bluuebunny/crossref_metadata_2025_split huggingface dataset:
A constructive treatment of Urysohn's Lemma in an apartness space
Authors: Bridges Douglas , Diener Hannes 
Published: October 2006

AbstractThis paper is dedicated to Prof. Dr. Günter Asser, whose work in founding this journal and maintaining it over many difficult years has been a major contribution to the activities of the mathematical logic community.At first (maybe even at second) sight it appears highly unlikely that Urysohn's Lemma has any significant constructive content. However, working in the context of an apartness space and using functions whose values are a generalisation of the reals, rather than real numbers, enables us to produce a significant constructive version of that lemma. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A nonstandard proof of a lemma from constructive measure theory
Authors: Ross David A. 
Published: October 2006

AbstractSuppose that fn is a sequence of nonnegative functions with compact support on a locally compact metric space, that T is a nonnegative linear functional, and that $ \sum ^\infty _{n=1}$ T fn < T f0. A result of Bishop, foundational to a constructive theory of functional analysis, asserts the existence of a point x such that $ \sum ^\infty _{n=1}$ fn (x) < f 0(x). This paper extends this result to arbitrary Hausdorff spaces, and gives short proofs using nonstandard analysis. While such arguments used are not themselves constructive, they can illuminate where the difficulty lies in finding the point x. An algorithm for constructing x is then given, with a nonstandard proof that the algorithm converges to a correct value. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
FMR fine structure – A tool to investigate the spatial magnetic phase separation phenomena in manganites
Authors: Martyanov Oleg , Yudanov Valerii , Lee Roman , Volkov Nikita , Sablina Klara 
Published: October 2006

AbstractAn original approach is proposed to study the magnetic phase separation phenomenon. It is based on the registration of the noise‐like FMR Fine Structure (FMR FS) caused by the magnetic interparticle dipole–dipole interaction between spatially separated ferromagnetic regions. Data obtained for a La0.7Pb0.3MnO3 single crystal point to the existence of spatially separated ferromagnetic regions. It is shown that FMR FS of the La0.7Pb0.3MnO3 single crystal is temperature reversible and disappears at the maximum of magnetoresistance. magnified imageThe FMR FS of La0.7Pb0.3MnO3 single crystal (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Immobilization Techniques for Mono‐ and Oligosaccharide Microarrays
Authors: Monzo Alex , Guttman András 
Published: October 2006

AbstractMono‐ and oligosaccharide microarrays play an essential role in the analysis of many important biological processes, such as DNA–sugar interactions, protein–sugar interactions, and sugar–sugar interactions. Based on the earlier success of DNA and protein microarrays, similar technologies emerged in the past years for sugar immobilization in order to fabricate carbohydrate microarrays. Efficient immobilization of various mono‐ and oligosaccharides of interest onto solid surfaces is indispensable for successful preparation of carbohydrate microarrays. In this paper, we review the different techniques available for covalent and noncovalent immobilization of conjugated and nonconjugated simple and complex sugars onto a palette of various surfaces. We also give a short overview on some of the future prospects of this emerging field.
Reorganization of highly preorganized hosts upon cation complexation: Ab initio study of fluorospherands
Authors: Elroby Shabaan A. K. , Lee Kyu Hwan , Oh Jung Soo , Chung Hwan Won , Cho Seung Joo , Paek Kyungsoo 
Published: October 2006

AbstractFluorospherands (F‐spherands) are highly preorganized hosts composed of fluorobenzene or 4‐methylfluorobenzene units attached to one another at their 2,6‐positions. To understand the intrinsic factors affecting cation complexation, we investigated the complexation behavior between F‐spherands and cations using density functional theory (DFT) at the level of B3LYP/6‐31G**. The F6‐spherand (C6H3F)6, (1) has a highly preorganized spherical cavity, which can encapsulate Li+ and Na+. Its cavity is not big enough for K+ and NH, which prefer external binding. Plausible conformations were studied for F8‐spherand (C6H3F)8. Conformer of D2d symmetry (2b) is more stable than that of D4d (2a), in agreement with NMR experiments. The cavity size of F8‐spherand is big enough to encapsulate all cations studied. However, the cavity size of 2b is smaller than that of 2a, which resulted in the guest selectivity. Upon complexation, 2b conformation is more stable for Li+ and Na+, while 2a conformation is preferred for larger cations such as K+ and NH. Thus, the ab initio calculations over these highly preorganized fluorospherands give important insights into their host–guest chemistry. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Cervical length assessment in women with idiopathic polyhydramnios
Authors: Hershkovitz R. , Sheiner E. , Maymon E. , Erez O. , Mazor M. 
Published: October 2006

