bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Genetic and Phenotypic Diversity of Invasive Nontypeable
Haemophilus influenzae
Authors: Erwin Alice L. , Nelson Kevin L. , Mhlanga-Mutangadura Tendai , Bonthuis Paul J. , Geelhood Jennifer L. , Morlin Gregory , Unrath William C. T. , Campos Jose , Crook Derrick W. , Farley Monica M. , Henderson Frederick W. , Jacobs Richard F. , Mühlemann Kathrin , Satola Sarah W. , van Alphen Loek , Golomb Miriam , Smith Arnold L. 
Published: August 2005

ABSTRACT

The ability of unencapsulated (nontypeable)
Haemophilus influenzae
(NTHi) to cause systemic disease in healthy children has been recognized only in the past decade. To determine the extent of similarity among invasive nontypeable isolates, we compared strain R2866 with 16 additional NTHi isolates from blood and spinal fluid, 17 nasopharyngeal or throat isolates from healthy children, and 19 isolates from middle ear aspirates. The strains were evaluated for the presence of several genetic loci that affect bacterial surface structures and for biochemical reactions that are known to differ among
H. influenzae
strains. Eight strains, including four blood isolates, shared several properties with R2866: they were biotype V (indole and ornithine decarboxylase positive, urease negative), contained sequence from the adhesin gene
hia
, and lacked a genetic island flanked by the
infA
and
ksgA
genes. Multilocus sequence typing showed that most biotype V isolates belonged to the same phylogenetic cluster as strain R2866. When present, the
infA-ksgA
island contains lipopolysaccharide biosynthetic genes, either
lic2B
and
lic2C
or homologs of the
losA
and
losB
genes described for
Haemophilus ducreyi
. The island was found in most nasopharyngeal and otitis isolates but was absent from 40% of invasive isolates. Overall, the 33
hmw
-negative isolates were much more likely than
hmw
-containing isolates to have tryptophanase, ornithine decarboxylase, or lysine decarboxylase activity or to contain the
hif
genes. We conclude (i) that invasive isolates are genetically and phenotypically diverse and (ii) that certain genetic loci of NTHi are frequently found in association among NTHi strains.
Characterization of the
dapA
-
nlpB
Genetic Locus Involved in Regulation of Swarming Motility, Cell Envelope Architecture, Hemolysin Production, and Cell Attachment Ability in
Serratia marcescens
Authors: Soo Po-Chi , Wei Jun-Rong , Horng Yu-Tze , Hsieh Shang-Chen , Ho Shen-Wu , Lai Hsin-Chih 
Published: August 2005

ABSTRACT

Swarming migration of
Serratia marcescens
requires both flagellar motility and cellular differentiation and is a population-density-dependent behavior. While the
flhDC
and quorum-sensing systems have been characterized as important factors regulating
S. marcescens
swarming, the underlying molecular mechanisms are currently far from being understood.
Serratia
swarming is thermoregulated and is characterized by continuous surface migration on rich swarming agar surfaces at 30°C but not at 37°C. To further elucidate the mechanisms, identification of specific and conserved regulators that govern the initiation of swarming is essential. We performed transposon mutagenesis to screen for
S. marcescens
strain CH-1 mutants that swarmed at 37°C. Analysis of a “precocious-swarming” mutant revealed that the defect in a conserved

dapA
Sm

-nlpB
Sm

genetic locus which is closely related to the synthesis of bacterial cell wall peptidoglycan is responsible for the aberrant swarming phenotype. Further complementation and gene knockout studies showed that

nlpB
Sm

, which encodes a membrane lipoprotein, NlpB

Sm

, but not

dapA
Sm

, is specifically involved in swarming regulation. On the other hand,

dapA
Sm

but not

nlpB
Sm

is responsible for the determination of cell envelope architecture, regulation of hemolysin production, and cellular attachment capability. While the

nlpB
Sm

mutant showed similar cytotoxicity to its parent strain, the

dapA
Sm

mutant significantly increased in cytotoxicity. We present evidence that DapA

Sm

is involved in the determination of cell-envelope-associated phenotypes and that NlpB

Sm

is involved in the regulation of swarming motility.
Anti-LcrV Antibody Inhibits Delivery of Yops by
Yersinia pestis
KIM5 by Directly Promoting Phagocytosis
Authors: Cowan Clarissa , Philipovskiy Alexander V. , Wulff-Strobel Christine R. , Ye Zhan , Straley Susan C. 
Published: August 2005

