bluuebunny/crossref_metadata_2025 huggingface dataset:
Maternal hemoglobin level and fetal outcome at low and high altitudes
Authors: Gonzales Gustavo F. , Steenland Kyle , Tapia Vilma
Published: September 2009

Both, low (<7 g/dl) and high (>14.5 g/dl), maternal hemoglobin (Hb) levels have been related to poor fetal outcome. Most studies have been done at low altitude (LA). Here, we have sought to determine whether this relationship exists at both high and low altitude, and also whether there is an adverse effect of high altitude (HA) on fetal outcome independent of level of maternal hemoglobin. The study is based on a retrospective multicenter analysis of 35,449 pregnancies at LA and six other cities above 3000 meters. In analyses of all women at both LA and HA, those with Hb <9 g/dl had odds ratios (ORs) and 95% confidence intervals (CI) of 4.4 (CI: 2.8–6.7), 2.5 (CI: 1.9–3.2), and 1.4 (CI: 1.1–1.9) for stillbirths, preterm, and small for gestational age (SGA) births, respectively, compared with women with 11–12.9 g/dl of Hb, after adjustment for confounders. These risks by hemoglobin level differed little between women at LA and HA, suggesting that no correction of the definition of anemia is necessary for women at HA. Women living at high altitude with hemoglobin >15.5 g/dl had higher risks for stillbirths (OR: 1.3; CI: 1.05–1.3), preterm (OR: 1.5; CI 1.3–1.8), and SGA births (OR: 2.1, CI 1.8–2.3). There was also a significant adverse effect of living at HA, independent of hemoglobin level for all three outcomes (OR: 3.9, 1.7, and 2.3; CI: 2.8–5.2, 1.5–1.9, and 2.1–2.5) for stillbirths, preterms, and SGA respectively, after adjusting for hemoglobin level. Both, high and low maternal hemoglobin levels were related to poor pregnancy outcome, with similar effect of low hemoglobin in both LA and HA. Our data suggest, that maternal hemoglobin above 11 g/dl but below 13 g/dl is the area of minimal risk of poor adverse outcomes. Living at HA had an adverse effect independent of hemoglobin level.
Functional significance of muscarinic receptor expression within the proximal and distal rat vagina
Authors: Basha Maureen , LaBelle Edward F. , Northington Gina M. , Wang Tanchun , Wein Alan J. , Chacko Samuel
Published: September 2009

Information regarding the role of cholinergic nerves in mediating vaginal smooth muscle contraction is sparse, and in vitro studies of the effects of muscarinic agonists on vaginal smooth muscle are discrepant. The goal of this study was to determine the expression of muscarinic receptors in the vaginal wall of the rat. In addition, we sought to determine the effect of the muscarinic receptor agonist carbachol on contractility and inositol phosphate production of the proximal and distal rat vaginal muscularis. RT-PCR analysis indicated that both M2and M3receptor transcripts were expressed within the proximal and distal rat vagina. Carbachol dose-dependently (10−7–10−4M) contracted the rat vaginal muscularis with a greater maximal contractile response in the proximal vagina ( P < 0.01) compared with the distal vagina. The contractile responses of the rat vaginal muscularis to carbachol were dose dependently inhibited by the M3antagonist para-fluoro-hexahydrosiladefenidol, and a pKBof 7.78 and 7.95 was calculated for the proximal and distal vagina, respectively. Inositol phosphate production was significantly increased in both regions of the vagina following 20-min exposure to 50 μM carbachol with higher levels detected in the proximal vagina compared with the distal ( P < 0.05). Preliminary experiments indicated the presence of M2and M3receptors in the human vaginal muscularis as well as contraction of human vaginal muscularis to carbachol, indicating that our animal studies are relevant to human tissue. Our results provide strong evidence for the functional significance of M3receptor expression in the vaginal muscularis.
Mesangial cell-derived factors alter monocyte activation and function through inflammatory pathways: possible pathogenic role in diabetic nephropathy
Authors: Min Danqing , Lyons J. Guy , Bonner James , Twigg Stephen M. , Yue Dennis K. , McLennan Susan V.
Published: September 2009

Infiltration of macrophages to the kidney is a feature of early diabetic nephropathy. For this to happen monocytes must become activated, migrate from the circulation, and infiltrate the mesangium. This process involves degradation of extracellular matrix, a process mediated by matrix metalloproteinases (MMPs). In the present study we investigate the expression of proinflammatory cytokines TNF-α, IL-6, and MMP-9 in glomeruli of control and diabetic rodents and use an in vitro coculture system to examine whether factors secreted by mesangial cells in response to a diabetic milieu can induce monocyte MMP-9 expression and infiltration. After 8 wk of diabetes, the glomerular level of TNF-α, IL-6, and macrophage number and colocalization of MMP-9 with macrophage were increased ( P < 0.01). Coculture of THP1 monocytes and glomerular mesangial cells in 5 or 25 mM glucose increased MMP-9 (5 mM: 65% and 25 mM: 112%; P < 0.05) and conditioned media degradative activity (5 mM: 30.0% and 25 mM: 33.5%: P < 0.05). These effects were reproduced by addition of mesangial cell conditioned medium to THP1 cells. High glucose (25 mM) increased TNF-α, IL-6, and monocyte chemoattractant protein-1 in mesangial cell conditioned medium. These cytokines all increased adhesion and differentiation of THP1 cells ( P < 0.05), but only TNF-α and IL-6 increased MMP-9 expression (50- and 60-fold, respectively; P < 0.05). Our results show that mesangial cell-secreted factors increase monocyte adhesion, differentiation, MMP expression, and degradative capacity. High glucose could augment these effects by increasing mesangial cell proinflammatory cytokine secretion. This mesangial cell-monocyte interaction may be important in activating monocytes to migrate from the circulation to the kidney in the early stages of diabetic nephropathy.
Synergistic and antagonistic interactions in the rat forelimb: acute effects of coactivation
Authors: Maas Huub , Huijing Peter A.
Published: September 2009

