bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gamma-ray bursts from quark stars
Authors: Paczyński B. , Haensel P. 
Published: August 2005

Abstract
Long gamma-ray bursts (GRBs) are believed to be related to the explosion of Type Ic supernovae, which have been stripped of their hydrogen and helium envelopes. There appear to be two types of these explosions: those that are approximately spherical (GRB 980425/SN 1998bw), and which are associated with weak bursts; and the classical GRBs which generate ultrarelativistic jets (GRB 030329/SN 2003dh). If this bimodality is real, Swift will provide clear evidence for it.
We propose that classical powerful GRBs, which generate ultrarelativistic outflows, are a result of the formation of quark stars. Quark stars may provide additional energy for the explosion of Type Ic supernovae, but far more important is the creation of a surface which acts as a membrane that cannot be penetrated by baryons. A surface of a quark star allows only ultrarelativistic matter to escape: photons, neutrinos, electron–positron pairs and magnetic fields. The formation of a quark star follows several minutes after the initial core collapse. Possible evidence for this time delay is provided by BATSE precursors to GRBs, as analysed by Lazzati.
Constraints on the dark energy equation of state from the imprint of baryons on the power spectrum of clusters
Authors: Angulo R. , Baugh C. M. , Frenk C. S. , Bower R. G. , Jenkins A. , Morris S. L. 
Published: August 2005

Abstract
Acoustic oscillations in the baryon–photon fluid leave a signature in the matter power spectrum. The overall shape of the spectrum and the wavelength of the oscillations depend upon the sound horizon scale at recombination. Using the Λ cold dark matter Hubble Volume simulation, we show that the imprint of baryons is visible in the power spectrum of cluster-mass dark matter haloes, in spite of significant differences between the halo power spectrum and the prediction of linear perturbation theory. A measurement of the sound horizon scale can constrain the dark energy equation of state. We show that a survey of clusters at intermediate redshift (z∼ 1), like the Sunyaev–Zel'dovich survey proposed by the South Pole Telescope or a red sequence photometric survey with VISTA or the Dark Energy Survey, could potentially constrain the sound horizon scale to an accuracy of ∼2 per cent, in turn fixing the ratio of the pressure of the dark energy to its density (w) to better than ∼10 per cent. Our approach does not require knowledge of the cluster mass, unlike those that depend upon the abundance of clusters.
The origin of long-period Alfvén waves in the solar wind
Authors: Zaqarashvili T. V. , Belvedere G. 
Published: August 2005

Abstract
We suggest that the observed long-period Alfvén waves in the solar wind may be generated in the solar interior as a result of the pulsation of the Sun in the fundamental radial mode. The period of this pulsation is about 1 h. The pulsation causes a periodic variation of density and large-scale magnetic field, which affects the Alfvén speed in the solar interior. Consequently, Alfvén waves with half the frequency of pulsation (i.e. with double the period) can be parametrically amplified in the interior below the convection zone as a result of the recently suggested swing wave–wave interaction. Therefore the amplified Alfvén waves have periods of several hours. The waves can propagate upwards through the convection zone to the solar atmosphere and cause the observed long-period Alfvén oscillations in the solar wind.
Cosmic backgrounds from miniquasars
Authors: Salvaterra Ruben , Haardt Francesco , Ferrara Andrea 
Published: August 2005

Abstract
A large population of intermediate-mass black holes (IMBHs) might be produced at early cosmic times as a leftover of the evolution of the very massive first stars. Accretion on to IMBHs provides a source of (re)ionizing radiation. We show that the baryon mass fraction locked into IMBHs and their growth is strongly constrained by the observed residual soft X-ray background (SXRB) intensity. Thus, unless they are extremely X-ray quiet, miniquasars must be quite rare and/or have a short shining phase. As a byproduct, we find that miniquasars cannot be the only source of reionization and that their alleged contribution to the near-infrared bands is completely negligible.
An Integrated Approach to Identifying the Salinity Source Contaminating a Ground‐Water Supply
Authors: Knuth Martin , Jackson Jim L. , Whittemore Donald O. 
Published: August 2005