ABSTRACT

LcrV of
Yersinia pestis
is a major protective antigen proposed for inclusion in subunit plague vaccines. One way that anti-LcrV antibody is thought to protect is by inhibiting the delivery of toxins called Yops to host cells. The present study characterizes the relation between this inhibition and the phagocytosis of the bacteria. J774A.1 cells were infected with
Y. pestis
KIM5 in the presence of a protective polyclonal anti-LcrV antibody or a nonprotective polyclonal anti-YopM antibody, and delivery of YopH and YopE into the cytoplasm was assayed by immunoblotting. The ability to inhibit the delivery of these Yops depended upon having antibody bound to the cell surface; blocking conditions that prevented the binding of antibody to Fc receptors prevented the inhibition of Yop delivery. Anti-LcrV antibody also promoted phagocytosis of the yersiniae, whereas F(ab′)
2
fragments did not. Further, anti-LcrV antibody could not inhibit the delivery of Yops into cells that were unable to phagocytose due to the presence of cytochalasin D. However, Yops were produced only by extracellular yersiniae. We hypothesize that anti-LcrV antibody does not directly inhibit Yop delivery but instead causes phagocytosis, with consequent inhibition of Yop protein production in the intracellular yersiniae. The prophagocytic effect of anti-LcrV antibody extended to mouse polymorphonuclear neutrophils (PMNs) in vitro, and PMNs were shown to be critical for protection: when PMNs in mice were ablated, the mice lost all ability to be protected by anti-LcrV antibody.
Gene Expression Profile Analysis of
Porphyromonas gingivalis
during Invasion of Human Coronary Artery Endothelial Cells
Authors: Rodrigues Paulo H. , Progulske-Fox Ann 
Published: August 2005

ABSTRACT

Microarrays were used to identify genes of
Porphyromonas gingivalis
W83 differentially expressed during invasion of primary human coronary artery endothelial cells. Analyses of microarray images indicated that 62 genes were differentially regulated. Of these, 11 genes were up-regulated and 51 were down-regulated. The differential expression of 16 selected genes was confirmed by real-time PCR.
Analysis of Cellular Phenotypes That Mediate Genetic Resistance to Tuberculosis Using a Radiation Bone Marrow Chimera Approach
Authors: Majorov Konstantin B. , Eruslanov Evgeny B. , Rubakova Elvira I. , Kondratieva Tatiana K. , Apt Alexander S. 
Published: August 2005

ABSTRACTAdoptive transfer of bone marrow cells from tuberculosis-resistant (I/St × A/Sn)F1donor mice into lethally irradiated susceptible I/St recipients changed their phenotype following infection with virulentMycobacterium tuberculosis. Compared to I/St→I/St control animals, F1→I/St chimeras demonstrated (i) prolonged survival time, (ii) increased antimycobacterial function of lung macrophages, (iii) elevated gamma interferon production by lung cells, and (iv) decreased infiltration of the lungs with CD4+and CD8+T cells and Ly-6G+neutrophils.
Measurements of Ocean Surface Backscattering Using an Airborne 94-GHz Cloud Radar—Implication for Calibration of Airborne and Spaceborne W-Band Radars
Authors: Li Lihua , Heymsfield Gerald M. , Tian Lin , Racette Paul E. 
Published: August 2005

AbstractBackscattering properties of the ocean surface have been widely used as a calibration reference for airborne and spaceborne microwave sensors. However, at millimeter-wave frequencies, the ocean surface backscattering mechanism is still not well understood, in part, due to the lack of experimental measurements. During the Cirrus Regional Study of Tropical Anvils and Cirrus Layers-Florida Area Cirrus Experiment (CRYSTAL-FACE), measurements of ocean surface backscattering were made using a 94-GHz (W band) cloud radar on board a NASA ER-2 high-altitude aircraft. This unprecedented dataset enhances our knowledge about the ocean surface scattering mechanism at 94 GHz. The measurement set includes the normalized ocean surface cross section over a range of the incidence angles under a variety of wind conditions. It was confirmed that even at 94 GHz, the normalized ocean surface radar cross section, σo, is insensitive to surface wind conditions near a 10° incidence angle, a finding similar to what has been found in the literature for lower frequencies. Analysis of the radar measurements also shows good agreement with a quasi-specular scattering model at low incidence angles. The results of this work support the proposition of using the ocean surface as a calibration reference for airborne millimeter-wave cloud radars and for the ongoing NASA CloudSat mission, which will use a 94-GHz spaceborne cloud radar for global cloud measurements.
Numerical and Physical Diffusion: Can Wave Prediction Models Resolve Directional Spread?
Authors: Ardhuin F. , Herbers T. H. C. 
Published: August 2005