The goals of the present study were 1) to assess effects of antagonist coactivation on mechanical interactions between synergistic muscles, and 2) to quantify the extent of epimuscular myofascial force transmission between synergistic and antagonistic muscles in the rat forelimb. Connective tissues enveloping the muscle bellies in the antebrachium were left intact. Forces exerted at the distal tendons of flexor carpi ulnaris (FCU), palmaris longus (PL), and extensor carpi ulnaris (ECU) muscles were measured at various FCU lengths for two different stimulation protocols: 1) simultaneous stimulation of ulnar/median nerve complex (exciting all wrist flexors, including synergistic FCU and PL) and radial nerve (exciting all wrist extensors, including antagonistic ECU); and 2) stimulation of the ulnar/median nerve exclusively. PL and ECU were kept at a constant length. In addition, muscle forces were measured during stimulation of one of the indicated nerves, with later addition of stimulation of the second nerve during the maintained tetanic contraction. Coactivation of antagonistic muscles increased FCU isometric forces (on average, by 10% of optimal force) and PL forces (on average, by 13% of maximal force), but mechanical interaction between FCU and PL was unchanged. Changing the length and relative position of FCU significantly affected PL (by 20%) as well as ECU forces (by 8%). In addition, distal tetanic force of FCU kept at a constant high length was determined by the order of nerve stimulation onset. These results indicate effects of myofascial pathways between synergistic and antagonistic muscles in the rat forelimb. Coactivation may enhance the stiffness of connective tissues between muscles, but the present data suggest that activation of all wrist flexors already preloaded the myofascial pathways to the greatest extent. The stimulation order effects were explained by dynamic features of muscle and connective tissues (i.e., length-history dependence and viscoelasticity).
Cellular localization of D‐lactate dehydrogenase and NADH oxidase from Archaeoglobus fulgidus
Authors: Reddy Pagala Vishwajeeth , Park Joohye , Reed David W. , Hartzell Patricia L.
Published: September 2009

Members of the genus Archaeoglobus are hyperthermophilic sulfate reducers with an optimal growth temperature of 83 °C. Archaeoglobus fulgidus can utilize
simple compounds including D‐lactate, L‐lactate and pyruvate as the sole substrate for carbon and electrons for dissimilatory sulfate reduction. Previously we showed that this organism makes a D‐lactate dehydrogenase (Dld) that requires FAD and Zn2+ for activity. To determine the cellular location and topology of Dld and to identify proteins that interact with Dld, an antibody directed against Dld was prepared. Immunocytochemical studies using gold particle‐coated secondary antibodies show that more than 85% of Dld is associated with the membrane. A truncated form of Dld was detected in immunoblots of whole cells treated with protease, showing that Dld is an integral membrane protein and that a significant portion of Dld, including part of the FAD‐binding pocket, is outside the membrane facing the S‐layer. The gene encoding Dld is part of an operon that includes noxA2, which encodes one of several NADH oxidases in A. fulgidus. Previous studies have shown that NoxA2 remains bound to Dld during purification. Thin sections of A. fulgidus probed simultaneously with antibodies against Dld and NoxA2 show that both proteins co‐localized to the same sites in the membrane. Although these data show a tight interaction between NoxA2 and Dld, the role of NoxA2 in electron transport reactions is unknown. Rather, NoxA2 may protect proteins involved in electron transfer by reducing O2 to H2O2 or H2O.
The ultrastructure of Ignicoccus: Evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon
Authors: Rachel Reinhard , Wyschkony Irith , Riehl Sabine , Huber Harald
Published: September 2009

A novel genus of hyperthermophilic, strictly chemolithotrophic archaea, Ignicoccus, has been described recently, with (so far) three isolates in pure culture. Cells were prepared for ultrastructural investigation by cultivation in cellulose capillaries and processing by high‐pressure freezing, freeze‐substitution and embedding in Epon. Cells prepared in accordance with this protocol consistently showed a novel cell envelope structure previously unknown among the Archaea: a cytoplasmic membrane; a periplasmic space with a variable width of 20 to 400 nm, containing membrane‐bound vesicles; and an outer sheath, approximately 10 nm wide, resembling the outer membrane of gram‐negative bacteria. This sheath contained three types of particles: numerous tightly, irregularly packed single particles, about 8 nm in diameter; pores with a diameter of 24 nm, surrounded by tiny particles, arranged in a ring with a diameter of 130 nm; and clusters of up to eight particles, each particle 12 nm in diameter. Freeze‐etched cells exhibited a smooth surface, without a regular pattern, with frequent fracture planes through the outer sheath, indicating the presence of an outer membrane and the absence of an S‐layer. The study illustrates the novel complex architecture of the cell envelope of Ignicoccus as well as the importance of elaborate preparation procedures for ultrastructural investigations.
Identification and analysis of proton‐translocating pyrophosphatases in the methanogenic archaeon Methanosarcina mazei
Authors: Bäumer Sebastian , Lentes Sabine , Gottschalk Gerhard , Deppenmeier Uwe
Published: September 2009

