bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory Interactions among Adhesin Gene Systems of Uropathogenic
Escherichia coli
Authors: Lindberg Stina , Xia Yan , Sondén Berit , Göransson Mikael , Hacker Jörg , Uhlin Bernt Eric 
Published: November 2007

ABSTRACT

Uropathogenic
Escherichia coli
strain J96 carries multiple determinants for fimbrial adhesins. The regulatory protein PapB of P fimbriae has previously been implicated in potential coregulatory events. The
focB
gene of the F1C fimbria determinant is highly homologous to
papB
; the translated sequences share 81% identity. In this study we investigated the role of PapB and FocB in regulation of the F1C fimbriae. By using gel mobility shift assays, we showed that FocB binds to sequences in both the
pap
and
foc
operons in a somewhat different manner than PapB. The results of both in vitro cross-linking and in vivo oligomerization tests indicated that FocB could function in an oligomeric fashion. Furthermore, our results suggest that PapB and FocB can form heterodimers and that these complexes can repress expression of the
foc
operon. The effect of FocB on expression of type 1 fimbriae was also tested. Taken together, the results that we present expand our knowledge about a regulatory network for different adhesin gene systems in uropathogenic
E. coli
and suggest a hierarchy for expression of the fimbrial adhesins.
Comparison of Seven Techniques for Typing International Epidemic Strains of
Clostridium difficile
: Restriction Endonuclease Analysis, Pulsed-Field Gel Electrophoresis, PCR-Ribotyping, Multilocus Sequence Typing, Multilocus Variable-Number Tandem-Repeat Analysis, Amplified Fragment Length Polymorphism, and Surface Layer Protein A Gene Sequence Typing
Authors: Killgore George , Thompson Angela , Johnson Stuart , Brazier Jon , Kuijper Ed , Pepin Jacques , Frost Eric H. , Savelkoul Paul , Nicholson Brad , van den Berg Renate J. , Kato Haru , Sambol Susan P. , Zukowski Walter , Woods Christopher , Limbago Brandi , Gerding Dale N. , McDonald L. Clifford 
Published: November 2007

ABSTRACT

Using 42 isolates contributed by laboratories in Canada, The Netherlands, the United Kingdom, and the United States, we compared the results of analyses done with seven
Clostridium difficile
typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing (
slpA
ST), PCR-ribotyping, restriction endonuclease analysis (REA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). We assessed the discriminating ability and typeability of each technique as well as the agreement among techniques in grouping isolates by allele profile A (AP-A) through AP-F, which are defined by toxinotype, the presence of the binary toxin gene, and deletion in the
tcdC
gene. We found that all isolates were typeable by all techniques and that discrimination index scores for the techniques tested ranged from 0.964 to 0.631 in the following order: MLVA, REA, PFGE,
slpA
ST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain of
C. difficile
(BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and no
tcdC
gene deletion). REA,
slpA
ST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion in
tcdC
) in a single group that excluded other APs. PFGE, AFLP, and MLVA grouped two, one, and two different non-AP-B isolates, respectively, with their AP-B isolates. All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks.
In Vitro Bactericidal Activity of
Streptococcus pneumoniae
and Bactericidal Susceptibility of
Staphylococcus aureus
Strains Isolated from Cocolonized versus Noncocolonized Children
Authors: Regev-Yochay Gili , Malley Richard , Rubinstein Ethan , Raz Meir , Dagan Ron , Lipsitch Marc 
Published: November 2007

ABSTRACT

Streptococcus pneumoniae
is bactericidal to
Staphylococcus aureus
in vitro. To determine whether this in vitro effect accounts for the inverse relation between
S. pneumoniae
and
S. aureus
colonization reported in previous epidemiologic studies, we compared
S. pneumoniae
and
S. aureus
strains from cocolonized children to those from noncocolonized children. Cocolonizing pneumococci were less bactericidal and cocolonizing staphylococci less susceptible to this effect; however, the magnitude of the effect was small. Thus, in vitro killing is not the major determinant of the pattern of cocolonization.
The Traditions of Ancient Logic-cum-Grammar in the Middle Ages—What's the Problem?
Authors: Ebbesen Sten 
Published: November 2007