AbstractObjectiveThe aims of the study were to determine cervical length among patients with polyhydramnios and to assess the relationship between the severity of polyhydramnios, cervical length and gestational age at delivery.Patients and methodsA prospective study was designed including 92 consecutive singleton pregnancies with polyhydramnios between 24 and 40 weeks' gestation. Cervical length was measured using transvaginal sonography. Polyhydramnios was defined when amniotic fluid index (AFI) was equal to or greater than 20 cm. A single sonologist performed all the examinations of the cervical length and the AFI.ResultsThe median cervical length and AFI were 37.5 (range, 7–52) mm and 28.8 (range, 20–43) cm, respectively. A significant gradual shortening of the cervical length was observed with advancing gestational age (P = 0.027). No significant association was found between AFI and cervical length (P = 0.24). A cut‐off of 15 mm (n = 5) was associated with a significantly lower gestational age at delivery (30 ± 2.6 weeks vs. 37.2 ± 4.2 weeks, respectively, P < 0.001).ConclusionsWomen with polyhydramnios have a gradual shortening of cervical length with advancing gestational age. However, this finding is not related to the severity of polyhydramnios. Copyright © 2006 ISUOG. Published by John Wiley & Sons, Ltd.
GenoProfiler: batch processing of high-throughput capillary fingerprinting data
Authors: You Frank M. , Luo Ming-Cheng , Gu Yong Qiang , Lazo Gerard R. , Deal Karin , Dvorak Jan , Anderson Olin D. 
Published: October 2006

AbstractSummary: High-throughput content fingerprinting techniques employing capillary electrophoresis place new demands on the editing of fingerprint files for the downstream contig assembly program, FPC. A cross-platform software application, GenoProfiler, was developed for automated editing of sized fingerprinting profiles generated by the ABI Genetic Analyzers. The batch-processing module extracts the sized fragment information directly from the ABI raw trace files, or from data files exported from GeneMapper or other size calling software, removes the background noise and undesired fragments, and generates fragment size files compatible with the FPC software.Availability: Contact: oandersn@pw.usda.gov
Acute Effects of Vigabatrin on Brain GABA and Homocarnosine in Patients with Complex Partial Seizures
Authors: Petroff Ognen A. C. , Hyder Fahmeed , Collins Theresa , Mattson Richard H. , Rothman Douglas L. 
Published: October 2006

Summary: Purpose: The acute, subacute, and chronic effects of vigabatrin (VGB) were studied in patients with refractory complex partial seizures. VGB increases human brain γ‐aminobutyric acid (GABA) and the related metabolites, homocarnosine and 2‐pyrrolidinone. Methods: In vivo measurements of GABA and homocarnosine were made of a 14‐cc volume in the occipital cortex by using 1H spectroscopy with a 2.1‐Tesla magnetic resonance spectrometer and an 8‐cm surface coil. Six patients (three women) were studied serially during the initiation and maintenance of VGB as adjunct therapy. Results: The first, 3 g dose of VGB increased brain GABA by 2.0 μmol/g within 81 min of oral administration. After 2 h, median edited GABA remained essentially the same for 2 days. The response to the second, 3‐g dose of VGB given at 48 h was considerably less than that to the first dose, with a median increase of 0.5 μmol/g within 72 min. After 2–3 months, rechallenging patients taking 1.5‐g VGB twice daily with 6 g increased GABA by 0.4 μmol/g within 87 min. Homocarnosine increased more gradually than GABA to above‐normal levels after a week of VGB therapy. Conclusions: VGB promptly elevates brain GABA and presumably offers partial protection against further seizures within hours of the first oral dose. Once‐a‐day dosing is sufficient to increase GABA. Patients may be expected to experience the effects of increased homocarnosine within 1 week.
REM Sleep Components Predict the Response to Initial Treatment of Infantile Spasms
Authors: Kohyama Jun , Sugimoto Junko , Itoh Masahiro , Sakuma Hiroshi , Shimohira Masayuki , Hasegawa Takeshi , Iwakawa Yoshihide 
Published: October 2006

