bluuebunny/crossref_metadata_2025_split huggingface dataset:
A menagerie of non-finitely based process semantics
over BPA* – from ready simulation to completed traces
Authors: ACETO LUCA , FOKKINK WAN , INGÓLFSDÓTTIR ANNA 
Published: July 2002

Fokkink and Zantema (Fokkink and Zantema 1994) have shown that
bisimulation
equivalence has a finite equational axiomatization over the language of
Basic Process
Algebra with the binary Kleene star operation (BPA*). In
light of this positive result on the
mathematical tractability of bisimulation equivalence over BPA*,
a natural question to ask is
whether any other (pre)congruence relation in van Glabbeek's
linear time/branching time
spectrum is finitely (in)equationally axiomatizable over it. In this paper,
we prove that,
unlike bisimulation equivalence, none of the preorders and equivalences
in van Glabbeek's
linear time/branching time spectrum, whose discriminating power lies
in between that of
ready simulation and that of completed traces, has a finite equational
axiomatization. This
we achieve by exhibiting a family of (in)equivalences that holds in ready
simulation
semantics (which is the finest semantics that we consider) and whose instances
cannot all be
proved by means of any finite set of (in)equations that is sound in completed
trace semantics
(which is the coarsest semantics that is appropriate for the
language BPA*). To this end, for
every finite collection of (in)equations that are sound in completed trace
semantics, we build
a model in which some of the (in)equivalences of the family under consideration
fail. The
construction of the model mimics the one used by Conway (Conway 1971, p.
105) in his
proof of a result, originally due to Redko, to the effect that infinitely
many equations are
needed to axiomatize equality of regular expressions.Our non-finite axiomatizability results apply to the language BPA* over
an arbitrary
non-empty set of actions. In particular, we show that completed trace equivalence
is not
finitely based over BPA* even when the set of actions
is a singleton. Our proof of this result
may be adapted to the standard language of regular expressions to yield
a solution to an
open problem posed by Salomaa (Salomaa 1969, p. 143).Another semantics that is usually considered in process theory is trace
semantics. Trace
semantics is, in general, not preserved by sequential composition, and
is therefore
inappropriate for the language BPA*. We show that, if the set of
actions is a singleton, trace
equivalence and preorder are preserved by all the operators in the signature
of BPA*, and
coincide with simulation equivalence and preorder, respectively. In that
case, unlike all the
other semantics considered in this paper, trace semantics have finite,
complete equational
axiomatizations over closed terms.
Measuring salt and freezing temperature on roads
Authors: Turunen Markus 
Published: July 2002

AbstractPractical monitoring of the amount of salt spread on the road surface for de‐icing purposes is technically difficult, especially if it has to be done in a commercially viable way. Possible solutions to this problem are discussed. As it has become customary to refer to the freezing temperature of a salted road, the physical meaning of such a temperature is scrutinised. It turns out that the meaning and the definition of freezing temperature are not clear, and that it also does not have the significance that is often associated with it. Some experimental results of salt measurements on a road are presented. Copyright © 1997 Royal Meteorological Society.
A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping
Authors: Murphy William J. , Sun Shan , Chen Zhang-qun , Yuhki Naoya , Hirschmann Deborah , Menotti-Raymond Marilyn , O'Brien Stephen J. 
Published: July 2002

Ordered gene maps of mammalian species are becoming increasingly valued in assigning gene variants to function in human and animal models, as well as recapitulating the natural history of genome organization. To extend this power to the domestic cat, a radiation hybrid (RH) map of the cat was constructed integrating 424 Type I-coding genes with 176 microsatellite markers, providing coverage over all 20 feline chromosomes. Alignment of parallel RH maps of human and cat reveal 100 conserved segments ordered (CSOs) between the species, nearly three times the number observed with reciprocal chromosome painting analyses. The observed number is equivalent to theoretical predictions of the number of conserved segments to be found between cat and human, implying that 300–400 Type I gene markers is sufficient to reveal nearly all conserved segments for species that exhibit the most frequently observed “slow” rate of genome reorganization. The cat–human RH map comparisons provide a new genomic tool for comparative gene mapping in the cat and related Felidae, and provide confirmation that the cat genome organization is remarkably conserved compared with human. These data demonstrate that ordered RH-based gene maps provide the most precise assessment of comparing genomes, short of contig construction or full-sequence determination.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AZ081249–AZ081287andAW646734–AW646956.]
Temperature-Induced Extended Helix/Random Coil Transitions in a Group 1 Late Embryogenesis-Abundant Protein from Soybean
Authors: Soulages Jose L. , Kim Kangmin , Walters Christina , Cushman John C. 
Published: July 2002