AbstractClashes between bits of non-homogeneous theories inherited from antiquity were an important factor in the formation of medieval theories in logic and grammar, but the traditional categories of Aristotelianism, Stoicism and Neoplatonism are not quite adequate to describe the situation. Neoplatonism is almost irrelevant in logic and grammar, while there might be reasons to introduce a new category, LAS = Late Ancient Standard, with two branches: (1) logical LAS = Aristotle + Boethius, and (2) grammatical LAS = Stoics &c. → Apollonius → Priscian.
Res Meaning a Thing Thought: The Influence of the Ars donati
Authors: Grondeux Anne 
Published: November 2007

AbstractDuring the fourth century C. E. Donatus borrowed from the Greek tradition the idea of replacing res corporalis with res in the definition of the noun, because of the usual equivalence between pragma and res. This change had important consequences, such as a new distinction between corpus and res, as well as a new meaning proposed for the word res. This new meaning happened to be questioned by later commentators, because masters of grammar seemed to reject the Donatian distinction between corpus and res, and consider that corpus is rather included inside res, before being later accepted by Sedulius and Remigius, perhaps under the influence of the common expression res verbi. However, the word remained poly-semic in spite of Donatus' attempt, as can be seen in the Glosulae in Priscianum (s. XII).
The Nonlinear Transient Atmospheric Response to Tropical Forcing
Authors: Lin Hai , Derome Jacques , Brunet Gilbert 
Published: November 2007

Abstract
Ensemble integrations using a primitive-equation dry atmospheric model were performed to investigate the atmospheric transient response to tropical thermal forcings that resemble El Niño and La Niña. The response develops in the North Pacific within 1 week after the integration. The signal in the North Atlantic and Europe is established by the end of the second week. Significant asymmetry was found between the responses in El Niño and La Niña that is similar to the observations, that is, one feature is that the 550-hPa positive height response in the North Pacific of the La Niña run is located about 30° west of the negative response of the El Niño run; another feature is that the responses in the North Atlantic and Europe for the La Niña and El Niño cases have similar patterns with the same polarity. The first feature is established within 2 weeks of the integration, while the second feature develops starting from the end of the second week. Several factors contribute to this nonlinearity of the response. In the Tropics, the shape of the Rossby wave response and the zonal extent of the Kelvin wave are not symmetric between El Niño and La Niña, which seems to be associated with the dependence of the wave property on the modified zonal mean flow. This is especially important in the equatorial region to the west of the forcing, which is likely responsible for the phase shift of the major extratropical response in the North Pacific. The transient eddy activity in the extratropics feeds back to the response and helps to maintain the nonlinearity.
Fifty-Seven-Year California Reanalysis Downscaling at 10 km (CaRD10). Part II: Comparison with North American Regional Reanalysis
Authors: Kanamaru Hideki , Kanamitsu Masao 
Published: November 2007

Abstract
The California Reanalysis Downscaling at 10 km (CaRD10) was compared with the North American Regional Reanalysis (NARR), which is a data assimilation regional analysis at 32-km resolution and 3-hourly output using the Eta Model for the period 1979 through the present using the NCEP/Department of Energy (DOE) reanalysis as lateral boundary conditions. The objectives of this comparison are twofold: 1) to understand the efficacy of regional downscaling and horizontal resolution and 2) to estimate the uncertainties in regional analyses due to system differences.
The large-scale component of atmospheric analysis is similar in CaRD10 and NARR. The CaRD10 daily winds fit better to station observations than NARR over ocean where daily variability is large and over land. The daily near-surface temperature comparison shows a similar temporal correlation with observations in CaRD10 and NARR. Several synoptic examples such as the Catalina eddy, coastally trapped wind reversal, and Santa Ana winds are better produced in CaRD10 than NARR. These suggest that the horizontal resolution of the model has a large influence on the regional analysis, and the near-surface observation is not properly assimilated in the current state-of-the-art regional data assimilation system.
The CaRD10 near-surface temperature and winds on monthly and hourly scales are similar to NARR with more regional details available in CaRD10. The Southwestern monsoon is poorly reproduced in CaRD10 because of the position of the lateral boundary. The spatial pattern of the two precipitation analyses is similar, but CaRD10 shows smaller-scale features despite a positive bias. The trends of 500-hPa height and precipitation are similar in the two analyses but the near-surface temperature trend spatial patterns do not agree, suggesting the importance of regional topography, model physics, and land surface schemes. A comparison of a major storm event shows that both analyses suffer from budget residual. CaRD10’s large precipitation is related to wind direction, spatial distribution of precipitable water, and a large moisture convergence.
Dynamical downscaling forced by a global analysis is a computationally economical approach to regional-scale long-term climate analysis and can provide a high-quality climate analysis comparable to current state-of-the-art data-assimilated regional reanalysis. However, uncertainties in regional analyses can be large and caution should be exercised when using them for climate applications.
Radiative and Convective Driving of Tropical High Clouds
Authors: Kubar Terence L. , Hartmann Dennis L. , Wood Robert 
Published: November 2007