Abstract
A new semi-Lagrangian advection scheme called multistep ray advection is proposed for solving the spectral energy balance equation of ocean surface gravity waves. Existing so-called piecewise ray methods advect wave energy over a single time step using “pieces” of ray trajectories, after which the spectrum is updated with source terms representing various physical processes. The generalized scheme presented here allows for an arbitrary number N of advection time steps along the same rays, thus reducing numerical diffusion, and still including source-term variations every time step. Tests are performed for alongshore uniform bottom topography, and the effects of two types of discretizations of the wave spectrum are investigated, a finite-bandwidth representation and a single frequency and direction per spectral band. In the limit of large N, both the accuracy and computation cost of the method increase, approaching a nondiffusive fully Lagrangian scheme. Even for N = 1 the semi-Lagrangian scheme test results show less numerical diffusion than predictions of the commonly used first-order upwind finite-difference scheme. Application to the refraction and shoaling of narrow swell spectra across a continental shelf illustrates the importance of controlling numerical diffusion. Numerical errors in a single-step (Δt = 600 s) scheme implemented on the North Carolina continental shelf (typical swell propagation time across the shelf is about 3 h) are shown to be comparable to the angular diffusion predicted by the wave–bottom Bragg scattering theory, in particular for narrow directional spectra, suggesting that the true directional spread of swell may not always be resolved in existing wave prediction models, because of excessive numerical diffusion. This diffusion is effectively suppressed in cases presented here with a four-step semi-Lagrangian scheme, using the same value of Δt.
The Atmospheric Radiation Measurement Program Cloud Profiling Radars: An Evaluation of Signal Processing and Sampling Strategies
Authors: Kollias Pavlos , Albrecht Bruce A. , Clothiaux Eugene E. , Miller Mark A. , Johnson Karen L. , Moran Kenneth P. 
Published: August 2005

Abstract
The U.S. Department of Energy (DOE) Atmospheric Radiation Measurements (ARM) program operates millimeter-wavelength cloud radars (MMCRs) in several specific locations within different climatological regimes. These vertically pointing cloud profiling radars supply the three most important Doppler spectrum moment estimates, which are the radar reflectivity (or zero moment), the mean Doppler velocity (or first moment), and the Doppler spectrum width (or second moment), as a function of time and height. The ARM MMCR Doppler moment estimates form the basis of a number of algorithms for retrieving cloud microphysical and radiative properties. The retrieval algorithms are highly sensitive to the quality and accuracy of the MMCR Doppler moment estimates. The significance of these sensitivities should not be underestimated, because the inherent physical variability of clouds, instrument-induced noise, and sampling strategy limitations all potentially introduce errors into the Doppler moment estimates. In this article, the accuracies of the first three Doppler moment estimates from the ARM MMCRs are evaluated for a set of typical cloud conditions from the three DOE ARM program sites. Results of the analysis suggest that significant errors in the Doppler moment estimates are possible in the current configurations of the ARM MMCRs. In particular, weakly reflecting clouds with low signal-to-noise ratios (SNRs), as well as turbulent clouds with nonzero updraft and downdraft velocities that are coupled with high SNR, are shown to produce degraded Doppler moment estimates in the current ARM MMCR operational mode processing strategies. Analysis of the Doppler moment estimates and MMCR receiver noise characteristics suggests that the introduction of a set of quality control criteria is necessary for identifying periods of degraded receiver performance that leads to larger uncertainties in the Doppler moment estimates. Moreover, the temporal sampling of the ARM MMCRs was found to be insufficient for representing the actual dynamical states in many types of clouds, especially boundary layer clouds. New digital signal processors (DSPs) are currently being developed for the ARM MMCRs. The findings presented in this study will be used in the design of a new set of operational strategies for the ARM MMCRs once they have been upgraded with the new DSPs.
Measurement of Wind Waves and Wave-Coherent Air Pressures on the Open Sea from a Moving SWATH Vessel
Authors: Donelan Mark A. , Dobson Fred W. , Graber Hans C. , Madsen Niels , McCormick Cyril 
Published: August 2005

Abstract
The design and implementation on a Small Waterline Area Twin Hull (SWATH) vessel of a complete system for measuring the directional distribution of wind waves and the concomitant fluctuations of air pressure and wind speed immediately above them are described. Data taken with the system on board the Canadian Coast Guard Ship Frederick G. Creed during the 1999 Shoaling Waves Experiment (SHOWEX) are used to calculate the wave-supported fluxes of momentum and energy between the air and the sea.
Métissage and Bricolage in the Making of African Christian Identities
Authors: Mary André 
Published: August 2005