Abstract
Group 1 late embryogenesis-abundant (LEA) proteins are a subset of hydrophilins that are postulated to play important roles in protecting plant macromolecules from damage during freezing, desiccation, or osmotic stress. To better understand the putative functional roles of group 1 LEA proteins, we analyzed the structure of a group 1 LEA protein from soybean (Glycine max). Differential scanning calorimetry of the purified, recombinant protein demonstrated that the protein assumed a largely unstructured state in solution. In the presence of trifluoroethanol (50% [w/v]), the protein acquired a 30% α-helical content, indicating that the polypeptide is highly restricted to adopt α-helical structures. In the presence of sodium dodecyl sulfate (1% [w/v]), 8% of the polypeptide chain adopted an α-helical structure. However, incubation with phospholipids showed no effect on the protein structure. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein existed in equilibrium between two conformational states. Ultraviolet absorption spectroscopy studies also showed that the protein became more hydrated upon heating. Furthermore, circular dichroism spectral measurements indicated that a minimum of 14% of amino acid residues existed in a solvent-exposed, left-handed extended helical or poly (l-proline)-type (PII) conformation at 20°C with the remainder of the protein being unstructured. The content of PII-like structure increased as temperature was lowered. We hypothesize that by favoring the adoption of PII structure, instead of the formation of α-helical or β-sheet structures, group 1 LEA proteins retain a high content of surface area available for interaction with the solvent. This feature could constitute the basis of a potential role of LEA proteins in preventing freezing, desiccation, or osmotic stress damage.
A Putative Mg Chelatase Subunit from Arabidopsis thaliana cv C24 (Sequence and Transcript Analysis of the Gene, Import of the Protein into Chloroplasts, and in Situ Localization of the Transcript and Protein
Authors: Gibson LCD. , Marrison J. L. , Leech R. M. , Jensen P. E. , Bassham D. C. , Gibson M. , Hunter C. N. 
Published: July 2002

Abstract
We have isolated and sequenced a cDNA from Arabidopsis thaliana cv C24 that encodes a putative Mg chelatase subunit. The deduced amino acid sequence shows a very high level of identity to a gene previously characterized from Antirrhinum majus (olive) and also high similarity to bchH, a bacterial gene involved in the Mg chelatase reaction of bacteriochlorophyll biosynthesis. We suggest that this gene be called CHL H. Northern blot analyses were used to investigate the expression of CHL H, another putative Mg chelatase gene, ch-42, and ferrochelatase. The CHL H transcript was observed to undergo a dramatic diurnal variation, rising almost to its maximum level by the end of the dark period, then increasing slightly at the onset of the light and declining steadily to a minimum by the end of the light period; in contrast, transcripts for ch-42 and ferrochelatase remained constant. A model is proposed in which the CHL H protein plays a role in regulating the levels of chlorophyll during this cycle. In situ hybridization revealed that the transcripts are located over the surface of the chloroplasts, a feature in common with transcripts for the ch-42 gene. The CHL H protein was imported into the stromal compartment of the chloroplast and processed in an in vitro assay. Immunoblotting showed that the distribution of CHL H protein between the stroma and chloroplast membranes varies depending on the concentration of Mg2+. In situ immunofluorescence was used to establish that the CHL H and CH-42 proteins are localized within the chloroplast in vivo.
K+-Selective Inward-Rectifying Channels and Apoplastic pH in Barley Roots1
Authors: Amtmann Anna , Jelitto Till C. , Sanders Dale 
Published: July 2002

