or related motifs that are also often repeated in ligand proteins. The structures, calcium coordination, and peptide binding modes of five monomeric EH domains have recently been elucidated, providing insights into their mechanisms of action.
Gla
‐Domain
Authors: Brown Mark A , Stenflo Johan
Published: April 2006

The term ‘Gla‐domain’ is used to describe the γ‐carboxyglutamic acid (Gla)‐containing region of certain vitamin K–dependent proteins such as prothrombin and factor IX. The domain comprises the first 45 or so amino acids at the N‐terminus of these proteins and contains 9–13 Gla residues that can bind divalent metal cations in a cooperative manner, the most physiologically important being Ca
2+
. Binding of Ca
2+
by the Gla residues induces a conformational transition in the domain that allows it to bind to phospholipid‐containing membranes, a requisite step for the biological functioning of the proteins. Gla residues are also found in two proteins of bone and the extracellular matrix (bone Gla protein or osteocalcin, and matrix Gla protein), and in neurotoxic peptides synthesized by molluscs of the genus
Conus
, but these polypeptides are not considered to have a Gla‐domain as such, and will not be discussed here.
PhospholipaseA2
Authors: Betzel Christian , Singh Tej P , Georgieva Dessislava , Genov Nicolay
Published: April 2006

Phospholipase A2s (phosphatidesn‐2 acylhydrolase, EC 3.1.1.4, PLA2) hydrolyze specifically thesn‐2 ester bond of phospholipids (PL). With some exceptions, they are Ca2+‐dependent enzymes. PLA2s are present in many organs and body fluids of vertebrates, invertebrates, and insects. They play an important role in the phospholipid digestion, remodeling, and metabolism, and are involved in human diseases such as acute pancreatitis, rheumatoid arthritis, respiratory distress, and acute chest syndrome. This review summarizes recent data on the biological function, amino acid sequence, classification, structure–function relationships, and 3D structures of PLA2s. Special attention is paid to the pharmacological activities of the snake venom enzymes. These hydrolases exert their activity through specific protein–protein interactions. Two types of structurally and functionally distinct receptors, N‐ and M‐type, were identified during the last decade and characterized. PLA2binding to its protein receptor can lead to cell damage, tissue necrosis, and other undesirable processes. The ‘interfacial activation’ of the enzymes and their participation in the interfacial catalysis are discussed. Protection of cell membranes from PLA2s is of medical importance.
Structural Calcium (Trypsin, Subtilisin)
Authors: Gilliland Gary L , Teplyakov Alexey
Published: April 2006

The presence of structural calcium in trypsin and subtilisin does not play a role in catalysis, but instead, stabilizes the structures. Trypsin and subtilisin are two large families of serine proteases with different folds that take advantage of the stabilizing effects of binding calcium ions. Representative structures of the different calcium binding sites found in each protein family are described along with the implications for the presence of the ions. This article reviews the details, the energetics, and the roles that calcium plays in the structures of both these families of enzymes.
Cytochrome

c

′
Authors: Romão Maria João , Archer Margarida
Published: April 2006

Cytochromes c′ are heme proteins presumably involved in electron transport and the name cytochrome c′ is used to distinguish these high‐spin heme proteins from the low‐spin mitochondrial cytochromes
c
. The heme group is covalently bound by thioether bonds between the two vinyl groups of the heme and the two cysteinyl side chains in a sequence, ‐Cys‐X‐Y‐Cys‐His‐, typical of cytochromes
c
. The histine occupies the fifth axial coordination position. Most cytochromes c′ are isolated as homodimers of ca 2 × 14 kDa and each monomer consists of an anti‐parallel four‐α‐helical bundle, which defines the heme‐binding pocket.
Cytochromec554
Authors: Iverson Tina M , Hendrich Michael P , Arciero David M , Hooper Alan B , Rees Douglas C
Published: April 2006

Cytochrome c554(cyt c554) is a tetra‐hemec‐type cytochrome that participates in the nitrification pathway ofNitrosomonas europaea. In this process, cyt c554functions as the electron acceptor from the enzyme hydroxylamine oxidoreductase that catalyzes the oxidation of hydroxylamine to nitrite. Cyt c554is a predominantly α‐helical protein with four covalently attached hemes. The four hemes are arranged in two pairs, such that the planes of the porphyrin rings are nearly parallel and overlapping at the edges. This type of heme‐stacking has been observed in two other nitrogen cycle proteins: hydroxylamine oxidoreductase and cytochrome c nitrite reductase, an enzyme that catalyzes the reduction of nitrite to ammonia. The relatively unusual spectral properties of cyt c554may reflect interactions between these pairs of stacked hemes.
Arthromyces Peroxidase
Authors: Fukuyama Keiichi
Published: April 2006

