bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive Output Force Tracking Control of Hydraulic Cylinders With Applications to Robot Manipulators
Authors: Zhu Wen-Hong , Piedboeuf Jean-Claude
Published: June 2005

An adaptive output force control scheme for hydraulic cylinders is proposed by using direct output force measurement through loadcells. Due to the large and somewhat uncertain piston friction force, cylinder chamber pressure control with Coulomb-viscous friction prediction may not be sufficient enough to achieve a precise output force control. In the proposed approach, the output force error resulting from direct measurement is used not only for feedback control, but also to update the parameters of an appropriate friction model which includes the Coulomb-viscous friction force in sliding motion and the output force dependent friction force in presliding motion. The L2 and L∞ stability is guaranteed for both the pressure force error and the output force error. Under bounded desired output force and its derivative, asymptotic stability of both the pressure force error and the output force error is also guaranteed. The experimental results demonstrate that a good pressure force control system does not necessarily guarantee a good output force control, and that adaptive friction compensation is superior to fixed-parameter friction compensation. The output force control transfer functions of a robot joint driven by two hydraulic cylinders in pull–pull configuration are limited by ±1.5dB up to 20Hz, tested in free motion and in rigid constraint. The excellent output force (joint torque) control performance implies the dynamic equivalency between a hydraulic cylinder and an electrically-driven motor within the prespecified bandwidth. This allows to emulate an electrically-driven robot by a hydraulic robot.
Robust Control for Uncertain Takagi–Sugeno Fuzzy Systems with Time-Varying Input Delay
Authors: Lee Ho Jae , Park Jin Bae , Joo Young Hoon
Published: June 2005

A control problem of Takagi–Sugeno fuzzy systems with a time-varying input delay and norm-bounded uncertainties is addressed. The input delay is well-known in making the closed-loop stabilization difficult. A sufficient condition for the robust fuzzy-model-based stabilization is derived based on the Lyapunov–Razumikhin stability theorem, without the assumption of the variation rate on the delay. A constructive design scheme is presented in the form of the iterative convex optimization problem. The effectiveness of the proposed method is demonstrated by a numerical simulation of a nonlinear mass-spring-damper system.
Tip-Over Stability of Manipulator-Like Mobile Hydraulic Machines
Authors: Abo-Shanab R. F. , Sepehri N.
Published: June 2005

This paper describes the development of a simulation model for studying the tip-over stability of a typical heavy-duty hydraulic log-loader machine. The model takes into account the dynamics of (i) the base that can potentially rock back and forth, (ii) the combined vehicle suspension and ground/tire compliance, (iii) the friction between the tires and the ground, and (iv) the hydraulic actuators’ functions. The results demonstrate the effects of the manipulator movements, the flexibility of the contact between the base and the ground, the hydraulic compliance, and the friction properties between the wheels and the ground, on the stability of the machine. Particularly, it is shown that the flexibility of the contact between the base and the ground reduces the machine stability, whereas the flexibility at the manipulator joints due the hydraulic compliance improves the machine stability.
Characterization and Modeling of Printed Wiring Board Warpage and its Effect on LGA Separable Interconnects
Authors: Cepeda-Rizo J. , Yeh Hsien-Yang , Teneketges N.
Published: June 2005

The paper presents a study on printed wiring board (PWB) warpage caused by the mechanical fastening of separable interconnects, known as land grid array (LGA) package assemblies. Out-of-plane displacement of the PWB were measured and characterized, as well as force-per-pin values of the LGA, and correlations were made between the two. Classical laminate theory was utilized to describe the warpage behavior of the assembly and a model was presented to solve the out-of-plane displacements. An overall assessment of the assembly was made and compared to the mechanical specification of the LGA.
Behavior of Short Lateral Dead Ends on Pipeline Transients: A Lumped Parameter Model and an Analytical Solution
Authors: Wang Xiao-Jian , Lambert Martin F. , Simpson Angus R.
Published: May 2005

By integrating the continuity equation over a short lateral dead end, the effects of a short lateral dead end side branch on pipeline fluid transients can be lumped into a node. The analytical solution to a linearized equation shows that a pipeline transient can be expressed as a Fourier series and presence of a lateral dead end reduces the frequencies of the harmonic components. The impact of the lateral dead end on the observed transients depends on a parameter Sd, which is related to the location of the lateral dead end, the relative volume, and the wave speed of the lateral dead end with respect to the pipeline. A lumped parameter approach that can be incorporated into the method of characteristics has also been developed in this paper. It has been found that it is possible to take account of the effects of a short lateral dead end in an accurate and computational efficient manner.
New Physically Based Approach of Mass Conservation Correction in Level Set Formulation for Incompressible Two-Phase Flows
Authors: Majumder Snehamoy , Chakraborty Suman
Published: May 2005

A novel physically based mass conservation model is developed in the framework of a level set method, as an alternative to the Heaviside function based formulation classically employed in the literature. In the proposed “volume fraction based level set approach,” expressions for volume fraction function for each interfacial computational cell are developed, and are subsequently correlated with the corresponding level set functions. The volume fraction function, derived from a physical basis, is found to be mathematically analogous to the Heaviside function, except for a one-dimensional case. The results obtained are compared with the benchmark experimental and numerical results reported in the literature. Finally, transient evolution of a circular bubble in a developing shear flow and rising bubbles in a static fluid, are critically examined. The Cox angle and the deformation parameter characterizing the bubble evolution are critically examined. An excellent satisfaction of the mass conservation requirements is observed in all case studies undertaken.
Measurement of Stiffness and Damping Characteristics of Computer Keyboard Keys
Authors: Nagurka Mark , Marklin Richard
Published: June 2005