AbstractUsing satellite cloud data from the Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) and collocated precipitation rates from the Advanced Microwave Scanning Radiometer (AMSR), it is shown that rain rate is closely related to the amount of very thick high cloud, which is a better proxy for precipitation than outgoing longwave radiation (OLR). It is also shown that thin high cloud, which has a positive net radiative effect on the top-of-atmosphere (TOA) energy balance, is nearly twice as abundant in the west Pacific compared to the east Pacific. For a given rain rate, anvil cloud is also more abundant in the west Pacific. The ensemble of all high clouds in the east Pacific induces considerably more TOA radiative cooling compared to the west Pacific, primarily because of more high, thin cloud in the west Pacific. High clouds are also systematically colder in the west Pacific by about 5 K.The authors examine whether the anvil cloud temperature is better predicted by low-level equivalent potential temperature (ΘE), or by the peak in upper-level convergence associated with radiative cooling in clear skies. The temperature in the upper troposphere where ΘE is the same as that at the lifting condensation level (LCL) seems to influence the temperatures of the coldest, thickest clouds, but has no simple relation to anvil cloud. It is shown instead that a linear relationship exists between the median anvil cloud-top temperature and the temperature at the peak in clear-sky convergence. The radiatively driven clear-sky convergence profiles are thus consistent with the warmer anvil clouds in the EP versus the WP.
Bronchial epithelial spheroids: an alternative culture model to investigate epithelium inflammation-mediated COPD
Authors: Deslee Gaetan , Dury Sandra , Perotin Jeanne M , Al Alam Denise , Vitry Fabien , Boxio Rachel , Gangloff Sophie C , Guenounou Moncef , Lebargy François , Belaaouaj Abderrazzaq 
Published: November 2007

AbstractBackgroundChronic obstructive pulmonary disease (COPD) is characterized by abnormal lung inflammation that exceeds the protective response. Various culture models using epithelial cell lines or primary cells have been used to investigate the contribution of bronchial epithelium in the exaggerated inflammation of COPD. However, these models do not mimicin vivosituations for several reasons (e.g, transformed epithelial cells, protease-mediated dissociation of primary cells, etc.). To circumvent these concerns, we developed a new epithelial cell culture model.MethodsUsing non transformed non dissociated bronchial epithelium obtained by bronchial brushings from COPD and non-COPD smokers, we developed a 3-dimensional culture model, bronchial epithelial spheroids (BES). BES were analyzed by videomicroscopy, light microscopy, immunofluorescence, and transmission electron microscopy. We also compared the inflammatory responses of COPD and non-COPD BES. In our study, we chose to stimulate BES with lipopolycaccharide (LPS) and measured the release of the pro-inflammatory mediators interleukin-8 (IL-8) and leukotriene B4 (LTB4) and the anti-inflammatory mediator prostaglandin E2 (PGE2).ResultsBES obtained from both COPD and non-COPD patients were characterized by a polarized bronchial epithelium with tight junctions and ciliary beating, composed of basal cells, secretory cells and ciliated cells. The ciliary beat frequency of ciliated cells was not significantly different between the two groups. Of interest, BES retained their characteristic features in culture up to 8 days. BES released the inflammatory mediators IL-8, PGE2 and LTB4 constitutively and following exposure to LPS. Interestingly, LPS induced a higher release of IL-8, but not PGE2 and LTB4 in COPD BES (p < 0.001) which correlated with lung function changes.ConclusionThis study provides for the first time a compelling evidence that the BES model provides an unaltered bronchial surface epithelium. More importantly, BES represent an attractive culture model to investigate the mechanisms of injuring agents that mediate epithelial cell inflammation and its contribution to COPD pathogenesis.
Epidermal growth factor potentiates in vitro metastatic behaviour of human prostate cancer PC-3M cells: involvement of voltage-gated sodium channel
Authors: Uysal-Onganer Pinar , Djamgoz Mustafa BA 
Published: November 2007