Abstract
Recent structure-function analysis of heterologously expressed K+-selective inward-rectifying channels (KIRCs) from plants has revealed that external protons can have opposite effects on different members of the same gene family. An important question is how the diverse response of KIRCs to apoplastic pH is reflected at the tissue level. Activation of KIRCs by acid external pH is well documented for guard cells, but no other tissue has yet been studied. In this paper we present, for the first time to our knowledge, in planta characterization of the effects of apoplastic pH on KIRCs in roots. Patch-clamp experiments on protoplasts derived from barley (Hordeum vulgare) roots showed that a decrease in external pH shifted the half-activation potential to more positive voltages and increased the limit conductance. The resulting enhancement of the KIRC current, together with the characteristic voltage dependence, strongly relates the KIRC of barley root cells to AKT1-type as opposed to AKT3-type channels. Measurements of cell wall pH in barley roots with fluorescent dye revealed a bulk apoplastic pH close to the pK values of KIRC activation and significant acidification of the apoplast after the addition of fusicoccin. These results indicate that channel-mediated K+ uptake may be linked to development, growth, and stress responses of root cells via the activity of H+-translocating systems.
Inhibition of Plant Asparagine Synthetase by Monoterpene Cineoles
Authors: Romagni Joanne G. , Duke Stephen O. , Dayan Franck E. 
Published: July 2002

Abstract
Asparagine (Asn) synthetase (AS) is the key enzyme in Asn biosynthesis and plays an important role in nitrogen mobilization. Despite its important physiological function, little research has been done documenting inhibitors of plant AS. Plant growth inhibition caused by the natural monoterpene 1,4-cineole and its structurally related herbicide cinmethylin was reversed 65% and 55%, respectively, by providing 100 μm Asn exogenously. Reversion of the phytotoxic effect was dependent on the concentration of Asn. The presence of either 1,4-cineole or cinmethylin stimulated root uptake of [14C]Asn by lettuce (Lactuca sativa) seedlings. Although the physiological responses suggested that both compounds affected Asn biosynthesis, biochemical analysis of AS activity showed that the natural monoterpene was a potent inhibitor (I50 = approximately 0.5 μm) of the enzyme, whereas the commercial product was not inhibitory up to levels of 10 mm. Analysis of the putative metabolite, 2-hydroxy-1,4-cineole, showed that the cis-enantiomer was much more active than the trans-enantiomer, suggesting that the hydroxyl group was involved in the specific ligand/active site interaction. This is the first report that AS is a suitable herbicide target site, and that cinmethylin is apparently a proherbicide that requires metabolic bioactivation via cleavage of the benzyl-ether side chain.
Early H2O2 Accumulation in Mesophyll Cells Leads to Induction of Glutathione during the Hyper-Sensitive Response in the Barley-Powdery Mildew Interaction
Authors: Vanacker Helene , Carver Tim L.W. , Foyer Christine H. 
Published: July 2002

Abstract
H2O2 production and changes in glutathione, catalase, and peroxidase were followed in whole-leaf extracts from the susceptible (AlgS [Algerian/4* (F14) Man.(S)]; ml-a1allele) and resistant (AlgR [Algerian/4* (F14) Man.(R)];Ml-a1 allele) barley (Hordeum vulgare) isolines between 12 and 24 h after inoculation with powdery mildew (Blumeria graminis [DC]. Speer [syn. Erysiphe graminis DC] f.sp hordei Marchal). Localized papilla responses and cell death hypersensitive responses were not observed within the same cell. In hypersensitive response sites, H2O2 accumulation first occurred in the mesophyll underlying the attacked epidermal cell. Subsequently, H2O2 disappeared from the mesophyll and accumulated around attacked epidermal cells. In AlgR, transient glutathione oxidation coincided with H2O2accumulation in the mesophyll. Subsequently, total foliar glutathione and catalase activities transiently increased in AlgR. These changes, absent from AlgS, preceded inoculation-dependent increases in peroxidase activity that were observed in both AlgR and AlgS at 18 h. An early intercellular signal precedes H2O2, and this elicits anti-oxidant responses in leaves prior to events leading to death of attacked cells.
Fluoroquinolone Resistance in Anaerobic Bacteria following Exposure to Levofloxacin, Trovafloxacin, and Sparfloxacin in an In Vitro Pharmacodynamic Model
Authors: Ross Gigi H. , Wright David H. , Hovde Laurie Baeker , Peterson Marnie L. , Rotschafer John C. 
Published: July 2002

ABSTRACT

This investigation explored pharmacodynamic characteristics of fluoroquinolones against
Bacteroides thetaiotamicron
and the potential for development of resistance. An in vitro model was used to generate kill curves with three fluoroquinolones at various area under the concentration-time curve (AUC)/MIC ratios. Concentration-independent killing was observed. Increases in MICs were noted following exposure to fluoroquinolones at AUC/MIC ratios of 6 to 14.
Branched-Chain Amino Acid Biosynthesis Is Essential for Optimal Growth of
Streptococcus thermophilus
in Milk
Authors: Garault P. , Letort C. , Juillard V. , Monnet V. 
Published: July 2002