To determine the stiffness and damping of computer keyboard keys, a computer-controlled test rig that can measure computer key displacement, velocity, and contact force has been designed. The test rig, consisting of a single-axis stage carrying a probe for contacting keys, has been used to collect contact force and motion data as computer keys are depressed and released at constant velocities up to 80mm∕s. Keys that employ a rubber-dome under their caps to achieve the necessary compliance and toggling action were tested. The results demonstrate a nonlinear stiffness force versus displacement characteristic at a given speed and the presence of damping-type forces that increase with key depression speed at a given displacement. In particular, the results indicate that the peak force at the 80mm∕s rate of depression increases relative to the quasistatic (0.5mm∕s) force level by over 12% for the “Enter,” “K,” and “Spacebar” keys. This paper describes the hardware and software configuration, and presents sample results of the stiffness and damping characteristics of keys during depression-return stroke tests.
Influence of Wall Proximity on the Lift and Drag of a Particle in an Oscillatory Flow
Authors: Fischer Paul F. , Leaf Gary K. , Restrepo Juan M.
Published: May 2005

We report on the lift and drag forces on a stationary sphere subjected to a wall-bounded oscillatory flow. We show how these forces depend on two parameters, namely, the distance between the particle and the bounding wall, and on the frequency of the oscillatory flow. The forces were obtained from numerical solutions of the unsteady incompressible Navier–Stokes equations. For the range of parameters considered, a spectral analysis found that the forces depended on a small number of degrees of freedom. The drag force manifested little change in character as the parameters varied. On the other hand, the lift force varied significantly: We found that the lift force can have a positive as well as a negative time-averaged value, with an intermediate range of external forcing periods in which enhanced positive lift is possible. Furthermore, we determined that this force exhibits a viscous-dominated and a pressure-dominated range of parameters.
Adaptive Method of Helicopter Track and Balance
Authors: Wang Shengda , Danai Kourosh , Wilson Mark
Published: June 2005

An adaptive method of helicopter track and balance is introduced to improve the search for the required blade adjustments. In this method, an interval model is used to represent the range of effect of blade adjustments on helicopter vibration, instead of exact values, to cope with the nonlinear and stochastic nature of aircraft vibration. The coefficients of the model are initially defined according to sensitivity coefficients between the blade adjustments and helicopter vibration, to include the ‘a priori’ knowledge of the process. The model coefficients are subsequently transformed into intervals and updated after each tuning iteration to improve the model’s estimation accuracy. The search for the required blade adjustments is performed according to this model by considering the vibration estimates of all of the flight regimes to provide a comprehensive solution for track and balance. The effectiveness of the proposed method is evaluated in simulation using a series of neural networks trained with actual vibration data. The results indicate that the proposed method improves performance according to several criteria representing various aspects of track and balance.
A New Model for Springback Prediction for Aluminum Sheet Forming
Authors: Gau Jenn-Terng , Kinzel Gary L.
Published: June 2005

A new model for springback, based on isotropic and kinematic hardening models, the Mroz multiple surfaces model, and observations from experimental data, is proposed in this paper. In this model, a material parameter (CM), which is significant after reverse yielding, is suggested to handle the Bauschinger effect. A simple, low-cost, multiple-bending experiment has been developed to determine CM for aluminum alloys AA6022-T4 and AA6111-T4. The new model fits available experimental results better than the isotropic and kinematic hardening models and the Mroz multiple surfaces model.
The New Grain Formation During Warm and Hot Deformation of Copper
Authors: Wusatowska-Sarnek Agnieszka M.
Published: June 2005

Initial stage of dynamic recrystallization (DRX) under warm and hot deformation was investigated in polycrystalline copper. At the onset of DRX at intermediate deformation temperatures (i.e., high values of Zener–Hollomon parameter Z) large orientation gradients are developed near grain boundaries, and conversely smaller gradients at high temperatures (i.e., low Z values). The frequency of thermally activated grain boundary motion coupled with various levels of local orientation gradients lead to the operation of different mechanisms of DRX nucleation. At warm deformation equiaxed grains with moderate- to high-angle boundaries are evolved at near the pre-existed boundary as a result of increasing density of geometrically necessary boundaries and progressive rotation of subgrains with little accompanying boundary migration, while at hot deformation grain boundary bulging accompanied with twinning takes place.
The Effect of Mean Stress on the Fatigue Behavior of Woven-Roving Glass Fiber-Reinforced Polyester Subjected to Torsional Moments
Authors: Nasr Mohamed N. A. , Abouelwafa M. N. , Gomaa A. , Hamdy A. , Morsi E.
Published: June 2005

