bluuebunny/crossref_metadata_2025_split 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

AbstractThe 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

AbstractTwo multi-component scores (Fibrotest
Increased free malondialdehyde concentrations in smokers normalise with a mixed fruit and vegetable juice concentrate: a pilot study
Authors: Bamonti Fabrizia , Novembrino Cristina , Ippolito Silvia , Soresi Enzo , Ciani Alberto , Lonati Silvia , Scurati-Manzoni Elisabetta , Cighetti Giuliana 
Published: April 2006

Abstract
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

ABSTRACTTo 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

Abstract
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.
Credit Constraints and Contract Enforcement
Authors: Powers Dennis 
Published: April 2006

Abstract
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.
Geographic structure of human genetic variation: medical and evolutionary implications
Authors: Bertorelle Giorgio , Barbujani Guido 
Published: April 2006

Abstract

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

Abstract

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

Abstract
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

AbstractProtein 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

Abstract

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

AbstractMetallothioneins (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

Abstract

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

AbstractThe 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

Abstract

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

AbstractPhospholipase 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

Abstract
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

Abstract

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

AbstractCytochrome 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

AbstractHeme 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

Abstract
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

Abstract

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.