AbstractAn integrated approach involving geohydrological, geochemical, and geophysical methods was used to determine the source of salinity contaminating a ground‐water supply in an area of Ohio where three possible sources existed: road salting, naturally saline ground waters at depth, and formation brines placed in surface pits during drilling of a gas well. Changes in chloride concentrations during pumping tests of contaminated wells indicated that the main source of salinity was derived from within the water‐table aquifer. Mixing curves of Br/Cl versus chloride concentration were used to determine which of each of the three salinity sources was the primary source affecting different well waters. The major source affecting the ground‐water supply was found to be the formation brines associated with the gas well drilling.Geophysical surveys using electromagnetic induction (Geonics EM–31) and dipole‐dipole electrical resistivity methods provided a three‐dimensional view of the brine contamination plume in the unsaturated and saturated zones in the area of the gas well. The plume location and orientation confirmed that the formation brine from the blow‐down pits used during drilling of a nearby gas well was the primary source polluting the ground‐water supply in the study area.
A Compatible Single‐Phase/Two‐Phase Numerical Model: 2. Application to a Coastal Aquifer in Mexico
Authors: Rivera Alfonso , Ledoux Emmanuel , Sauvagnac Serge 
Published: August 2005

AbstractThe application of a numerical model to a coastal aquifer is presented including the simulation of single‐phase and two‐phase fluid flow. The single‐phase part of the model solves the diffusivity equation and helps to identify certain parameters of the aquifer and to simulate the flow field (fresh water) under different conditions. The two‐phase part of the model solves the partial differential equations describing the motion of salt water and fresh water separated by a sharp interface.The model was calibrated using the observed piezometry of the aquifer for the fresh‐water flow field. Simulations were made for both steady‐and unsteady‐state conditions to establish the position and movement of the interface under different schemes of pumping. Results show that the model reproduces very accurately the flow field of fresh water. It identifies the potential salt‐water intrusion (upconing) into some of the pumping wells, thus helping in the identification of optimal pumping schemes.
Hydrocarbon Thickness Fluctuations in Monitoring Wells
Authors: Kemblowski M. W. , Chiang C. Y. 
Published: August 2005

AbstractHydrocarbon thickness measurements in monitoring wells are used to estimate the hydrocarbon volume in the subsurface and to evaluate the efficiency of hydrocarbon recovery. It is commonly assumed that the formation hydrocarbon thickness is linearly related to the measured one. However, field data quite frequently show hydrocarbon thickness fluctuations that are not related to either hydrocarbon recovery or its release.It is postulated that these fluctuations are related to hydrocarbon/ground‐water interface elevation changes, and can be explained by two mechanisms: (1) difference in the residual saturation of hydrocarbons entrapped below and above the “interface,” and (2) preferred flow of the liquids through the monitoring well.
The Chemical Evolution of Ground Water in the Milk River Aquifer, Canada
Authors: Hendry M. Jim , Schwartz Franklin W. 
Published: August 2005

AbstractWell‐defined trends are observed in the ion composition of ground water from the Milk River aquifer. Ground water from the area of the subcrop has higher concentrations of Na+, SO42‐, Ca2+, and Mg2+ than immediately downgradient. Away from the area of subcrop, Na+, Cl‐, HCO3‐ + CO32‐, and CH4 concentrations increase systematically with increased residence time, pH decreases, and Mg2+ and Ca2+ concentrations are typically low (less than 0.1 mmol/1). Geologic changes play an important role in producing these chemical patterns. The first major geologic change was the erosion of the overlying confining beds in the recharge area about 5 × 105 years ago, enabling meteoric water with low concentrations of Na+ and Cl‐ to enter the aquifer and displace preexisting water. The second major change was the deposition of glacial till in the area of the Milk River about 30,000 to 40,000 years ago. Water recharging through the till to the aquifer developed characteristically high concentrations of Na+, SO42‐, Ca2+, and Mg2+. Downgradient of the area of subcrop, the trends in Na+ and Cl‐ are controlled by diffusion from the underlying confining shale. Analyses of ground‐water and gas samples for sulfate reducers and ground‐water and gas samples for sulfide and H2S, respectively, suggest that SO42‐ reduction is not a major process. Geochemical modeling suggests that CO2 gas is added to the ground water with increased residence time in the aquifer. The increase in CO2, CH4, and dissolved inorganic carbon can be attributed to methane fermentation. Geochemical modeling suggests that cation exchange plays a minor role in the chemical evolution of the ground waters.
The
yliA
, -
B
, -
C
, and -
D
Genes of
Escherichia coli
K-12 Encode a Novel Glutathione Importer with an ATP-Binding Cassette
Authors: Suzuki Hideyuki , Koyanagi Takashi , Izuka Shunsuke , Onishi Akiko , Kumagai Hidehiko 
Published: August 2005