The effect of torsional mean stress on the fatigue behavior of glass fiber-reinforced polyester (GFRP) is studied by testing thin-walled, woven-roving tubular specimens with two fiber orientations, [±45°]2s and [0,90°]2s, at negative stress ratios (R),R=−1,−0.75,−0.5,−0.25, 0. The [±45°]2s specimens were found to have higher fatigue strength than the [0,90°]2s specimens at all stress ratios. This is attributed to the difference in local stress components, the [±45°]2s specimens being subjected to tension-compression local stress components, while the [0,90°]2s specimens being subjected to pure local shear stress. For the studied stress ratios; the mean stress component had a detrimental effect on the amplitude component for the [±45°]2s specimens; while it was ineffective for the [0,90°]2s specimens in a certain region in the mean-amplitude diagram, region (1), then it had a detrimental effect in the rest of the diagram, region (2). The S–N curves for positive stress ratios were extrapolated from those for negative stress ratios, which were found experimentally, for the [0,90°]2s specimens. The positive stress ratio points, having the same local stress state as the negative ones, showed an acceptable behavior tending to decrease the amplitude component for the same life.
Penetration of Human-Induced Warming into the World's Oceans
Authors: Barnett Tim P. , Pierce David W. , AchutaRao Krishna M. , Gleckler Peter J. , Santer Benjamin D. , Gregory Jonathan M. , Washington Warren M.
Published: June 2005

A warming signal has penetrated into the world's oceans over the past 40 years. The signal is complex, with a vertical structure that varies widely by ocean; it cannot be explained by natural internal climate variability or solar and volcanic forcing, but is well simulated by two anthropogenically forced climate models. We conclude that it is of human origin, a conclusion robust to observational sampling and model differences. Changes in advection combine with surface forcing to give the overall warming pattern. The implications of this study suggest that society needs to seriously consider model predictions of future climate change.
Genomic Sequencing of Pleistocene Cave Bears
Authors: Noonan James P. , Hofreiter Michael , Smith Doug , Priest James R. , Rohland Nadin , Rabeder Gernot , Krause Johannes , Detter J. Chris , Pääbo Svante , Rubin Edward M.
Published: June 2005

Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of ∼1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach used here establishes the feasibility of ancient DNA genome sequencing programs.
Tricksy Business: Transcriptome Analysis Reveals the Involvement of Thioredoxin A in Redox Homeostasis, Oxidative Stress, Sulfur Metabolism, and Cellular Differentiation inBacillus subtilis
Authors: Smits Wiep Klaas , Dubois Jean-Yves F. , Bron Sierd , van Dijl Jan Maarten , Kuipers Oscar P.
Published: June 2005

Thioredoxins are important thiol-reactive proteins. Most knowledge about this class of proteins is derived from proteome studies, and little is known about the global transcriptional response of cells to various thioredoxin levels. InBacillus subtilis, thioredoxin A is encoded bytrxAand is essential for viability. In this study, we report the effects of minimal induction of a strain carrying an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducibletrxAgene (ItrxA) on transcription levels, as determined by DNA macroarrays. The effective depletion of thioredoxin A leads to the induction of genes involved in the oxidative stress response (but not those dependent on PerR), phage-related functions, and sulfur utilization. Also, several stationary-phase processes, such as sporulation and competence, are affected. The majority of these phenotypes are rescued by a higher induction level of ItrxA, leading to an approximately wild-type level of thioredoxin A protein. A comparison with other studies shows that the effects of thioredoxin depletion are distinct from, but show some similarity to, oxidative stress and disulfide stress. Some of the transcriptional effects may be linked to thioredoxin-interacting proteins. Finally, thioredoxin-linked processes appear to be conserved between prokaryotes and eukaryotes.
Mutations in Cytochrome Assembly and Periplasmic Redox Pathways inBordetella pertussis
Authors: Feissner Robert E. , Beckett Caroline S. , Loughman Jennifer A. , Kranz Robert G.
Published: June 2005

Transposon mutagenesis ofBordetella pertussiswas used to discover mutations in the cytochromecbiogenesis pathway called system II. Using a tetramethyl-p-phenylenediamine cytochromecoxidase screen, 27 oxidase-negative mutants were isolated and characterized. Nine mutants were still able to synthesizec-type cytochromes and possessed insertions in the genes for cytochromecoxidase subunits (ctaC, -D, and -E), hemeabiosynthesis (ctaB), assembly of cytochromecoxidase (sco2), or ferrochelatase (hemZ). Eighteen mutants were unable to synthesize allc-type cytochromes. Seven of these had transposons indipZ(dsbD), encoding the transmembrane thioreduction protein, and all seven mutants were corrected for cytochromecassembly by exogenous dithiothreitol, which was consistent with the cytochromeccysteinyl residues of the CXXCH motif requiring periplasmic reduction. The remaining 11 insertions were located in theccsBAoperon, suggesting that with the appropriate thiol-reducing environment, the CcsB and CcsA proteins comprise the entire system II biosynthetic pathway. Antiserum to CcsB was used to show that CcsB is absent inccsAmutants, providing evidence for a stable CcsA-CcsB complex. No mutations were found in the genes necessary for disulfide bond formation (dsbAordsbB). To examine whether the periplasmic disulfide bond pathway is required for cytochromecbiogenesis inB. pertussis, a targeted knockout was made indsbB. The DsbB−mutant makes holocytochromesclike the wild type does and secretes and assembles the active periplasmic alkaline phosphatase. AdipZmutant is not corrected by adsbBmutation. Alternative mechanisms to oxidize disulfides inB. pertussisare analyzed and discussed.
Peculiar Properties of DsbA in Its Export across the
Escherichia coli
Cytoplasmic Membrane
Authors: Shimohata Nobuyuki , Akiyama Yoshinori , Ito Koreaki
Published: June 2005