Analysis of genome sequence data from the methanogenic archaeon Methanosarcina mazei Gö1 revealed the existence of two open reading frames encoding proton‐translocating pyrophosphatases (PPases). These open reading frames are linked by a 750‐bp intergenic region containing TC‐rich stretches and are transcribed in opposite directions. The corresponding polypeptides are referred to as Mvp1 and Mvp2 and consist of 671 and 676 amino acids, respectively. Both enzymes represent extremely hydrophobic, integral membrane proteins with 15 predicted transmembrane segments and an overall amino acid sequence similarity of 50.1%. Multiple sequence alignments revealed that Mvp1 is closely related to eukaryotic PPases, whereas Mvp2 shows highest homologies to bacterial PPases. Northern blot experiments with RNA from methanol‐grown cells harvested in the mid‐log growth phase indicated that only Mvp2 was produced under these conditions. Analysis of washed membranes showed that Mvp2 had a specific activity of 0.34 U mg (protein)–1. Proton translocation experiments with inverted membrane vesicles prepared from methanol‐grown cells showed that hydrolysis of 1 mol of pyrophosphate was coupled to the translocation of about 1 mol of protons across the cytoplasmic membrane. Appropriate conditions for mvp1 expression could not be determined yet. The pyrophosphatases of M. mazei Gö1 represent the first examples of this enzyme class in methanogenic archaea and may be part of their energy‐conserving system. Abbreviations: DCCD, N,N′‐dicyclohexylcarbodiimide; PPase, inorganic pyrophosphatase; PPi, inorganic pyrophosphate; Δp, proton motive force.
Common evolutionary origins of mechanosensitive ion channels in Archaea, Bacteria and cell‐walled Eukarya
Authors: Kloda Anna , Martinac Boris
Published: September 2009

The ubiquity of mechanosensitive (MS) channels triggered a search for their functional homologs in Archaea. Archaeal MS channels were found to share a common ancestral origin with bacterial MS channels of large and small conductance, and sequence homology with several proteins that most likely function as MS ion channels in prokaryotic and eukaryotic cell‐walled organisms. Although bacterial and archaeal MS channels differ in conductive and mechanosensitive properties, they share similar gating mechanisms triggered by mechanical force transmitted via the lipid bilayer. In this review, we suggest that MS channels of Archaea can bridge the evolutionary gap between bacterial and eukaryotic MS channels, and that MS channels of Bacteria, Archaea and cell‐walled Eukarya may serve similar physiological functions and may have evolved to protect the fragile cellular membranes in these organisms from excessive dilation and rupture upon osmotic challenge.
Getting on target: The archaeal signal recognition particle
Authors: Zwieb Christian , Eichler Jerry
Published: September 2009

Protein translocation begins with the efficient targeting of secreted and membrane proteins to complexes embedded within the membrane. In Eukarya and Bacteria, this is achieved through the interaction of the signal recognition particle (SRP) with the nascent polypeptide chain. In Archaea, homologs of eukaryal and bacterial SRP‐mediated translocation pathway components have been identified. Biochemical analysis has revealed that although the archaeal system incorporates various facets of the eukaryal and bacterial targeting systems, numerous aspects of the archaeal system are unique to this domain of life. Moreover, it is becoming increasingly clear that elucidation of the archaeal SRP pathway will provide answers to basic questions about protein targeting that cannot be obtained from examination of eukaryal or bacterial models. In this review, recent data regarding the molecular composition, functional behavior and evolutionary significance of the archaeal signal recognition particle pathway are discussed.
Molecular analysis of the role of two aromatic aminotransferases and a broad‐specificity aspartate aminotransferase in the aromatic amino acid metabolism of Pyrococcus furiosus
Authors: Ward Donald E. , de Vos William M. , van der Oost John
Published: September 2009

The genes encoding aromatic aminotransferase II (AroAT II) and aspartate aminotransferase (AspAT) from Pyrococcus furiosus have been identified, expressed in Escherichia coli and the recombinant proteins characterized. The AroAT II enzyme was specific for the transamination reaction of the aromatic amino acids, and uses α‐ketoglutarate as the amino acceptor. Like the previously characterized AroAT I, AroAT II has highest efficiency for phenylalanine (k
cat/K
m = 923 s–1 mM–1). Northern blot analyses revealed that AroAT I was mainly expressed when tryptone was the primary carbon and energy source. Although the expression was significantly lower, a similar trend was observed for AroAT II. These observations suggest that both AroATs are involved in amino acid degradation. Although AspAT exhibited highest activity with aspartate and α‐ketoglutarate (k
cat ~105 s–1), it also showed significant activity with alanine, glutamate and the aromatic amino acids. With aspartate as the amino donor, AspAT catalyzed the amination of α‐ketoglutarate, pyruvate and phenylpyruvate. No activity was detected with either branched‐chain amino acids or α‐keto acids. The AspAT gene (aspC) was expressed as a polycistronic message as part of the aro operon, with expression observed only when the aromatic amino acids were absent from the growth medium, indicating a role in the biosynthesis of the aromatic amino acids.
Calcium‐induced aggregation of archaeal bipolar tetraether liposomes derived from the thermoacidophilic archaeon Sulfolobus acidocaldarius
Authors: Kanichay Roby , Boni Lawrence T. , Cooke Peter H. , Khan Tapan K.
Published: September 2009