ABSTRACT

Lactic acid bacteria are nutritionally demanding bacteria which need, among other things, amino acids for optimal growth. We identified the branched-chain amino acid (BCAA) biosynthesis pathway as an essential pathway for optimal growth of
Streptococcus thermophilus
in milk. Through random insertional mutagenesis, we isolated and characterized two mutants for which growth in milk is affected as a consequence of
ilvB
and
ilvC
gene interruptions. This situation demonstrates that the BCAA biosynthesis pathway is active in
S. thermophilus
. BCAA biosynthesis is necessary but not sufficient for optimal growth of
S. thermophilus
and is subject to retro-inhibition processes. The specificity of the BCAA biosynthesis pathway in
S. thermophilus
lies in the independent transcription of the
ilvC
gene encoding a keto acid reductoisomerase acting on acetolactate at the junction of the BCAA and acetoin biosynthesis pathways. The possible advantages for
S. thermophilus
of keeping this biosynthesis pathway active could be linked either to adaptation of the organism to milk, which is different than that of other dairy bacteria, or to the role of the pathway in maintaining the internal pH.
Successional Development of Sulfate-Reducing Bacterial Populations and Their Activities in a Wastewater Biofilm Growing under Microaerophilic Conditions
Authors: Ito Tsukasa , Okabe Satoshi , Satoh Hisashi , Watanabe Yoshimasa 
Published: July 2002

ABSTRACT

A combination of fluorescence in situ hybridization, microprofiles, denaturing gradient gel electrophoresis of PCR-amplified 16S ribosomal DNA fragments, and 16S rRNA gene cloning analysis was applied to investigate successional development of sulfate-reducing bacteria (SRB) community structure and in situ sulfide production activity within a biofilm growing under microaerophilic conditions (dissolved oxygen concentration in the bulk liquid was in the range of 0 to 100 μM) and in the presence of nitrate. Microelectrode measurements showed that oxygen penetrated 200 μm from the surface during all stages of biofilm development. The first sulfide production of 0.32 μmol of H
2
S m
−2
s
−1
was detected below ca. 500 μm in the 3rd week and then gradually increased to 0.70 μmol H
2
S m
−2
s
−1
in the 8th week. The most active sulfide production zone moved upward to the oxic-anoxic interface and intensified with time. This result coincided with an increase in SRB populations in the surface layer of the biofilm. The numbers of the probe SRB385- and 660-hybridized SRB populations significantly increased to 7.9 × 10
9
cells cm
−3
and 3.6 × 10
9
cells cm
−3
, respectively, in the surface 400 μm during an 8-week cultivation, while those populations were relatively unchanged in the deeper part of the biofilm, probably due to substrate transport limitation. Based on 16S rRNA gene cloning analysis data, clone sequences that related to
Desulfomicrobium hypogeium
(99% sequence similarity) and
Desulfobulbus elongatus
(95% sequence similarity) were most frequently found. Different molecular analyses confirmed that
Desulfobulbus
,
Desulfovibrio
, and
Desulfomicrobium
were found to be the numerically important members of SRB in this wastewater biofilm.
Microbial Iron Respiration Can Protect Steel from Corrosion
Authors: Dubiel M. , Hsu C. H. , Chien C. C. , Mansfeld F. , Newman D. K. 
Published: July 2002

ABSTRACT

Microbiologically influenced corrosion (MC) of steel has been attributed to the activity of biofilms that include anaerobic microorganisms such as iron-respiring bacteria, yet the mechanisms by which these organisms influence corrosion have been unclear. To study this process, we generated mutants of the iron-respiring bacterium
Shewanella oneidensis
strain MR-1 that were defective in biofilm formation and/or iron reduction. Electrochemical impedance spectroscopy was used to determine changes in the corrosion rate and corrosion potential as a function of time for these mutants in comparison to the wild type. Counter to prevailing theories of MC, our results indicate that biofilms comprising iron-respiring bacteria may reduce rather than accelerate the corrosion rate of steel. Corrosion inhibition appears to be due to reduction of ferric ions to ferrous ions and increased consumption of oxygen, both of which are direct consequences of microbial respiration.
Bacillus
Probiotics: Spore Germination in the Gastrointestinal Tract
Authors: Casula Gabriella , Cutting Simon M. 
Published: July 2002