Export of DsbA, a protein disulfide bond-introducing enzyme, across the
Escherichia coli
cytoplasmic membrane was studied with special reference to the effects of various mutations affecting translocation factors. It was noted that both the internalized precursor retaining the signal peptide and the periplasmic mature product fold rapidly into a protease-resistant structure and they exhibited anomalies in sodium dodecyl sulfate-polyacrylamide gel electrophoresis in that the former migrated faster than the latter. The precursor, once accumulated, was not exported posttranslationally. DsbA export depended on the SecY translocon, the SecA ATPase, and Ffh (signal recognition particle), but not on SecB. SecY mutations, such as
secY39
and
secY205
, that severely impair translocation of a number of secretory substrates by interfering with SecA actions only insignificantly impaired the DsbA export. In contrast,
secY125
, affecting a periplasmic domain and impairing a late step of translocation, exerted strong export inhibition of both classes of proteins. These results suggest that DsbA uses not only the signal recognition particle targeting pathway but also a special route of translocation through the translocon, which is hence suggested to actively discriminate preproteins.
The
Haloferax volcanii
FtsY Homolog Is Critical for Haloarchaeal Growth but Does Not Require the A Domain
Authors: Haddad Alex , Rose R. Wesley , Pohlschröder Mechthild
Published: June 2005

The targeting of many Sec substrates to the membrane-associated translocation pore requires the cytoplasmic signal recognition particle (SRP). In
Eukarya
and
Bacteria
it has been shown that membrane docking of the SRP-substrate complex occurs via the universally conserved SRP receptor (Srα/β and FtsY, respectively). While much has been learned about the archaeal SRP in recent years, few studies have examined archaeal Srα/FtsY homologs. In the present study the FtsY homolog of
Haloferax volcanii
was characterized in its native host. Disruption of the sole chromosomal copy of
ftsY
in
H. volcanii
was possible only under conditions where either the full-length haloarchaeal FtsY or an amino-terminally truncated version of this protein lacking the A domain, was expressed in
trans
. Subcellular fractionation analysis of
H. volcanii ftsY
deletion strains expressing either one of the complementing proteins revealed that in addition to a cytoplasmic pool, both proteins cofractionate with the haloarchaeal cytoplasmic membrane. Moreover, membrane localization of the universally conserved SRP subunit SRP54, the key binding partner of FtsY, was detected in both
H. volcanii
strains. These analyses suggest that the
H. volcanii
FtsY homolog plays a crucial role but does not require its A domain for haloarchaeal growth.
Expression Levels Influence Ribosomal Frameshifting at the Tandem Rare Arginine Codons AGG_AGG and AGA_AGA in
Escherichia coli
Authors: Gurvich Olga L. , Baranov Pavel V. , Gesteland Raymond F. , Atkins John F.
Published: June 2005

The rare codons AGG and AGA comprise 2% and 4%, respectively, of the arginine codons of
Escherichia coli
K-12, and their cognate tRNAs are sparse. At tandem occurrences of either rare codon, the paucity of cognate aminoacyl tRNAs for the second codon of the pair facilitates peptidyl-tRNA shifting to the +1 frame. However, AGG_AGG and AGA_AGA are not underrepresented and occur 4 and 42 times, respectively, in
E. coli
genes. Searches for corresponding occurrences in other bacteria provide no strong support for the functional utilization of frameshifting at these sequences. All sequences tested in their native context showed 1.5 to 11% frameshifting when expressed from multicopy plasmids. A cassette with one of these sequences singly integrated into the chromosome in stringent cells gave 0.9% frameshifting in contrast to two- to four-times-higher values obtained from multicopy plasmids in stringent cells and eight-times-higher values in relaxed cells. Thus, +1 frameshifting efficiency at AGG_AGG and AGA_AGA is influenced by the mRNA expression level. These tandem rare codons do not occur in highly expressed mRNAs.
Analysis of
Pseudomonas putida
KT2440 Gene Expression in the Maize Rhizosphere: In Vitro Expression Technology Capture and Identification of Root-Activated Promoters
Authors: Ramos-González María Isabel , Campos María Jesús , Ramos Juan L.
Published: June 2005

Pseudomonas putida
KT2440, a paradigm organism in biodegradation and a good competitive colonizer of the maize rhizosphere, was the subject of studies undertaken to establish the genetic determinants important for its rhizospheric lifestyle. By using in vivo expression technology (IVET) to positively select single cell survival, we identified 28
rap
genes (
r
oot-
a
ctivated
p
romoters) preferentially expressed in the maize rhizosphere. The IVET system had two components: a mutant affected in aspartate-β-semialdehyde dehydrogenase (
asd
), which was unable to survive in the rhizosphere, and plasmid pOR1, which carries a promoterless
asd
gene. pOR1-borne transcriptional fusions of the
rap
promoters to the essential gene
asd
, which were integrated into the chromosome at the original position of the corresponding
rap
gene, were active and allowed growth of the
asd
strain in the rhizosphere. The fact that five of the
rap
genes identified in the course of this work had been formerly characterized as being related to root colonization reinforced the IVET approach. Up to nine
rap
genes encoded proteins either of unknown function or that had been assigned an unspecific role based on conservation of the protein family domains. Rhizosphere-induced fusions included genes with probable functions in the cell envelope, chemotaxis and motility, transport, secretion, DNA metabolism and defense mechanism, regulation, energy metabolism, stress, detoxification, and protein synthesis.
Sulfate-Dependent Repression of Genes That Function in Organosulfur Metabolism inBacillus subtilisRequires Spx
Authors: Erwin Kyle N. , Nakano Shunji , Zuber Peter
Published: June 2005