Previously, we showed that the proton permeability of small unilamellar vesicles (SUVs) composed of polar lipid fraction E (PLFE) from the thermoacidophilic archaeon Sulfolobus acidocaldarius was remarkably low and insensitive to temperature (Komatsu and Chong 1998). In this study, we used photon correlation spectroscopy to investigate the time dependence of PLFE SUV size as a function of Ca2+ concentration. In the absence of Ca2+, vesicle diameter changed little over 6 months. Addition of Ca2+, however, immediately induced formation of vesicle aggregates with an irregular shape, as revealed by confocal fluorescence microscopy. Aggregation was reversible upon addition of EDTA; however, the reversibility varied with temperature as well as incubation time with Ca2+. Freeze‐fracture electron microscopy showed that, after a long period of incubation (2 weeks) with Ca2+, the PLFE vesicles had not just aggregated, but had fused or coalesced. The initial rate of vesicle aggregation varied sigmoidally with Ca2+ concentration. At pH 6.6, the threshold calcium concentration (Cr) for vesicle aggregation at 25 and 40 °C was 11 and 17 mM, respectively. At pH 3.0, the Cr at 25 °C increased to 25 mM. The temperature dependence of Cr may be attributable to changes in membrane surface potential, which was –22.0 and –13.2 mV at 25 and 40 °C, respectively, at pH 6.6, as determined by 2‐(p‐toluidinyl)naphthalene‐6‐sulfonic acid fluorescence. The variation in surface potential with temperature is discussed in terms of changes in lipid conformation and membrane organization.
Minimal sulfur requirement for growth and sulfur‐dependent metabolism of the hyperthermophilic archaeon Staphylothermus marinus
Authors: Hao Xiaolei , Ma Kesen
Published: September 2009

Staphylothermus marinus is an anaerobic hyperthermophilic archaeon that uses peptides as carbon and energy sources. Elemental sulfur (S°) is obligately required for its growth and is reduced to H2S. The metabolic functions and mechanisms of S° reduction were explored by examining S°‐dependent growth and activities of key enzymes present in this organism. All three forms of S° tested—sublimed S°, colloidal S° and polysulfide—were used by S. marinus, and no other sulfur‐containing compounds could replace S°. Elemental sulfur did not serve as physical support but appeared to function as an electron acceptor. The minimal S° concentration required for optimal growth was 0.05% (w/v). At this concentration, there appeared to be a metabolic transition from H2 production to S° reduction. Some enzymatic activities related to S°‐dependent metabolism, including sulfur reductase, hydrogenase, glutamate dehydrogenase and electron transfer activities, were detected in cell‐free extracts of S. marinus. These results indicate that S° plays an essential role in the heterotrophic metabolism of S. marinus. Reducing equivalents generated by the oxidation of amino acids from peptidolysis may be transferred to sulfur reductase and hydrogenase, which then catalyze the production of H2S and H2, respectively.
The conserved adenosine in helix 6 of Archaeoglobus fulgidus signal recognition particle RNA initiates SRP assembly
Authors: Yin Jiaming , Huang Qiaojia , Pakhomova Olga N. , Hinck Andrew P. , Zwieb Christian
Published: September 2009

The signal recognition particle (SRP) RNA helix 6 of archaea and eukaryotes is essential for the binding of protein SRP19 and the assembly of a functional complex. The conserved adenosine at the third position of the tetraloop of helix 6 (A149) is crucial for the binding of protein SRP19 in the mammalian SRP. Here we investigated the significance of the equivalent adenosine residue at position 159 (A159) of Archaeoglobus fulgidus SRP RNA. The A159 of A. fulgidus and A149 of human SRP RNA were changed to C, G or U, and fragments containing helix 6 or helices 6 and 8 were synthesized by run‐off transcription with T7 RNA polymerase. The ability of recombinant A. fulgidus and human SRP19 to form ribonucleoprotein complexes was measured in vitro. The simultaneous presence of A149 and helix 8 is required for the high‐affinity binding of SRP19 to the human SRP RNA. In contrast, A. fulgidus SRP19 binds to the SRP RNA fragments with high affinity irrespective of the nature of the nucleotide, demonstrating that A159 does not directly participate in protein binding. Instead, as indicated by the resistance of the wild‐type A. fulgidus RNA towards digestion by RNase A, this residue allows the formation of a tightly folded RNA molecule. The high affinity between A. fulgidus SRP19 and RNA molecules that contain both helices 6 and 8 suggests that A159 is likely to initiate archaeal SRP assembly by forming a conserved tertiary RNA– RNA interaction.
Automated metabolic reconstruction for Methanococcus jannaschii
Authors: Tsoka Sophia , Simon David , Ouzounis Christos A.
Published: September 2009

We present the computational prediction and synthesis of the metabolic pathways in Methanococcus jannaschii from its genomic sequence using the PathoLogic software. Metabolic reconstruction is based on a reference knowledge base of metabolic pathways and is performed with minimal manual intervention. We predict the existence of 609 metabolic reactions that are assembled in 113 metabolic pathways and an additional 17 super‐pathways consisting of one or more component pathways. These assignments represent significantly improved enzyme and pathway predictions compared with previous metabolic reconstructions, and some key metabolic reactions, previously missing, have been identified. Our results, in the form of enzymatic assignments and metabolic pathway predictions, form a database (MJCyc) that is accessible over the World Wide Web for further dissemination among members of the scientific community.
Hydrolase and glycosynthase activity of endo‐1,3‐β‐glucanase from the thermophile Pyrococcus furiosus
Authors: Van Lieshout J. , Faijes M. , Nieto J. , Van Der Oost J. , Planas A.
Published: September 2009