Abstract

Background
Although a high level of functional voltage-gated sodium channel (VGSC) expression has been found in strongly metastatic human and rat prostate cancer (PCa) cells, the mechanism(s) responsible for the upregulation is unknown. The concentration of epidermal growth factor (EGF), a modulator of ion channels, in the body is highest in prostatic fluid. Thus, EGF could be involved in the VGSC upregulation in PCa. The effects of EGF on VGSC expression in the highly metastatic human PCa PC-3M cell line, which was shown previously to express both functional VGSCs and EGF receptors, were investigated. A quantitative approach, from gene level to cell behaviour, was used. mRNA levels were determined by real-time PCR. Protein expression was studied by Western blots and immunocytochemistry and digital image analysis. Functional assays involved measurements of transverse migration, endocytic membrane activity and Matrigel invasion.

Results
Exogenous EGF enhanced the cells' in vitro metastatic behaviours (migration, endocytosis and invasion). Endogenous EGF had a similar involvement. EGF increased VGSC Nav1.7 (predominant isoform in PCa) mRNA and protein expressions. Co-application of the highly specific VGSC blocker tetrodotoxin (TTX) suppressed the effect of EGF on all three metastatic cell behaviours studied.

Conclusion
1) EGF has a major involvement in the upregulation of functional VGSC expression in human PCa PC-3M cells. (2) VGSC activity has a significant intermediary role in potentiating effect of EGF in human PCa.
Dynacortin facilitates polarization of chemotaxing cells
Authors: Kabacoff Cathryn , Xiong Yuan , Musib Runa , Reichl Elizabeth M , Kim John , Iglesias Pablo A , Robinson Douglas N 
Published: November 2007

Abstract

Background

Cell shape changes during cytokinesis and chemotaxis require regulation of the actin cytoskeletal network. Dynacortin, an actin cross-linking protein, localizes to the cell cortex and contributes to cortical resistance, thereby helping to define the cell shape changes of cytokinesis. Dynacortin also becomes highly enriched in cortical protrusions, which are sites of new actin assembly.

Results

We studied the effect of dynacortin on cell motility during chemotaxis and on actin dynamics in vivo and in vitro. Dynacortin enriches with the actin, particularly at the leading edge of chemotaxing cells. Cells devoid of dynacortin do not become as polarized as wild-type control cells but move with similar velocities as wild-type cells. In particular, they send out multiple pseudopods that radiate at a broader distribution of angles relative to the chemoattractant gradient. Wild-type cells typically only send out one pseudopod at a time that does not diverge much from 0° on average relative to the gradient. Though dynacortin-deficient cells show normal bulk (whole-cell) actin assembly upon chemoattractant stimulation, dynacortin can promote actin assembly in vitro. By fluorescence spectroscopy, co-sedimentation and transmission electron microscopy, dynacortin acts as an actin scaffolder in which it assembles actin monomers into polymers with a stoichiometry of 1 Dyn2:1 actin under salt conditions that disfavor polymer assembly.

Conclusion

Dynacortin contributes to cell polarization during chemotaxis. By cross-linking and possibly stabilizing actin polymers, dynacortin also contributes to cortical viscoelasticity, which may be critical for establishing cell polarity. Though not essential for directional sensing or motility, dynacortin is required to establish cell polarity, the third core feature of chemotaxis.
Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach
Authors: Frabetti Flavia , Casadei Raffaella , Lenzi Luca , Canaider Silvia , Vitale Lorenza , Facchin Federica , Carinci Paolo , Zannotti Maria , Strippoli Pierluigi 
Published: November 2007

Abstract

Background
All standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. The aim of this work was to estimate mRNA open reading frame (ORF) 5' region sequence completeness in the model organism Danio rerio (zebrafish).