Oxidative stress inBacillus subtilisresults in the accumulation of Spx protein, which exerts both positive and negative transcriptional control over a genome-wide scale through its interaction with the RNA polymerase α subunit. Previous microarray transcriptome studies uncovered a unique class of genes that are controlled by Spx-RNA polymerase interaction under normal growth conditions that do not promote Spx overproduction. These genes were repressed by Spx when sulfate was present as a sole sulfur source. The genes include those of theytmI,yxeI, andssuoperons, which encode products resembling proteins that function in the uptake and desulfurization of organic sulfur compounds. Primer extension and analysis of operon-lacZfusion expression revealed that the operons are repressed by sulfate and cysteine; however, Spx functioned only in sulfate-dependent repression. Both theytmIoperon and the divergently transcribedytlI, encoding a LysR-type regulator that positively controlsytmIoperon transcription, are repressed by Spx in sulfate-containing media. The CXXC motif of Spx, which is necessary for redox sensitive control of Spx activity in response to oxidative stress, is not required for sulfate-dependent repression. TheyxeL-lacZandssu-lacZfusions were also repressed in an Spx-dependent manner in media containing sulfate as the sole sulfur source. This work uncovers a new role for Spx in the control of sulfur metabolism in a gram-positive bacterium under nonstressful growth conditions.
Catabolism of Benzoate and Phthalate in
Rhodococcus
sp. Strain RHA1: Redundancies and Convergence
Authors: Patrauchan Marianna A. , Florizone Christine , Dosanjh Manisha , Mohn William W. , Davies Julian , Eltis Lindsay D.
Published: June 2005

Genomic and proteomic approaches were used to investigate phthalate and benzoate catabolism in
Rhodococcus
sp. strain RHA1, a polychlorinated biphenyl-degrading actinomycete. Sequence analyses identified genes involved in the catabolism of benzoate (
ben
) and phthalate (
pad
), the uptake of phthalate (
pat
), and two branches of the β-ketoadipate pathway (
catRABC
and
pcaJIHGBLFR
). The regulatory and structural
ben
genes are separated by genes encoding a cytochrome P450. The
pad
and
pat
genes are contained on a catabolic island that is duplicated on plasmids pRHL1 and pRHL2 and includes predicted terephthalate catabolic genes (
tpa
). Proteomic analyses demonstrated that the β-ketoadipate pathway is functionally convergent. Specifically, the
pad
and
pat
gene products were only detected in phthalate-grown cells. Similarly, the
ben
and
cat
gene products were only detected in benzoate-grown cells. However,
pca
-encoded enzymes were present under both growth conditions. Activity assays for key enzymes confirmed these results. Disruption of
pcaL
, which encodes a fusion enzyme, abolished growth on phthalate. In contrast, after a lag phase, growth of the mutant on benzoate was similar to that of the wild type. Proteomic analyses revealed 20 proteins in the mutant that were not detected in wild-type cells during growth on benzoate, including a CatD homolog that apparently compensated for loss of PcaL. Analysis of completed bacterial genomes indicates that the convergent β-ketoadipate pathway and some aspects of its genetic organization are characteristic of rhodococci and related actinomycetes. In contrast, the high redundancy of catabolic pathways and enzymes appears to be unique to RHA1 and may increase its potential to adapt to new carbon sources.
Regulation and Function of Cytochrome
c
′ in
Rhodobacter sphaeroides
2.4.3
Authors: Choi Peter S. , Grigoryants Vladimir M. , Abruña Hector D. , Scholes Charles P. , Shapleigh James P.
Published: June 2005

Cytochrome
c
′ (Cyt
c
′) is a
c
-type cytochrome with a pentacoordinate heme iron. The gene encoding this protein in
Rhodobacter sphaeroides
2.4.3, designated
cycP
, was isolated and sequenced. Northern blot analysis and β-galactosidase assays demonstrated that
cycP
transcription increased as oxygen levels decreased and was not repressed under denitrifying conditions as observed in another
Rhodobacter
species. CO difference spectra performed with extracts of cells grown under different conditions revealed that Cyt
c
′ levels were highest during photosynthetic denitrifying growth conditions. The increase in Cyt
c
′ under this condition was higher than would be predicted from transcriptional studies. Electron paramagnetic resonance analysis of whole cells demonstrated that Cyt
c
′ binds NO during denitrification. Mass spectrometric analysis of nitrogen oxides produced by cells and purified protein did not indicate that Cyt
c
′ has NO reductase activity. Taken together, these results suggest a model where Cyt
c
′ in
R. sphaeroides
2.4.3 may shuttle NO to the membrane, where it can be reduced.
Gene Conversion Tracts Associated with Crossovers in
Rhizobium etli
Authors: Santoyo Gustavo , Martínez-Salazar Jaime M. , Rodríguez César , Romero David
Published: June 2005