Pyrococcus furiosus laminarinase (LamA, PF0076) is an endo‐glycosidase that hydrolyzes β‐1,3‐gluco‐oligosaccharides, but not β‐1,4‐gluco‐oligosaccharides. We studied the specificity of LamA towards small saccharides by using 4‐methylumbelliferyl β‐glucosides with different linkages. Besides endo‐activity, wild‐type LamA has some exo‐activity, and catalyzes the hydrolysis of mixed‐linked oligosaccharides (Glcβ4Glcβ3Glcβ‐MU (Glc = glucosyl, MU = 4‐methylumbelliferyl)) with both β‐1,4 and β‐1,3 specificities. The LamA mutant E170A had severely reduced hydrolytic activity, which is consistent with Glu170 being the catalytic nucleophile. The E170A mutant was active as a glycosynthase, catalyzing the condensation of α‐laminaribiosyl fluoride to different acceptors. The best condensation yields were found at pH 6.5 and 50 °C, but did not exceed 30%. Depending on the acceptor, the synthase generated either a β‐1,3 or a β‐1,4 linkage.
Active site of Zn2+‐dependent sn‐glycerol‐1‐phosphate dehydrogenase from Aeropyrum pernix K1
Authors: Han Jin-Suk , Ishikawa Kazuhiko
Published: September 2009

The enzyme sn‐glycerol‐1‐phosphate dehydrogenase (Gro1PDH, EC 1.1.1.261) is key to the formation of the enantiomeric configuration of the glycerophosphate backbone (sn‐glycerol‐1‐phosphate) of archaeal ether lipids. This enzyme catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol‐1‐phosphate. To date, no information about the active site and catalytic mechanism of this enzyme has been reported. Using the sequence and structural information for glycerol dehydrogenase, we constructed six mutants (D144N, D144A, D191N, H271A, H287A and D191N/H271A) of Gro1PDH from Aeropyrum pernix K1 and examined their characteristics to clarify the active site of this enzyme. The enzyme was found to be a zinc‐dependent metalloenzyme, containing one zinc ion for every monomer protein that was essential for activity. Site‐directed mutagenesis of D144 increased the activity of the enzyme. Mutants D144N and D144A exhibited low affinity for the substrates and higher activity than the wild type, but their affinity for the zinc ion was the same as that of the wild type. Mutants D191N, H271A and H287A had a low affinity for the zinc ion and a low activity compared with the wild type. The double mutation, D191N/ H271A, had no enzyme activity and bound no zinc. From these results, it was clarified that residues D191, H271 and H287 participate in the catalytic activity of the enzyme by binding the zinc ion, and that D144 has an effect on substrate binding. The structure of the active site of Gro1PDH from A. pernix K1 seems to be similar to that of glycerol dehydrogenase, despite the differences in substrate specificity and biological role.
Identification of replication origins in archaeal genomes based on the Z‐curve method
Authors: Zhang Ren , Zhang Chun-Ting
Published: September 2009

The Z‐curve is a three‐dimensional curve that constitutes a unique representation of a DNA sequence, i.e., both the Z‐curve and the given DNA sequence can be uniquely reconstructed from the other. We employed Z‐curve analysis to identify one replication origin in the Methanocaldococcus jannaschii genome, two replication origins in the Halobacterium species NRC‐1 genome and one replication origin in the Methanosarcina mazei genome. One of the predicted replication origins of Halobacterium species NRC‐1 is the same as a replication origin later identified by in vivo experiments. The Z‐curve analysis of the Sulfolobus solfataricus P2 genome suggested the existence of three replication origins, which is also consistent with later experimental results. This review aims to summarize applications of the Z‐curve in identifying replication origins of archaeal genomes, and to provide clues about the locations of as yet unidentified replication origins of the Aeropyrum pernix K1, Methanococcus maripaludis S2, Picrophilus torridus DSM 9790 and Pyrobaculum aerophilum str. IM2 genomes.
Existence and Uniform Decay of Weak Solutions for Nonlinear Thermoelastic System with Memory
Authors: Haihong Liu , Ning Su
Published: September 2009

A nonlinear thermoelastic system with memory is considered, which is derived from a physical model with vibration in temperature environment. By some skillful and technical arguments, results of existence, uniqueness, and uniform decay on this generalized system are obtained.
Entropy Generation and Human Aging: Lifespan Entropy and Effect of Diet Composition and Caloric Restriction Diets
Authors: Silva Carlos A. , Annamalai Kalyan
Published: September 2009

The first and second laws of thermodynamic were applied to statistical databases on nutrition and human growth in order to estimate the entropy generation over the human lifespan. The calculations were performed for the cases of variation in the diet composition and calorie restriction diets; and results were compared to a base case in which lifespan entropy generation was found to be 11 404 kJ/K per kg of body mass, predicting a lifespan of 73.78 and 81.61 years for the average male and female individuals respectively. From the analysis of the results, it was found that changes of diet % of fat and carbohydrates do not have a significant impact on predicted lifespan, while the diet % of proteins has an important effect. Reduction of diet protein % to the minimum recommended in nutrition literature yields an average increase of 3.3 years on the predicted lifespan. Changes in the calorie content of the diet also have an important effect, yielding a % increase in lifespan equal or higher than the % reduction in the diet caloric content. This correlates well experimental data on small mammal and insects, in which lifespan has been increased by diet restriction.
Caenorhabditis elegans F09E10.3 Encodes a Putative 3‐Oxoacyl‐Thioester Reductase of Mitochondrial Type 2 Fatty Acid Synthase FASII that Is Functional in Yeast
Authors: Gurvitz Aner
Published: September 2009