Heme peroxidase catalyzes the oxidation of a variety of compounds by utilizing hydrogen peroxide. The resting peroxidase reacts with hydrogen peroxide to yield an intermediate compound I, which is reduced to the resting stateviathe second intermediate compound II, by the use of reducing substrates. The reducing substrates include naturally occurring organic compounds such as phenols and ascorbic acid, diagnostic reagents such as luminol and 4‐amino‐antipyrine, as well as inorganic compounds such as halide ions, ferrocyanide, and isothiocyanate.Arthromycesperoxidase is a class II peroxidase in the plant peroxidase superfamily, and has the characteristics of giving extraordinarily high chemiluminescence in the oxidation of luminol.
Purple Acid Phosphatase
Authors: Vogel Andreas , Spener Friedrich , Krebs Bernt
Published: April 2006

Purple acid phosphatases (PAPs) hydrolyzing activated phosphoric acid esters and anhydrides have in common a two‐metal center with a tyrosine‐Fe(III) charge transfer transition responsible for the color. In the mammalian enzymes from the spleen, macrophages, osteoclasts, and uterine fluids, the second metal in the active site is Fe(II); whereas, the plant enzyme kidney bean PAP (kbPAP) has an Fe(III)–Zn(II) active center. The structure of the homodimeric 111‐kDa kbPAP shows the active site at the carboxy end of two sandwiched β–α–β–α–β motifs. The two metal ions are bridged monodentately by Asp164. The iron is further coordinated by Tyr167, His325, and Asp135, and the zinc by His286, His323, and Asn201. The active‐site structure is consistent with proposals on the mechanism of phosphate ester hydrolysis by nucleophilic attack on the phosphate by an Fe(III)‐coordinated hydroxide ion. Protein isolation, biological functions, sequences, activity, comparison of mammalian and plant PAPs, and the functional aspects of both types are discussed extensively.
Cytochrome

b

1
– Bacterioferritin
Authors: Frolow Felix , Kalb(Gilboa) Aaron Joseph
Published: April 2006

Cytochrome b1, also known as bacterioferritin, has been isolated from

Escherichia coli

, as well as many other bacteria. This large 400‐kD protein is composed of 24 identical subunits arranged in a shell of cubic (
432
) symmetry and contains at least three distinct forms of iron:

12 heme irons coordinated by pairs of methionine sulfurs from contiguous twofold symmetry related subunits

48 iron atoms, two in each subunit, occupying a
quasi‐
symmetric binuclear metal‐binding site

several thousand bulk iron atoms that may be deposited as a microcrystalline polymeric mineral in the hollow interior of the ferritin‐like protein shell.
Methylmalonyl
Co
A
Mutase
Authors: Gruber Karl , Kratky Christoph
Published: April 2006

The 5′‐adenosylcobalamin dependent methylmalonyl‐CoA mutase (MCM) catalyzes the reversible and stereospecific equilibration of (
2R
)‐methylmalonyl CoA and succinyl CoA through a radical mechanism. Its occurrence ranges from bacteria to mammals, where it is required for the metabolism or biosynthesis of propionate. MCM from

Propionibacterium shermanii

is an αβ‐heterodimer of total molecular weight 150 kDa, containing an inactive β‐subunit along with an active α‐subunit, the latter binding one adenosylcobalamin molecule close to the active site. The protein was found to occur in two fundamentally different conformations: in the presence of substrates it crystallizes in a “closed” conformation, whereas in the absence of substrates an “open” conformation is observed. This dramatic conformational change suggests a mechanism for the first step of the MCM‐catalyzed reaction cycle, i.e. the substrate‐induced homolysis of the Co–C bond.
Dimethylsulfoxide Reductase
Authors: Li Hung‐Kei , Schindelin Hermann
Published: April 2006