Gene conversion has been defined as the nonreciprocal transfer of information between homologous sequences. Despite its broad interest for genome evolution, the occurrence of this mechanism in bacteria has been difficult to ascertain due to the possible occurrence of multiple crossover events that would mimic gene conversion. In this work, we employ a novel system, based on cointegrate formation, to isolate gene conversion events associated with crossovers in the nitrogen-fixing bacterium
Rhizobium etli
. In this system, selection is applied only for cointegrate formation, with gene conversions being detected as unselected events. This minimizes the likelihood of multiple crossovers. To track the extent and architecture of gene conversions, evenly spaced nucleotide changes were made in one of the nitrogenase structural genes (
nifH
), introducing unique sites for different restriction endonucleases. Our results show that (i) crossover events were almost invariably accompanied by a gene conversion event occurring nearby; (ii) gene conversion events ranged in size from 150 bp to 800 bp; (iii) gene conversion events displayed a strong bias, favoring the preservation of incoming sequences; (iv) even small amounts of sequence divergence had a strong effect on recombination frequency; and (v) the MutS mismatch repair system plays an important role in determining the length of gene conversion segments. A detailed analysis of the architecture of the conversion events suggests that multiple crossovers are an unlikely alternative for their generation. Our results are better explained as the product of true gene conversions occurring under the double-strand break repair model for recombination.
A Region ofBacillus subtilisCodY Protein Required for Interaction with DNA
Authors: Joseph Pascale , Ratnayake-Lecamwasam Manoja , Sonenshein Abraham L.
Published: June 2005

Bacillus subtilisCodY protein is the best-studied member of a novel family of global transcriptional regulators found ubiquitously in low-G+C gram-positive bacteria. As for many DNA-binding proteins, CodY appears to have a helix-turn-helix (HTH) motif thought to be critical for interaction with DNA. This putative HTH motif was found to be highly conserved in the CodY homologs. Site-directed mutagenesis was used to identify amino acids within this motif that are important for DNA recognition and binding. The effects of each mutation on DNA binding in vitro and on the regulation of transcription in vivo from two target promoters were tested. Each of the mutations had similar effects on binding to the two promoters in vitro, but some mutations had differential effects in vivo.
Mutagenesis at Two Distinct Phosphate-Binding Sites Unravels Their Differential Roles in Regulation of Rubisco Activation and Catalysis
Authors: Marcus Yehouda , Altman-Gueta Hagit , Finkler Aliza , Gurevitz Michael
Published: June 2005

Orthophosphate (P
i
) has two antagonistic effects on ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), stimulation of activation and inhibition of catalysis by competition with the substrate RuBP. The enzyme binds P
i
at three distinct sites, two within the catalytic site (where 1P and 5P of ribulose 1,5-bisphosphate [RuBP] bind), and the third at the latch site (a positively charged pocket involved in active-site closure during catalysis). We examined the role of the latch and 5P sites in regulation of Rubisco activation and catalysis by introducing specific mutations in the enzyme of the cyanobacterium
Synechocystis
sp. strain PCC 6803. Whereas mutations at both sites abolished the P
i
-stimulated Rubisco activation, substitution of residues at the 5P site, but not at the latch site, affected the P
i
inhibition of Rubisco catalysis. Although some of these mutations substantially reduced the catalytic turnover of Rubisco and increased the

K
m

(RuBP), they had little to moderate effect on the rate of photosynthesis and no effect on photoautotrophic growth. These findings suggest that in cyanobacteria, Rubisco does not limit photosynthesis to the extent previously estimated. These results indicate that both the latch and 5P sites participate in regulation of Rubisco activation, whereas P
i
binding only at the 5P site inhibits catalysis in a competitive manner.
Crystal Structure of the “PhoU-Like” Phosphate Uptake Regulator from
Aquifex aeolicus
Authors: Oganesyan Vaheh , Oganesyan Natalia , Adams Paul D. , Jancarik Jaru , Yokota Hisao A. , Kim Rosalind , Kim Sung-Hou
Published: June 2005

The
phoU
gene of
Aquifex aeolicus
encodes a protein called PHOU_AQUAE with sequence similarity to the PhoU protein of
Escherichia coli.
Despite the fact that there is a large number of family members (more than 300) attributed to almost all known bacteria and despite PHOU_AQUAE's association with the regulation of genes for phosphate metabolism, the nature of its regulatory function is not well understood. Nearly one-half of these PhoU-like proteins, including both PHOU_AQUAE and the one from
E. coli
, form a subfamily with an apparent dimer structure of two PhoU domains on the basis of their amino acid sequence. The crystal structure of PHOU_AQUAE (a 221-amino-acid protein) reveals two similar coiled-coil PhoU domains, each forming a three-helix bundle. The structures of PHOU_AQUAE proteins from both a soluble fraction and refolded inclusion bodies (at resolutions of 2.8 and 3.2Å, respectively) showed no significant differences. The folds of the PhoU domain and Bag domains (for a class of cofactors of the eukaryotic chaperone Hsp70 family) are similar. Accordingly, we propose that gene regulation by PhoU may occur by association of PHOU_AQUAE with the ATPase domain of the histidine kinase PhoR, promoting release of its substrate PhoB. Other proteins that share the PhoU domain fold include the coiled-coil domains of the STAT protein, the ribosome-recycling factor, and structural proteins like spectrin.
Pseudomonas syringae
Type III Chaperones ShcO1, ShcS1, and ShcS2 Facilitate Translocation of Their Cognate Effectors and Can Substitute for Each Other in the Secretion of HopO1-1
Authors: Guo Ming , Chancey Scott T. , Tian Fang , Ge Zhengxiang , Jamir Yashitola , Alfano James R.
Published: June 2005