Caenorhabditis elegans F09E10.3 (dhs-25) was identified as encoding a 3‐oxoacyl‐thioester reductase, potentially of the mitochondrial type 2 fatty acid synthase (FASII) system. Mitochondrial FASII is a relatively recent discovery in metazoans, and the relevance of this process to animal physiology has not been elucidated. A good animal model to study the role of FASII is the nematode C. elegans. However, the components of nematode mitochondrial FASII have hitherto evaded positive identification. The nematode F09E10.3 protein was ectopically expressed without an additional mitochondrial targeting sequence in Saccharomyces cerevisiae mutant cells lacking the homologous mitochondrial FASII enzyme 3‐oxoacyl‐ACP reductase Oar1p. These yeast oar1Δ mutants are unable to respire, grow on nonfermentable carbon sources, or synthesize sufficient levels of lipoic acid. Mutant yeast cells producing a full‐length mitochondrial F09E10.3 protein contained NAD+‐dependent 3‐oxoacyl‐thioester reductase activity and resembled the corresponding mutant overexpressing native Oar1p for the above‐mentioned phenotype characteristics. This is the first identification of a metazoan 3‐oxoacyl‐thioester reductase (see Note Added in Proof).
Polycaprolactone Scaffolds Fabricated via Bioextrusion for Tissue Engineering Applications
Authors: Domingos Marco , Dinucci Dinuccio , Cometa Stefania , Alderighi Michele , Bártolo Paulo Jorge , Chiellini Federica
Published: September 2009

The most promising approach in Tissue Engineering involves the seeding of porous, biocompatible/biodegradable scaffolds, with donor cells to promote tissue regeneration.
Additive biomanufacturing processes are increasingly recognized as ideal techniques to produce 3D structures with optimal pore size and spatial distribution, providing an adequate mechanical support for tissue regeneration while shaping in‐growing tissues. This paper presents a novel extrusion‐based system to produce 3D scaffolds with controlled internal/external geometry for TE applications.The BioExtruder is a low‐cost system that uses a proper fabrication code based on the ISO programming language enabling the fabrication of multimaterial scaffolds. Poly(ε‐caprolactone) was the material chosen to produce porous scaffolds, made by layers of directionally aligned microfilaments. Chemical, morphological, and in vitro biological evaluation performed on the polymeric constructs revealed a high potential of the BioExtruder to produce 3D scaffolds with regular and reproducible macropore architecture, without inducing relevant chemical and biocompatibility alterations of the material.
Predictors of Response to Intradetrusor Botulinum Toxin-A Injections in Patients with Idiopathic Overactive Bladder
Authors: Cohen Brian L. , Caruso Daniel J. , Kanagarajah Prashanth , Gousse Angelo E.
Published: September 2009

Objectives. To evaluate whether there are any demographic or urodynamic differences in patients with idiopathic overactive bladder (I-OAB) that respond and do not respond to intradetrusor injections of botulinum toxin-A (BTX-A).Methods. This represents a secondary analysis of data collected from an investigator initiated randomized trial designed to evaluate clinical differences in outcomes for 100 versus 150 U BTX-A in patients with I-OAB. Preinjection demographic and urodynamic data were collected. Patients were evaluated 12 weeks after injection and were determined to be responders or nonresponders as defined by our criteria. Statistical comparisons were made between groups.Results. In patients with overactive bladder without incontinence (OAB-Dry), there were no variables that could be used to predict response to BTX-A. On univariate analysis, younger patients with overactive bladder with incontinence (OAB-Wet) were more likely to respond to BTX-A than older patients. However, this relationship was no longer statistically significant on multivariate analysis.Conclusions. We were unable to identify any preinjection demographic or urodynamic parameters that could aid in predicting which patients will achieve clinical response to BTX-A. Future studies are necessary to further evaluate this question.
Design of an Adaptive Predistorter for Solid State Power Amplifier in Wireless OFDM Systems
Authors: de Figueiredo Rui J. P. , Fang Lin , Lee Byung Moo
Published: September 2009

Orthogonal frequency division multiplexing (OFDM) is a powerful modulation choice for wideband wireless communication systems. However, its high peak‐to‐average power ratio greatly limits the high power amplifier (HPA) power efficiency. Here, we present the design of an adaptive predistorter to compensate the distortion caused by the HPA. Specifically, we deal with the implementation issue of the proposed predistorter in Lee and de Figueiredo′s work (2006). The performance improvement by predistorter is verified by both floating‐point simulation and fixed‐point simulation, where the latter includes the distortion effects from the hardware. The bit widths for OFDM signals, ADC, and DAC are evaluated, and the bit width of 10 is shown to be sufficient for the hardware design.
Lymphangitic Carcinomatosis as a Cause of Malignant Transient Pleural Transudate
Authors: Garcia Sevila Raquel , Barroso Encarnacion , Martin Concepcion , Aranda Ignacio , Romero Santiago
Published: September 2009

Although it is generally accepted that a malignant transient pleural transudate may appear during the early stages of lymphatic obstruction, cases demonstrating such probability are rare in literature. A 67-year-old woman was admitted to hospital because a lymphangitic carcinomatosis and a transudative infrapulmonary pleural effusion with a cytology positive for adenocarcinoma. One month later the effusion keeps being positive for adenocarcinoma but exudative in character. Lymphatic obstruction appears as the cause of the initial transudative characteristics of the pleural effusion.
Photoelectrocatalytic Degradation of Organic Pollutants in Aqueous Solution Using a Pt‐TiO2 Film
Authors: He Chun , Abou Asi Mudar , Xiong Ya , Shu Dong , Li Xiangzhong
Published: September 2009