Summary: Purpose: The phasic inhibition index (PII) is the rate of the simultaneous occurrence of rapid eye movement bursts (RBs) and phasic chin muscle activity (PCMA) during rapid eye movement sleep (REMS). PII is low insofar as physiologically occurring REM‐related phasic inhibition acts on chin muscles. Previously we found that PII was significantly higher in patients with infantile spasms (ISs) who had a recurrence of convulsions than in patients with ISs who exhibited no recurrence. We aimed to predict the response of patients with ISs to conventional anticonvulsants (AEDs) by means of REMS components including PII, expecting to facilitate avoidance of potentially hazardous hormonal therapy. Methods: REMS, recorded before the beginning of any medication, was retrospectively examined in 15 patients with ISs. The patients were classified into two groups according to the response to initial treatment with conventional AEDs. Conventional AEDs were enough to control the spasms in six good responders (GRs), whereas further hormonal therapy was required in nine poor responders (PRs) to control the spasms. Results: The amount of REMS was significantly lower in patients with ISs than in controls. GRs had less REMS than did PRs, although no significant difference was observed. Although the frequencies of RB and PCMA showed no significant differences among GRs, PRs, and controls, the average PII value in PRs (12.6 ± 3.4; mean ± SD) was significantly (p < 0.001) higher than that in GRs (6.1 ± 1.7). Conclusions: PII is a useful parameter for differentiating GRs from PRs.
Differences in Microbial Activity and Microbial Populations of Peat Associated with Suppression of Damping-Off Disease Caused by
Pythium sylvaticum
Authors: Hunter Paul J. , Petch Geoff M. , Calvo-Bado Leo A. , Pettitt Tim R. , Parsons Nick R. , Morgan J. Alun W. , Whipps John M. 
Published: October 2006

ABSTRACT

The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for
Pythium sylvaticum
-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of
P. sylvaticum
at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the
Rhizobium-Agrobacterium
group (specifically sequences similar to those for the genera
Ochrobactrum
and
Zoogloea
) and the
Acidobacteria
, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to
Basidiomycete
yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of
Cryptococcus
increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of
Pythium-
induced diseases in peats.
Synthetic Statistical Approach Reveals a High Degree of Richness of Microbial Eukaryotes in an Anoxic Water Column
Authors: Jeon S.-O. , Bunge J. , Stoeck T. , Barger K. J.-A. , Hong S.-H. , Epstein S. S. 
Published: October 2006

ABSTRACT
Molecular surveys suggest that communities of microbial eukaryotes are remarkably rich, because even large clone libraries seem to capture only a minority of species. This provides a qualitative picture of protistan richness but does not measure its real extent either locally or globally. Statistical analysis can estimate a community's richness, but the specific methods used to date are not always well grounded in statistical theory. Here we study a large protistan molecular survey from an anoxic water column in the Cariaco Basin (Caribbean Sea). We group individual 18S rRNA gene sequences into operational taxonomic units (OTUs) using different cutoff values for sequence similarity (99 to 50%) and systematically apply parametric models and nonparametric estimators to the OTU frequency data to estimate the total protistan diversity. The parametric models provided statistically sound estimates of protistan richness, with biologically meaningful standard errors, maximal data usage, and extensive model diagnostics and were preferable to the available nonparametric tools. Our clone library exceeded 700 clones but still covered only a minority of species and less than half of the larger protistan clades. Our estimates of total protistan richness portray the target community as very rich at all OTU levels, with hundreds of different populations apparently co-occurring in the small (3-liter) volume of our sample, as well as dozens of clades of the highest taxonomic order. These estimates are among the first for microbial eukaryotes that are obtained using state-of-the-art statistical methods and can serve as benchmark numbers for the local diversity of protists.
Prevalence of a Non-Male-Killing Spiroplasma in Natural Populations of
Drosophila hydei
Authors: Kageyama Daisuke , Anbutsu Hisashi , Watada Masayoshi , Hosokawa Takahiro , Shimada Masakazu , Fukatsu Takema 
Published: October 2006