The
Pseudomonas syringae
type III secretion system (TTSS) translocates effector proteins into plant cells. Several
P. syringae
effectors require accessory proteins called type III chaperones (TTCs) to be secreted via the TTSS. We characterized the
hopO1-1
,
hopS1
, and
hopS2
operons in
P. syringae
pv. tomato DC3000; these operons encode three homologous TTCs, ShcO1, ShcS1, and ShcS2. ShcO1, ShcS1, and ShcS2 facilitated the type III secretion and/or translocation of their cognate effectors HopO1-1, HopS1, and HopS2, respectively. ShcO1 and HopO1-1 interacted with each other in yeast two-hybrid and coimmunoprecipitation assays. Interestingly, ShcS1 and ShcS2 were capable of substituting for ShcO1 in facilitating HopO1-1 secretion and translocation and each TTC was able to bind the other's cognate effectors in yeast two-hybrid assays. Moreover, ShcO1, ShcS1, and ShcS2 all bound to the middle-third region of HopO1-1. The HopS2 effector possessed atypical
P. syringae
TTSS N-terminal characteristics and was translocated in low amounts. A site-directed HopS2 mutation that introduced a common N-terminal characteristic from other
P. syringae
type III secreted substrates increased HopS2 translocation, supporting the idea that this characteristic functions as a secretion signal. Additionally,
hopO1-2
and
hopT1-2
were shown to encode effectors secreted via the DC3000 TTSS. Finally, a DC3000
hopO1-1
operon deletion mutant produced disease symptoms similar to those seen with wild-type DC3000 but was reduced in its ability to multiply in
Arabidopsis thaliana
. The existence of TTCs that can bind to dissimilar effectors and that can substitute for each other in effector secretion provides insights into the nature of how TTCs function.
The Transcription Termination Factor Rho Is Essential and Autoregulated in
Caulobacter crescentus
Authors: Italiani Valéria C. S. , Marques Marilis V.
Published: June 2005

The impossibility of obtaining a
rho
null mutant and sensitivity to bicyclomycin have indicated that
rho
is essential for the viability of
Caulobacter crescentus
. Transcription gene fusions of sequences with serial deletions of the
rho
5′ untranslated region (5′-UTR) with a
lacZ
reporter gene indicated that
rho
is autoregulated at the level of attenuation of transcription in the 5′-UTR.
Patients undergoing coronary revascularisation: a missed opportunity for secondary prevention?
Authors: Fox D J , Kibiro M , Eichhöfer J , Curzen N P
Published: June 2005

Background

This study tested the hypothesis that the opportunity to start secondary prevention therapy before discharge after coronary revascularisation is being missed. The study assessed current prescribing practice and identified discrepancies in prescribing for patients managed by surgeons (especially) and cardiologists.

Methods

200 consecutive patients from the Manchester Heart Centre percutaneous coronary intervention (PCI) and coronary artery bypass (CABG) registries were identified (100 from each registry) and the notes analysed. All had undergone coronary revascularisation from February 2002 to March 2002. Data were analysed using SPSS for Windows, version 10.1.

Results

After exclusion of two patients with contraindications, 100% (98 of 98) of PCI patients and 92% (90 of 98) CABG patients were prescribed aspirin at discharge. Eight two per cent of eligible PCI patients and 70% of eligible CABG patients were prescribed β blockers at discharge. Ninety six per cent (96 of 100) of PCI patients and 73% (73 of 100) of CABG patients were prescribed statins of any dose at discharge, (p<0.001). Sixty five per cent of PCI but only 26% of CABG patients were discharged prescribed ACE inhibitors (eligible patients based on HOPE, heart outcomes prevention evaluation trial), (p<0.001).

Conclusions

Secondary prevention prescription after coronary revascularisation remains suboptimal in all but aspirin use. Patients in the PCI group were statistically more likely to be discharged prescribed a statin or an ACE inhibitor, or both, than patients after CABG. Both interventional cardiologists and (especially) cardiac surgeons must improve their use of secondary prevention therapy.
Pathophysiology of dyslipidaemia in the metabolic syndrome
Authors: Kolovou G D , Anagnostopoulou K K , Cokkinos D V
Published: June 2005

The insulin resistance/metabolic syndrome is characterised by the variable coexistence of hyperinsulinaemia, obesity, dyslipidaemia, and hypertension. The pathogenesis of the syndrome has multiple origins, but obesity and sedentary lifestyle coupled with diet and still largely unknown genetic factors clearly interact to produce the syndrome. Dyslipidaemia, the hallmark of the metabolic syndrome, includes increased flux of free fatty acids, raised triglycerides, apolipoprotein B, and small dense low density lipoprotein, and decreased high density lipoprotein cholesterol. The widely prevalent nature of the metabolic syndrome emphasises the importance of its diagnosis and treatment. This review analyses the clinical and dynamic features of this syndrome in the aspect of dyslipidaemia and its management.
Variations in the provision of resuscitation equipment: survey of acute hospitals
Authors: Hogh L , Kane I , Bhalla A , Ward M C
Published: June 2005

Background

There are wide variations in survival after cardiopulmonary resuscitation. The aim of this survey was to describe how equipment provision of resuscitation trolleys was deployed in a range of clinical ward areas.

Methods

The equipment in randomly selected resuscitation trolleys in all 14 South West Thames Region hospitals was surveyed. The gold standard for equipment provision was referenced from the document CPR Guidance for Clinical Practice and Training in Hospital.

Results

There were significant differences in the provision of circulation equipment (p = 0.004) and in the rates of drug items present (p = 0.001). There was no significant difference in provision of airways equipment (p = 0.24) or immediate access items (p = 0.55).