A series of Pt‐TiO2 films with nanocrystaline structure was prepared by a procedure of photodeposition and subsequent dip‐coating. The Pt‐TiO2 films were characterized by X‐ray diffraction, scanning electronic microscope, electrochemical characterization to examine the surface structure, chemical composition, and the photoelectrochemical properties. The photocatalytic activity of the Pt‐TiO2 films was evaluated in the photocatalytic (PC) and photoelectrocatalytic (PEC) degradation of formic acid in aqueous solution. Compared with a TiO2 film, the efficiency of formic acid degradation using the Pt‐TiO2 films was significantly higher in both the PC and PEC processes. The enhancement is attributed to the action of Pt deposits on the TiO2 surface, which play a key role by attracting conduction band photoelectrons. In the PEC process, the anodic bias externally applied on the illuminated Pt‐TiO2 films can further drive away the accumulated photoelectrons from the metal deposits and promote a process of interfacial charge transfer.
Concentration Polarization of High‐Density Lipoprotein and Its Relation with Shear Stress in an In Vitro Model
Authors: Meng Wei , Yu Fengxu , Chen Huaiqing , Zhang Jianmin , Zhang Eryong , Dian Ke , Shi Yingkang
Published: September 2009

The purpose of this study was to determine the concentration polarization of high‐density lipoprotein (HDL) at the surface of the carotid artery under conditions of steady flow and to establish its relationship with shear stress using an in vitro vascular simulation model of carotid bifurcation. Shear stress, HDL concentration at the surface, and the ratio of HDL concentration at the surface to concentration in bulk flow were measured at different locations within the model under high‐speed (1.451 m/s) and low‐speed (0.559 m/s) flow. HDL showed concentration polarization at the surface of the carotid artery model, particularly in the internal carotid artery sinus. With decreasing flow velocity, the shear stress at the surface also decreased, and HDL concentration polarization increased. The concentration polarization of HDL was negatively and strongly correlated with shear stress at both low‐ (r = −0.872, P < .001) and high‐speed flow (r = −0.592, P = .0018).
Multiple Sclerosis Lesion Detection Using Constrained GMM and Curve Evolution
Authors: Freifeld Oren , Greenspan Hayit , Goldberger Jacob
Published: September 2009

This paper focuses on the detection and segmentation of Multiple Sclerosis (MS) lesions in magnetic resonance (MRI) brain images. To capture the complex tissue spatial layout, a probabilistic model termed Constrained Gaussian Mixture Model (CGMM) is proposed based on a mixture of multiple spatially oriented Gaussians per tissue. The intensity of a tissue is considered a global parameter and is constrained, by a parameter‐tying scheme, to be the same value for the entire set of Gaussians that are related to the same tissue. MS lesions are identified as outlier Gaussian components and are grouped to form a new class in addition to the healthy tissue classes. A probability‐based curve evolution technique is used to refine the delineation of lesion boundaries. The proposed CGMM‐CE algorithm is used to segment 3D MRI brain images with an arbitrary number of channels. The CGMM‐CE algorithm is automated and does not require an atlas for initialization or parameter learning. Experimental results on both standard brain MRI simulation data and real data indicate that the proposed method outperforms previously suggested approaches, especially for highly noisy data.
Herpes Simplex Esophagitis in Immunocompetent Host: A Case Report
Authors: Geraci G. , Pisello F. , Modica G. , Li Volsi F. , Cajozzo M. , Sciumè C.
Published: September 2009

Introduction. Herpes simplex esophagitis is well recognized in immunosuppressed subjects, but it is infrequent in immunocompetent patients. We present a case of HSE in a 53-year-old healthy man. Materials and Methods. The patient was admitted with dysphagia, odynophagia, and retrosternal chest pain. An esophagogastroduodenoscopy revealed minute erosive area in distal esophagus and biopsies confirmed esophagitis and findings characteristic of Herpes Simplex Virus infection. Results. The patients was treated with high dose of protonpump inhibitor, sucralfate, and acyclovir, orally, with rapid resolution of symptoms. Discussion. HSV type I is the second most common cause of infectious esophagitis. The majority of symptomatic immunocompetent patients with HSE will present with an acute onset of esophagitis. Endoscopic biopsies from the ulcer edges should be obtained for both histopathology and viral culture. In immunocompetent host, HSE is generally a self-limited condition. Conclusions. HSE should be suspected in case of esophagitis without evident cause, even if the patient is immunocompetent. When the diagnosis of HSE is confirmed, careful history and assessment for an immune disorder such as HIV infection is crucial, to look for underlying immune deficiency.
The Emulsion Polymerization of Each of Vinyl Acetate and Butyl Acrylate Monomers Using bis (2-ethylhexyl) Maleate for Improving the Physicomechanical Properties of Paints and Adhesive Films
Authors: Shaffei K. A. , Moustafa A. B. , Hamed A. I.
Published: September 2009

Improving the water sensitivity of polyvinyl acetate PVAc films as well as pressure sensitivity, adhesion and washability of polybutyl acrylate were achieved by using bis (2-ethylhexyl) maleate (BEHM). The emulsion polymerization kinetics of vinyl acetate and butyl acrylate in presence of BEHM was studied. The order of the polymerization reaction with respect to the BEHM in presence of each of vinyl acetate and butyl acrylate was studied. The physicomechanical properties of the polyvinyl acetate films and vinyl acetate-butyl acrylate copolymer films were studied in presence of BEHM and the obtained results were matched with those prepared in the presence of pluronic F 108 and showed superior values. The obtained mean average molecular weights were found to be smaller in presence of BEHM assuring the presence of chain transfer reaction.
Molecular Cloning, Characterization, and Expression Analysis of the CXCR4 Gene from Turbot:Scophthalmus maximus
Authors: Jia Airong , Zhang Xiao-Hua
Published: September 2009