ABSTRACT

Spores of
Bacillus
species are being used commercially as probiotics and competitive exclusion agents. Unlike the more commonly used
Lactobacillus
-type probiotics, spores are dormant life forms. To address how spore probiotics might function we have investigated whether spores can germinate in the gastrointestinal tract by using a murine model. Using a genetically engineered chimeric gene,
ftsH-lacZ
, which is strongly expressed only in vegetative cells, we have developed a sensitive competitive reverse transcription-PCR assay which has enabled detection of as few as 10
2
vegetative bacteria in the mouse gut. Using this method we have administered doses of
ftsH-lacZ
spores to groups of mice and shown that spores can germinate in significant numbers in the jejunum and ileum. The levels of detection we obtained suggest that spores may colonize the small intestine, albeit briefly.
Standardized Method of Measuring
Acanthamoeba
Antibodies in Sera from Healthy Human Subjects
Authors: Chappell Cynthia L. , Wright John A. , Coletta Michael , Newsome Anthony L. 
Published: July 2002

ABSTRACT

Acanthamoeba
species can cause serious, debilitating, and sometimes life-threatening infections. Three groups have been identified using morphological and immunological comparisons. Previous serological studies have utilized a variety of antigen preparations and assay methods and reported disparate (3 to 100%) results. This study was designed to (i) optimize an enzyme-linked immunosorbent assay for detecting serum antibodies to each of the
Acanthamoeba
serogroups and (ii) test 55 healthy individuals for specific immunoglobulin G reactivity. The highest signal-to-background ratio was found when 3,000 fixed, intact trophozoites per well were used with a 1:10 serum dilution. Sera yielding optical densities of <0.25 against all three
Acanthamoeba
serogroups were used to define the cutoff for positive results. The highest background reactivity with these sera was seen with
Acanthamoeba polyphaga
(serogroup 2), followed by
Acanthamoeba culbertsoni
(serogroup 3) and
Acanthamoeba astronyxis
(serogroup 1). Of 55 subjects tested, the highest number of positive results was seen with
A. polyphaga
(81.8%), followed by
A. astronyxis
(52.8%) and
A. culbertsoni
(40%). Seven serum samples (12.7%) were negative for all three
Acanthamoeba
serogroups, 16 (29.1%) were positive for one serogroup only, 16 were positive for two serogroups, and 16 reacted to all three serogroups. Further analysis showed no significant associations between serogroup reactivity and age or gender. However, some ethnic differences were noted, especially with
A. polyphaga
antigens. In that case, serum samples from Hispanic subjects were 14.5 times less likely to be positive (
P
= 0.0025) and had lower mean absorbance values (
P
= 0.047) than those from Caucasian subjects. Overall, these data suggest that
Acanthamoeba
colonization or infection is more common than previously thought. Mild or asymptomatic infections may contribute to the observed serum reactivities.
Cystatin Capture Enzyme-Linked Immunosorbent Assay for Serodiagnosis of Human Clonorchiasis and Profile of Captured Antigenic Protein ofClonorchis sinensis
Authors: Kim Tae Yun , Kang Shin-Yong , Park Sun Hyo , Sukontason Kom , Sukontason Kabkaew , Hong Sung-Jong 
Published: July 2002

ABSTRACTEnzyme-linked immunosorbent assay (ELISA) with crude extracts of adultClonorchis sinensishas been reported to have a high degree of sensitivity with a moderate degree of specificity for the serodiagnosis of clonorchiasis. The cystatin capture ELISA was investigated for its usefulness for the serodiagnosis of human clonorchiasis. Cystatin bound specifically to cysteine proteinases in crude extracts of adultC. sinensisworms, and its binding capacity was not hindered competitively by the other proteinase inhibitors tested. The cystatin capture ELISA for clonorchiasis showed a higher degree of specificity than the conventional ELISA, which produced some cross-reactivities to sera from patients with cysticercosis, sparganosis, and opisthorchiasis. Immunoglobulin G antibodies toC. sinensiscysteine proteinases were produced in experimental rabbits at week 3, and their levels increased rapidly and remained at a plateau after 8 weeks of infection. Of the proteins from theC. sinensiscrude extract captured with cystatin, seven proteins were reactive with the serum from patients with clonorchiasis. The cystatin capture ELISA is indicated to be a sensitive and highly specific immunodiagnostic assay for serodiagnosis of human clonorchiasis.