Conclusions

There are variations in the provision of resuscitation equipment in many clinical areas. Hospitals need to review the procedures for ensuring adequate provision of resuscitation equipment in all clinical areas.
Pulmonary artery thrombosis in a patient with severe acute respiratory syndrome
Authors: Ng K H L , Wu A K L , Cheng V C C , Tang B S F , Chan C Y , Yung C Y , Luk S H , Lee T W , Chow L , Yuen K Y
Published: June 2005

Severe acute respiratory syndrome (SARS) is an emerging infectious disease with both pulmonary and extra-pulmonary manifestations. Although coagulation abnormalities are common in these patients, clinically overt thromboembolic events are rarely reported. This report describes the first case of pulmonary artery thrombosis in a patient with laboratory confirmed SARS.
CONFORMAL GENERATORS AND DOUBLY SPECIAL RELATIVITY THEORIES
Authors: LEIVA CARLOS
Published: May 2005

In this paper, the relation between the modified Lorenz boosts, proposed in the doubly relativity theories and a linear combination of Conformal Group generators in R1,d-1 is investigated. The introduction of a new generator is proposed in order to deform the Conformal Group to achieve the connection conjectured. The new generator is obtained through a formal dimensional reduction from a free massless particle living in a R2,d space. Due to this treatment it is possible to say that even DSR theories modify light-cone structure in R1,d-1, it could remains, in some cases, untouched in R2,d.
STRONG LENSING PROBABILITIES IN A COSMOLOGICAL MODEL WITH A RUNNING PRIMORDIAL POWER SPECTRUM
Authors: ZHANG TONG-JIE , YANG ZHI-LIANG , HE XIANG-TAO
Published: May 2005

The combination of the first-year Wilkinson Microwave Anisotropy Probe (WMAP) data with other finer scale cosmic microwave background (CMB) experiments (CBI and ACBAR) and two structure formation measurements (2dFGRS and Lyman α forest) suggest a ΛCDM cosmological model with a running spectral power index of primordial density fluctuations. Motivated by this new result on the index of primordial power spectrum, we present the first study on the predicted lensing probabilities of image separation in a spatially flat ΛCDM model with a running spectral index (RSI-ΛCDM model). It is shown that the RSI-ΛCDM model suppresses the predicted lensing probabilities on small splitting angles of less than about 4″ compared with that of standard power-law ΛCDM (PL-ΛCDM) model.
ONE-LOOP EFFECTIVE POTENTIAL FOR THE VACUUM GAUGE FIELD IN M3×S3×S1 SPACETIME
Authors: CHO YOSHINORI , SHIRAISHI KIYOSHI
Published: May 2005

We calculate the effective potential for the vacuum gauge field from the one-loop matter effect in M3×S3×S1 spacetime. This background geometry is motivated from the recent studies on gauged supergravities with a positive-definite potential, which admits a generalized Kaluza–Klein reduction. We investigate how symmetry breaking patterns through the Hosotani mechanism are affected by the ratio of the radii of S1 and S3.
CHARGED PERFECT FLUID CONFIGURATIONS WITH A DILATON FIELD
Authors: YAZADJIEV STOYTCHO S.
Published: May 2005

We examine static charged perfect fluid configurations in the presence of a dilaton field. A method for construction of interior solutions is given. An explicit example of an interior solution which matches continuously the external Gibbons–Maeda–Garfinkle–Horowitz–Strominger solution is presented. Extremely charged perfect fluid configurations with a dilaton are also examined. We show that there are two types of extreme configurations. For each type the field equations are reduced to a single nonlinear equation on a space of a constant curvature. In the particular case of a perfect fluid with a linear equation of state, the field equations of the first type configurations are reduced to a Helmholtz equation on a space with a constant curvature. An explicit example of an extreme configuration is given and discussed.
ELLIPTIC CMB SKY
Authors: GURZADYAN V. G. , DE BERNARDIS P. , DE TROIA G. , BIANCO C. L. , KASHIN A. L. , KULOGHLIAN H. , MASI S. , PIACENTINI F. , POLENTA G. , YEGORIAN G.
Published: May 2005

The ellipticity of the anisotropy spots of the Cosmic Microwave Background measured by the Wilkinson Microwave Anisotropy Probe (WMAP) has been studied. We find an average ellipticity of about 2, confirming with a far larger statistics similar results found first for the COBE-DMR CMB maps, and then for the BOOMERanG CMB maps. There are no preferred directions for the obliquity of the anisotropy spots. The average ellipticity is independent of temperature threshold and is present on scales both smaller and larger than the horizon at the last scattering. The measured ellipticity characteristics are consistent with being the effect of geodesics mixing occurring in a hyperbolic Universe, and can mark the emergence of CMB ellipticity as a new observable constant describing the Universe. There is no way of simulating this effect. Therefore we cannot exclude that the observed behavior of the measured ellipticity can result from a trivial topology in the popular flat Λ-CDM model, or from a nontrivial topology.
NONCOMMUTATIVE MANIFOLDS FROM THE HIGGS SECTOR OF COINCIDENT D-BRANES
Authors: ISIDRO JOSÉ M.
Published: May 2005

The Higgs sector of the low-energy physics of n coincident D-branes contains the necessary elements for constructing noncommutative manifolds. The coordinates orthogonal to the coincident branes, as well as their conjugate momenta, take values in the Lie algebra of the gauge group living inside the brane stack. In the limit when n→∞ (and in the absence of orientifolds), this is the unitary Lie algebra u(∞). Placing a smooth manifold [Formula: see text] orthogonally to the stack of coincident D-branes, one can construct a noncommutative C⋆-algebra that provides a natural definition of a noncommutative partner for the manifold [Formula: see text].