Chemokine receptor 4 (CXCR4) belongs to the large superfamily of G protein‐coupled receptors. The EST sequence of CXCR4 from turbot (Scophthalmus maximusL.) was obtained from a subtractive cDNA library. In the present study, the full‐length cDNA sequence of turbot CXCR4 was obtained, and sequence analysis indicated that its primary structure was highly similar to CXCR4 from other vertebrates. Quantitative real‐time PCR demonstrated that the highest expression level of turbot CXCR4 was in the spleen following injection with physiological saline (PS). After turbot were challenged withVibrio harveyi, the lowest expression level of CXCR4 was detected at 8 hours in the spleen and 12 hours in the head kidney, and then increased gradually to 36 hours. These findings suggested that CXCR4 may play a significant role in the immune response of turbot.
Selective Decoding Scheme‐MAC Protocol in Ad Hoc Networks with MIMO Links
Authors: Suleesathira Raungrong , Aksiripipatkul Jansilp , Assawinchaichote Wudhichai
Published: September 2009

A problem encountered in the IEEE 802.11 MAC is the collision of simultaneous transmissions from either neighboring nodes or hidden nodes within the same contention floor. This paper presents the selective decoding schemes in MAC (SDS‐MAC) protocol for MIMO ad hoc networks. It is able to mitigate interferences by means of a minimum mean‐squared error (MMSE) technique. As a result, it allows a pair of simultaneous transmissions to the same or different nodes to yield the network utilization increase. The decoding schemes and time line operations are properly selected corresponding to the transmission demand of neighboring nodes to avoid collision. Transmission demand can be determined by the number of RTS packets and type of CTS packets. Simulation results are given to illustrate the SDS‐MAC performance.
Exploiting Attitude Sensing in Vision-Based Navigation for an Airship
Authors: Mirisola Luiz G. B. , Dias Jorge
Published: September 2009

An Attitude Heading Reference System (AHRS) is used to compensate for rotational motion, facilitating vision-based navigation above smooth terrain by generating virtual images to simulate pure translation movement. The AHRS combines inertial and earth field magnetic sensors to provide absolute orientation measurements, and our recently developed calibration routine determines the rotation between the frames of reference of the AHRS and the monocular camera. In this way, the rotation is compensated, and the remaining translational motion is recovered by directly finding a rigid transformation to register corresponding scene coordinates. With a horizontal ground plane, the pure translation model performs more accurately than image-only approaches, and this is evidenced by recovering the trajectory of our airship UAV and comparing with GPS data. Visual odometry is also fused with the GPS, and ground plane maps are generated from the estimated vehicle poses and used to evaluate the results. Finally, loop closure is detected by looking for a previous image of the same area, and an open source SLAM package based in 3D graph optimization is employed to correct the visual odometry drift. The accuracy of the height estimation is also evaluated against ground truth in a controlled environment.
Permanence of a Semi‐Ratio‐Dependent Predator‐Prey System with Nonmonotonic Functional Response and Time Delay
Authors: Li Xuepeng , Yang Wensheng
Published: September 2009

Sufficient conditions for permanence of a semi‐ratio‐dependent predator‐prey system with nonmonotonic functional response and time delay    are obtained, where x1(t) and x2(t) stand for the density of the prey and the predator, respectively, and m ≠ 0 is a constant. τ(t) ≥ 0 stands for the time delays due to negative feedback of the prey population.
Cardiovascular Consequences When Nitric Oxide and Lipid Signaling Converge
Authors: Rudolph Volker , Freeman Bruce A.
Published: September 2009

Abstract:The identification of nitric oxide (•NO) as an endogenously produced free radical mediator of endothelial-dependent relaxation and host defense has fundamentally changed concepts of cell signal transduction. Ligand-receptor oriented paradigms of cell signaling were originally centered on the concept of a high affinity and specific interaction between a ligand and its receptor, resulting in the activation of secondary signaling events such as gene expression or modulation of catalytic protein function. While•NO ligation of the heme iron of soluble guanylate cyclase is consistent with this perspective, the readily diffusible and broadly reactive•NO is increasingly appreciated to react with a vast array of target molecules that mediate paracrine vasodilator actions, inhibition of thrombosis and neointimal proliferation, and both pro- and antiinflammatory signaling reactions that are not affected by inhibitors of soluble guanylate cyclase. There is an expanding array of functionally significant “off target” collateral reactions mediated by•NO that are guanylate cyclase-independent and rather are dictated by anatomic distribution and the formation of secondary•NO-derived species. These reactions are a critical element of redox-regulated signaling and are addressed herein in the context of the oxidation of unsaturated fatty acids to vascular and inflammatory signaling mediators. Because of their abundance and the intrinsic reactivity of unsaturated lipid intermediates and eicosanoid metabolism enzymes with•NO and other oxides of nitrogen, lipid signaling mechanisms are a significant target for regulation by•NO in the vascular compartment. This convergence of•NO and lipid signaling pathways thus adds another level of regulation to physiological responses such as vasodilation, thrombosis, and inflammation. Herein, interactions between•NO and lipid signaling events are placed in the context of cardiovascular regulation.
Early Modern Green Sickness and Pre-Freudian Hysteria
Authors: Schleiner Winfried
Published: September 2009

In early modern medicine, both green sickness (or chlorosis) and hysteria were understood to be gendered diseases, diseases of women. Green sickness, a disease of young women, was considered so serious that John Graunt, the father of English statistics, thought that in his time dozens of women died of it in London every year. One of the symptoms of hysteria was that women fell unconscious. The force of etymology and medical tradition was so strong that in one instance the gender of the patient seems to have been changed by the recorder to make the case fit medical theory.