ABSTRACT

Glutathione protects cells and organisms from oxygen species and peroxides and is indispensable for aerobically living organisms. Moreover, it acts against xenobiotics and drugs by the formation and excretion of glutathione
S
conjugates. In this study, we show that the
yliA
, -
B
, -
C
, and -
D
genes of
Escherichia coli
K-12 encode a glutathione transporter with the ATP-binding cassette. The transporter imports extracellular glutathione into the cytoplasm in an ATP-dependent manner. This transporter, along with γ-glutamyltranspeptidase, has an important role in
E. coli
growth with glutathione as a sole sulfur source.
A LysR-Type Regulator, CidR, Is Required for Induction of the
Staphylococcus aureus cidABC
Operon
Authors: Yang Soo-Jin , Rice Kelly C. , Brown Raquel J. , Patton Toni G. , Liou Linda E. , Park Yong Ho , Bayles Kenneth W. 
Published: August 2005

ABSTRACT

The
Staphylococcus aureus cidABC
and
lrgAB
operons have been shown to regulate murein hydrolase activity and affect antibiotic tolerance. The
cid
operon enhances murein hydrolase activity and antibiotic sensitivity, whereas the
lrg
operon inhibits these processes. Based on these findings and the structural similarities of the
cidA
and
lrgA
gene products to the bacteriophage holin family of proteins, we have proposed that the
cid
and
lrg
operons encode holin- and antiholin-like proteins, respectively, that function to control the murein hydrolase activity produced by the bacteria. Analysis of
cid
operon transcription revealed the presence of two transcripts, one spanning all three
cid
genes and whose expression is induced by growth in the presence of acetic acid and the other spanning
cidB
and
cidC
only that is produced in a sigma B-dependent manner. The
cidABC
operon lies immediately downstream from the
cidR
gene, encoding a potential LysR-type transcriptional regulator. In this study, we demonstrate that
cidR
is involved in the regulation of
cidABC
expression. Northern blot analyses revealed that the
cidR
gene product positively regulates
cidABC
expression by increasing transcription in the presence of acetic acid produced as a result of the metabolism of glucose. As expected for an operon that encodes a positive effector of murein hydrolase activity, the upregulation of
cidABC
expression resulted in increased murein hydrolase activity produced by these cells. Furthermore, it was demonstrated that antibiotic tolerance and stationary-phase survival of
S. aureus
are affected by the
cidR
gene. Taken together, these results demonstrate that the
cidR
gene product functions as a transcriptional activator of
cidABC
transcription in response to acetic acid accumulation in the growth medium.
ABC Transporter for Corrinoids inHalobacteriumsp. Strain NRC-1
Authors: Woodson Jesse D. , Reynolds April A. , Escalante-Semerena Jorge C. 
Published: August 2005

ABSTRACTWe report evidence for the existence of a putative ABC transporter for corrinoid utilization in the extremely halophilic archaeonHalobacteriumsp. strain NRC-1. Results from genetic and nutritional analyses ofHalobacteriumshowed that mutants with lesions in open reading frames (ORFs) Vng1370G, Vng1371Gm, and Vng1369G required a 105-fold higher concentration of cobalamin for growth than the wild-type or parent strain. The data support the conclusion that these ORFs encode orthologs of the bacterial cobalamin ABC transporter permease (btuC; Vng1370G), ATPase (btuD; Vng1371Gm), and substrate-binding protein (btuF; Vng1369G) components. Mutations in the Vng1370G, Vng1371Gm, and Vng1369G genes were epistatic, consistent with the hypothesis that their products work together to accomplish the same function. Extracts ofbtuFmutant strains grown in the presence of cobalamin did not contain any cobalamin molecules detectable by a sensitive bioassay, whereasbtuCDmutant strain extracts did. The data are consistent with the hypothesis that the BtuF protein is exported to the extracellular side of the cell membrane, where it can bind cobalamin in the absence of BtuC and BtuD. Our data also provide evidence for the regulation of corrinoid transport and biosynthesis.Halobacteriumsynthesized cobalamin in a chemically defined medium lacking corrinoid precursors. To the best of our knowledge, this is the first genetic analysis of an archaeal corrinoid transport system.
Adaptation to Disruption of the Electron Transfer Pathway for Fe(III) Reduction in
Geobacter sulfurreducens
Authors: Leang Ching , Adams L. A. , Chin K.-J. , Nevin K. P. , Methé B. A. , Webster J. , Sharma M. L. , Lovley D. R. 
Published: August 2005