Results
We implemented a novel automated approach (5'_ORF_Extender) that systematically compares available expressed sequence tags (ESTs) with all the zebrafish experimentally determined mRNA sequences, identifies additional sequence stretches at 5' region and scans for the presence of all conditions needed to define a new, extended putative ORF. Our software was able to identify 285 (3.3%) mRNAs with putatively incomplete ORFs at 5' region and, in three example cases selected (selt1a, unc119.2, nppa), the extended coding region at 5' end was cloned by reverse transcription-polymerase chain reaction (RT-PCR).

Conclusion
The implemented method, which could also be useful for the analysis of other genomes, allowed us to describe the relevance of the "5' end mRNA artifact" problem for genomic annotation and functional genomic experiment design in zebrafish.

Open peer review
This article was reviewed by Alexey V. Kochetov (nominated by Mikhail Gelfand), Shamil Sunyaev, and Gáspár Jékely. For the full reviews, please go to the Reviewers' Comments section.
Tissue is the issue-sarcoidosis following ABVD chemotherapy for Hodgkin's lymphoma: a case report
Authors: Subbiah Vivek , Ly Uyen K , Khiyami Amer , O'Brien Timothy 
Published: November 2007

Abstract
Thirty two year old Caucasian female presented 2 months post partum with fevers, cough and shortness of breath. CT scan of the chest to rule out pulmonary embolism revealed mediastinal lymphadenopathy. Biopsy of the nodes revealed classic Hodgkin's lymphoma and she received ABVD chemotherapy. She was in remission as confirmed by a PET/CT scan. Five months later she had another PET/CT scan which showed areas of hypermetabolism indicating a possible relapse. Biopsy revealed sarcoidosis. She received steroids and 18 months later remained in clinical remission. This rare case of sarcoid following classic Hodgkin's lymphoma illustrates that clinical presentation, physical exam, lab investigations and even PET/CT scans may not be able to discriminate between Hodgkin's lymphoma and sarcoidosis. Tissue biopsy and pathological diagnosis remain the gold standard.
Utilization of Nanometre-order Diameter Columns inside Porous Anodic Alumina for Chromatography Chip System
Authors: Yamashita Tomohisa , Kodama Shuji , Ohto Mikiya , Nakayama Eriko , Kemmei Tomoko , Muramoto Tatsuya , Yamaguchi Akira , Teramae Norio , Takayanagi Nobutaka 
Published: November 2007

Abstract
Porous anodic alumina (PAA) membranes were used as a nanometre-order diameter column for chromatography chip with acetonitrile–water mobile phase using gradient elution. In a chromatogram, 9-anthracenemethanol (AM), 9-anthracenecarboxylic acid (AC), and dansyl–glycine (DG) showed different retention times, indicating that PAA membranes are applicable to stationary phase for chromatography chip.
Synthesis, Structural Characterization, and Photolysis of Dibenzodehydro[16]annulenes Containing E–E σ Bonds (E = Si and Ge)
Authors: Mochida Kunio , Ohto Junichi , Masuda Matsuri , Nanjo Masato , Arii Hidekazu , Nakadaira Yasuhiro 
Published: November 2007

Abstract
Dibenzodehydro[16]annulenes containing silicon–silicon and germanium–germanium σ bonds were newly prepared, and their structures were established by spectroscopic methods and X-ray diffraction analysis. On the photolysis, these sila- and germa-cycles evolve the corresponding divalent species, silylene and germylene, respectively, and in addition, the germanes led to the ring contraction to give a fourteen-membered germacycle.
FloorScore—Flooring Products Certification Program for Indoor Air Quality
Authors: Freeman William H. 
Published: November 2007

Abstract
The purpose of this paper is to provide information on the development of a volatile organic compound (VOC) emissions testing program for hard surface floor covering products. After providing historical information on the development of VOC emissions testing programs for interior finishes, the paper discusses the factors considered and steps taken by the Resilient Floor Covering Institute (RFCI) to design the FloorScore Indoor Air Quality (IAQ) Certification Program.