ABSTRACT

Male-killing phenotypes are found in a variety of insects and are often associated with maternally inherited endosymbiotic bacteria. In several species of
Drosophila
, male-killing endosymbionts of the genus
Spiroplasma
have been found at low frequencies (0.1 to 3%). In this study, spiroplasma infection without causing male-killing was shown to be prevalent (23 to 66%) in Japanese populations of
Drosophila hydei
. Molecular phylogenetic analyses showed that
D. hydei
was infected with a single strain of spiroplasma, which was closely related to male-killing spiroplasmas from other
Drosophila
species. Artificial-transfer experiments suggested that the spiroplasma genotype rather than the host genotype was responsible for the absence of the male-killing phenotype. Infection densities of the spiroplasma in the natural host,
D. hydei
, and in the artificial host,
Drosophila melanogaster
, were significantly lower than those of the male-killing spiroplasma NSRO, which was in accordance with the hypothesis that a threshold infection density is needed for the spiroplasma-induced male-killing expression.
Blooms of Single Bacterial Species in a Coastal Lagoon of the Southwestern Atlantic Ocean
Authors: Piccini Claudia , Conde Daniel , Alonso Cecilia , Sommaruga Ruben , Pernthaler Jakob 
Published: October 2006

ABSTRACT

We investigated seasonal differences in community structure and activity (leucine incorporation) of the planktonic bacterial assemblage in the freshwater and brackish-water zones of a shallow coastal lagoon of the southwestern Atlantic Ocean.
Alphaproteobacteria
formed the dominant microbial group in both zones throughout the sampling period. After an intrusion of marine water, members of the SAR11 lineage became abundant in the brackish-water zone. These bacteria were apparently distributed over the lagoon during the following months until they constituted almost 30% of all prokaryotic cells at both sampling sites. At the first sampling date (March 2003) a single alphaproteobacterial species unrelated to SAR11,
Sphingomonas echinoides
, dominated the microbial assemblages in both zones of the lagoon concomitantly with a bloom of filamentous cyanobacteria. Pronounced maxima of leucine incorporation were observed once in each zone of the lagoon. In the freshwater zone, this highly active microbial assemblage was a mix of the typical bacteria lineages expected in aquatic systems. By contrast, a single bacterial genotype with >99% similarity to the facultative pathogen gammaproteobacterial species
Stenotrophomonas maltophilia
formed >90% of the bacterial assemblage (>10
7
cell ml
−1
) in the brackish-water zone at the time point of highest bacterial leucine incorporation. Moreover, these bacteria were equally dominant, albeit less active, in the freshwater zone. Thus, the pelagic zone of the studied lagoon harbored repeated short-term blooms of single bacterial species. This finding may have consequences for environmental protection.
Molecular Evidence for the Broad Distribution of Anaerobic Ammonium-Oxidizing Bacteria in Freshwater and Marine Sediments
Authors: Penton C. Ryan , Devol Allan H. , Tiedje James M. 
Published: October 2006