ABSTRACT

Previous studies demonstrated that an outer membrane
c
-type cytochrome, OmcB, was involved in Fe(III) reduction in
Geobacter sulfurreducens
. An OmcB-deficient mutant was greatly impaired in its ability to reduce both soluble and insoluble Fe(III). Reintroducing
omcB
restored the capacity for Fe(III) reduction at a level proportional to the level of OmcB production. Here, we report that the OmcB-deficient mutant gradually adapted to grow on soluble Fe(III) but not insoluble Fe(III). The adapted OmcB-deficient mutant reduced soluble Fe(III) at a rate comparable to that of the wild type, but the cell yield of the mutant was only ca. 60% of that of the wild type under steady-state culturing conditions. Analysis of proteins and transcript levels demonstrated that expression of several membrane-associated cytochromes was higher in the adapted mutant than in the wild type. Further comparison of transcript levels during steady-state growth on Fe(III) citrate with a whole-genome DNA microarray revealed a significant shift in gene expression in an apparent attempt to adapt metabolism to the impaired electron transport to Fe(III). These results demonstrate that, although there are many other membrane-bound
c
-type cytochromes in
G. sulfurreducens
, increased expression of these cytochromes cannot completely compensate for the loss of OmcB. The concept that outer membrane cytochromes are promiscuous reductases that are interchangeable in function appears to be incorrect. Furthermore, the results indicate that there may be different mechanisms for electron transfer to soluble Fe(III) and insoluble Fe(III) oxides in
G. sulfurreducens
, which emphasizes the importance of studying electron transport to the environmentally relevant Fe(III) oxides.
E1 Enzyme of the Pyruvate Dehydrogenase Complex in
Corynebacterium glutamicum
: Molecular Analysis of the Gene and Phylogenetic Aspects
Authors: Schreiner Mark E. , Fiur Diana , Holátko Jiří , Pátek Miroslav , Eikmanns Bernhard J. 
Published: August 2005

ABSTRACT

The E1p enzyme is an essential part of the pyruvate dehydrogenase complex (PDHC) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the E2p enzyme within the complex. We analyzed the
Corynebacterium glutamicum aceE
gene, encoding the E1p enzyme, and constructed and characterized an E1p-deficient mutant. Sequence analysis of the
C. glutamicum aceE
gene and adjacent regions revealed that
aceE
is not flanked by genes encoding other enzymes of the PDHC. Transcriptional analysis revealed that
aceE
from
C. glutamicum
is monocistronic and that its transcription is initiated 121 nucleotides upstream of the translational start site. Inactivation of the chromosomal
aceE
gene led to the inability to grow on glucose and to the absence of PDHC and E1p activities, indicating that only a single E1p enzyme is present in
C. glutamicum
and that the PDHC is essential for the growth of this organism on carbohydrate substrates. Surprisingly, the E1p enzyme of
C. glutamicum
showed up to 51% identity to homodimeric E1p proteins from gram-negative bacteria but no similarity to E1 α- or β-subunits of heterotetrameric E1p enzymes which are generally assumed to be typical for gram-positives. To investigate the distribution of E1p enzymes in bacteria, we compiled and analyzed the phylogeny of 46 homodimeric E1p proteins and of 58 α-subunits of heterotetrameric E1p proteins deposited in public databases. The results revealed that the distribution of homodimeric and heterotetrameric E1p subunits in bacteria is not in accordance with the rRNA-based phylogeny of bacteria and is more heterogeneous than previously assumed.
Heat Shock Response ofArchaeoglobus fulgidus
Authors: Rohlin Lars , Trent Jonathan D. , Salmon Kirsty , Kim Unmi , Gunsalus Robert P. , Liao James C. 
Published: August 2005