Dimethylsulfoxide reductase is a molybdenum cofactor‐containing enzyme, which catalyzes the two‐electron reduction of dimethylsulfoxide to dimethylsulfide. The enzyme consists of a single polypeptide chain of 780 amino acids and contains no other cofactor besides the molybdenum cofactor. The overall fold of the enzyme is structurally organized into four domains, which are grouped around the cofactor. The molybdenum cofactor consists of two molybdopterin guanine dinucleotides, which are symmetrically ligating the molybdenum with their dithiolene groups. In the oxidized Mo(VI) form of the enzyme, an oxo group and a serine side chain complete the coordination sphere. The oxo group is the catalytically labile oxygen, which is replaced by an aquo or, possibly, a hydroxo ligand in the reduced Mo(IV) state.
Trimethylamine

N

‐Oxide Reductase
Authors: Iobbi‐Nivol Chantal , Haser Richard , Méjean Vincent , Czjzek Mirjam
Published: April 2006

Trimethylamine
N
‐oxide (TMAO) is a compound widely distributed in marine fish and invertebrates; and TMAO reducing enzymes are found not only in marine bacteria and photosynthetic bacteria living in ponds but also in enterobacteria. The various respiratory systems reducing TMAO, described so far, share a high level of homology either in their general structure, or in the regulation or mechanism of electron transfer. According to their content of molybdenum cofactor, the enzymes in charge of TMAO reduction are classified in the structural dimethylsulfoxide (DMSO) reductase family. TMAO reductases, however, in contrast to DMSO reductases are highly specific enzymes and reduce only their physiological substrate. The crystal structure was determined for the TMAO reductase from
Shewanella massilia
, and its structural differences with DMSO reductases in the environment of the active site. A tyrosine residue in the proximity of the molybdenum ion in DMSO reductases is absent in TMAO reductases and could be related to the differences in substrate specificities.
Rusticyanin
Authors: Shoham Menachem
Published: April 2006

Rusticyanin is a type 1 blue copper protein that functions as the major electron carrier in the iron respiratory electron transport chain ofThiobacillus ferrooxidans. This bacterium is the main cause of acid mine drainage. Rusticyanin is an extremophilic protein with redox activity as low as pH 0.5 and a redox potential of 680 mV, which is at least twice as high as for any other member of the family of cupredoxins. The ligands to the single copper ion are His85, Cys138, His143, and Met148. The three‐dimensional structure consists of a β‐sandwich of two mixed β‐sheets, one of six and one of seven strands, as well as a single amphipathic helix near the N‐terminus.
On the Fundamentals of Hydrological Sciences
Authors: Blöschl Günter
Published: April 2006

Although there is no universal theory in hydrology that starts from first principles, the various branches of hydrology show numerous common threads. They relate to the nature of the processes including their space–time variability, the general principles of hydrological measurements, and the types of methods for representing hydrological processes in a quantitative way, either statistically or deterministically. The purpose of this article is to provide some common ground for this Encyclopedia to highlight the particularities of the hydrological sciences.
Hydrologic Concepts of Variability and Scale
Authors: Woods Ross
Published: April 2006

All hydrological phenomena have significant variations in time and space. Typically, these variations are driven by variations in physiographic factors such as climate, soils, vegetation, topography, geology, as well as by human and animal activities. These externally driven variations then propagate through hydrological systems, leading to an extremely rich variety of hydrological variability apparent at different temporal and spatial scales, in different physical settings. Virtually any quantitative approach to this problem requires the selection of a limited set of spatial and temporal scales within a particular physiographic setting. Any particular choice of time and space scales has a major influence on which aspects of this hydrological variability are perceived. This article surveys hydrological variability in both time and space, across a range of scales.
Fractals and Similarity Approaches in Hydrology
Authors: Lanza Luca G , Gallant John
Published: April 2006

The application of fractals and similarity concepts in hydrology has given rise to a better understanding of the space‐time organization of forms and processes that are relevant to the hydrologic cycle. Indeed, a variety of literature results support the conjecture that scaling holds for most hydrological variables in time and space.

This chapter concentrates on fields where fractals and similarity approaches have proved helpful in fostering advances in specific hydrological studies. In particular, precipitation and drainage network morphology are addressed. A few specific applications to the study of natural forms and patterns relevant to the hydrological sciences are presented first, while the application of scaling concepts to the study of processes themselves is later discussed.

Because of its highly irregular behavior, the rainfall process is one ideal candidate to be approached by means of self‐similarity and/or (multi)fractal description models. Such models involve increasing complexity and computational burden as soon as the interest moves from the one‐dimensional time series to the three‐dimensional case, where the full space‐time pattern of rainfall is considered. Examples of recent interesting results are presented with reference to the one‐, two‐, and three‐dimensional approaches to rainfall modeling based on similarity concepts.