ABSTRACT

Previously available primer sets for detecting anaerobic ammonium-oxidizing (anammox) bacteria are inefficient, resulting in a very limited database of such sequences, which limits knowledge of their ecology. To overcome this limitation, we designed a new primer set that was 100% specific in the recovery of ∼700-bp 16S rRNA gene sequences with >96% homology to the “
Candidatus
Scalindua” group of anammox bacteria, and we detected this group at all sites studied, including a variety of freshwater and marine sediments and permafrost soil. A second primer set was designed that exhibited greater efficiency than previous primers in recovering full-length (1,380-bp) sequences related to “
Ca
. Scalindua,” “
Candidatus
Brocadia,” and “
Candidatus
Kuenenia.” This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments.
Quantitative Effect of
luxS
Gene Inactivation on the Fitness of
Helicobacter pylori
Authors: Lee Woo-Kon , Ogura Keiji , Loh John T. , Cover Timothy L. , Berg Douglas E. 
Published: October 2006

ABSTRACT

Furanone
metabolites called AI-2 (autoinducer 2), used by some bacterial species
for signaling and cell density-regulated changes in gene expression,
are made while regenerating
S
-adenosyl methionine (SAM) after
its use as a methyl donor. The
luxS
-encoded enzyme, in
particular, participates in this activated methyl cycle by generating
both a pentanedione, which is transformed chemically into these AI-2
compounds, and homocysteine, a precursor of methionine and SAM.
Helicobacter pylori
seems to contain the genes for this
activated methyl cycle, including
luxS
, but not genes for AI-2
uptake and transcriptional regulation. Here we report that deletion of
luxS
in
H. pylori
reference strain SS1 diminished its
competitive ability in mice and motility in soft agar, whereas no such
effect was seen with an equivalent
ΔluxS
derivative of
the unrelated strain X47. These different outcomes are consistent with
H. pylori
's considerable genetic diversity and are reminiscent
of phenotypes seen after deletion of another nonessential metabolic
gene, that encoding polyphosphate kinase 1. We suggest that synthesis
of AI-2 by
H. pylori
may be an inadvertent consequence of
metabolite flux in its activated methyl cycle and that impairment of
this cycle and/or pathways affected by it, rather than loss of quorum
sensing, is deleterious for some
H. pylori
strains. Also
tenable is a model in which AI-2 affects other microbes in
H.
pylori
's gastric ecosystem and thereby modulates the gastric
environment in ways to which certain
H. pylori
strains are
particularly
sensitive.
Identification of Virulence Genes Linked with Diarrhea Due to Atypical Enteropathogenic
Escherichia coli
by DNA Microarray Analysis and PCR
Authors: Afset Jan Egil , Bruant Guillaume , Brousseau Roland , Harel Josée , Anderssen Endre , Bevanger Lars , Bergh Kåre 
Published: October 2006

ABSTRACT

The role of atypical enteropathogenic
Escherichia coli
(EPEC) in childhood diarrhea is controversial. The aim of the present study was to search for genes linked with diarrhea in atypical EPEC strains from a case-control study among Norwegian children. Using DNA microarray analysis, genomic DNAs from strains isolated from children with (
n
= 37) and without (
n
= 20) diarrhea were hybridized against 242 different oligonucleotide probes specific for 182 virulence genes or markers from all known
E. coli
pathotypes. PCR was performed to test the strains for seven putative virulence genes not included in the microarray panel. The OI-122 gene
efa1/lifA
was the gene with the strongest statistical association with diarrhea (
P
= 0.0008). Other OI-122 genes (
set/ent
,
nleB
, and
nleE
) and genes with other locations (
lpfA
,
paa
,
ehxA
, and
ureD
) were also associated with diarrheal disease. The phylogenetic marker gene
yjaA
was negatively associated with diarrhea (
P
= 0.0004). Atypical EPEC strains could be classified in two main virulence groups based on their content of OI-122,
lpfA
, and
yjaA
genes. Among children with diarrhea, atypical EPEC isolates belonging to virulence group I (OI-122 and
lpfA
positive,
yjaA
negative) were the most common, while the majority of isolates from healthy children were classified as virulence group II strains (OI-122 negative,
lpfA
and
yjaA
positive;
P
< 0.001). In conclusion, using DNA microarray analysis to determine the virulence gene profile of atypical EPEC isolates, several genes were found to be significantly associated with diarrhea. Based on their composition of virulence genes, the majority of strains could be classified in two virulence groups, of which one was seen mainly in children with diarrhea.