ABSTRACTThe heat shock response of the hyperthermophilic archaeonArchaeoglobus fulgidusstrain VC-16 was studied using whole-genome microarrays. On the basis of the resulting expression profiles, approximately 350 of the 2,410 open reading frames (ORFs) (ca. 14%) exhibited increased or decreased transcript abundance. These span a range of cell functions, including energy production, amino acid metabolism, and signal transduction, where the majority are uncharacterized. One ORF called AF1298 was identified that contains a putative helix-turn-helix DNA binding motif. The gene product, HSR1, was expressed and purified fromEscherichia coliand was used to characterize specific DNA recognition regions upstream of twoA. fulgidusgenes, AF1298 and AF1971. The results indicate that AF1298 is autoregulated and is part of an operon with two downstream genes that encode a small heat shock protein, Hsp20, and cdc48, an AAA+ATPase. The DNase I footprints using HSR1 suggest the presence of acis-binding motif upstream of AF1298 consisting of CTAAC-N5-GTTAG. Since AF1298 is negatively regulated in response to heat shock and encodes a protein only distantly related to the N-terminal DNA binding domain of Phr ofPyrococcus furiosus, these results suggest that HSR1 and Phr may belong to an evolutionarily diverse protein family involved in heat shock regulation in hyperthermophilic and mesophilicArchaeaorganisms.
Gene Organization and Transcriptional Analysis of thetprJ,tprI,tprG, andtprFLoci inTreponema pallidumStrains Nichols and Sea 81-4
Authors: Giacani Lorenzo , Hevner Karin , Centurion-Lara Arturo 
Published: August 2005

ABSTRACTThetprgene family ofTreponema pallidumsubsp.pallidum, the causative agent of syphilis, has recently become the focus of intensive investigation. TprF and TprI sequences are highly conserved among different isolates and are the targets of strong humoral and cellular immune responses of the host, and immunization with a recombinant peptide from the amino terminus of these antigens has been shown to alter significantly lesion development following homologous challenge. This indicates that these antigens are expressed during infection and strongly suggests a key functionality.tprFandtprIare located immediately downstream of thetprGandtprJgenes, respectively, separated by very short intergenic spacers (55 nucleotides forG-Fand 56 nucleotides forJ-I). Preliminary analysis using gene-specific primers failed to amplifytprJin the Sea 81-4 isolate. In this study, sequence and transcriptional analysis of these loci showed a similar gene organization in the Nichols and Sea 81-4 strains, a complex pattern of transcription, and the presence of G homopolymeric repeats of variable lengths upstream of thetprF,tprI,tprG, andtprJtranscriptional start sites. However, distinctive features were also identified in the Sea 81-4 isolate, including atprG-like open reading frame in thetprJlocus, a frameshift and a premature termination in thetprGcoding sequence, a longertprG-tprFintergenic spacer, and absence of cotranscription of thetprG-tprFgenes.
The Toxin-Antitoxin System of the Streptococcal Plasmid pSM19035
Authors: Zielenkiewicz Urszula , Cegłowski Piotr 
Published: August 2005

ABSTRACT

pSM19035 of the pathogenic bacterium
Streptococcus pyogenes
is a low-copy-number plasmid carrying erythromycin resistance, stably maintained in a broad range of gram-positive bacteria. We show here that the ω
-ε-ζ
operon of this plasmid constitutes a novel proteic plasmid addiction system in which the ε and ζ genes encode an antitoxin and toxin, respectively, while ω plays an autoregulatory function. Expression of toxin Zeta is bactericidal for the gram-positive
Bacillus subtilis
and bacteriostatic for the gram-negative
Escherichia coli
. The toxic effects of ζ gene expression in both bacterial species are counteracted by proper expression of ε. The ε
-ζ
toxin-antitoxin cassette stabilizes plasmids in
E. coli
less efficiently than in
B. subtilis
.