English Métissage, bricolage, or hybridizing - the argument continues over the appropriateness of metaphors in the study of contemporary religious productions, and we are invited to question and confront the dialectical or "dialogical" processes which are at work in the appropriation of differences, and the handling of disputes which are part of these processes. A detour by way of all that is involved in the Christian invention of African identities, all that individuals and groups have invested in that invention, the remnant of the colonial encounter, all this contributes to the comparisons which are made in the present writing, and to its conclusions. When we speak of the post-modern re-enchantment with métissage, with its subversive transgressions exemplified by hybridization, or of our fascination with a vanishing bricolage which now is breaking up into simple collage, we may regret the way in which the fecundity of misunderstandings inherent in any encounter has been cancelled, and especially the ambivalent postures which beset the worlds of cultural mixture, and which contribute to their instability. French Métissage, bricolage ou hybridité, la dispute sur les métaphores dans l'approche des productions religieuses contemporaines invite à questionner et à confronter les processus dialectiques ou dialogiques qui sont à l'oeuvre dans l'appropriation des différences et la gestion des différends. Le détour par les enjeux de l'invention chrétienne des identités africaines au coeur de la rencontre coloniale nourrit la comparaison et les conclusions de cet article. Dans le ré-enchantement postmoderne des métissages, les transgressions subversives de l'hybridité ou dans l'éloge d'un bricolage qui dérive en simples collages, on peut regretter la manière dont se trouvent évacuées la fécondité des malentendus inhérents à toute rencontre et surtout les ambivalences de posture qui travaillent les mondes meêlés et entretiennent leur instabilité.
Coming to Terms with the Past: Religion and Identity in Wales
Authors: Chambers Paul , Thompson Andrew 
Published: August 2005

English The authors examine how Wales, a country in which, historically, national and religious identities were closely related, has been transformed by a process of secularization, and more recently by migration and political change. Recent discussions of change in Wales, however, have paid scant attention to the contemporary place of religions in Welsh society. Religion, if it is considered at all, is largely consigned to the past. The purpose of this paper is twofold. Firstly, we consider the changing nature of religion in Wales. In doing so, we draw on interviews with 40 representatives of faith groups to examine the public salience of religion in a society that might be characterized as post-Christian. Secondly, we explore the contemporary relationship between religion and national identity. French Les auteurs examinent comment le Pays de Galles, une région dans laquelle historiquement les identités nationale et religieuse étaient étroitement liées, a été traversé et transformé par un processus de sécularisation, et plus récemment par les migrations et un changement politique. Les récents débats portant sur le changement ont accordé peu d'attention à la place que tiennent aujourd'hui les religions dans la société galloise et la religion, lorsqu'on en parle, est généralement considérée comme un élément du passé. L'objectif de cet article est tout d'abord de traiter de l'évolution de la nature de la religion dans cette région. Pour ce faire, une quarantaine d'entretiens ont été réalisés avec des représentants de groupes de croyants pour y étudier l'importance de la religion dans la sphère publique d'une société qui pourrait être qualifiée de post-chrétienne. Est explorée ensuite la relation contemporaine qui existe entre la religion et l'identité nationale.
High-throughput scanning of breast tumor surgical specimens for low-level mutations
Authors: Wang Fengfei , Kaur Manjit , Liu Wei-Hua , Zhu Penny , Li Jin , Wang Lilin , Makrigiorgos G. Mike 
Published: August 2005

AbstractLarge numbers of mutations are postulated to occur as early events in carcinogenesis. For certain types of human tumors (mutator phenotypes) these mutations can be a driving force in generating clonogenic, causative genetic changes leading to multistage carcinogenesis. These low-level mutational events are highly significant due to their potential use as molecular markers for early identification of genomic instability that can lead to cancer and to their potential influence on the ability of tumors to resist drug treatment and/or metastasize. Detecting the presence and diversity of such genetic changes in human tumors is desirable due to their potential prognostic value. However, identification of these low-frequency genetic changes is difficult, since most mutations exist at mutant/wild-type ratios of <10
Cardiovascular risk-associated allele frequencies for 15 genes in healthy elderly French and Chinese
Authors: Xia Yongjing , Baum Larry , Pang C. P. , Siest Gérard , Visvikis Sophie 
Published: August 2005

AbstractIn order to investigate possible ethnic differences in genetic and environmental determinants, we investigated several cardiovascular disease-associated genetic variations in successful ageing populations of France (Nancy) and China (Hong Kong). Allelic frequencies of these genetic variations were compared between healthy elderly Chinese (n=103) and French populations (n=100). A multi-locus assay was used to genotype 15 genes for 29 biallelic sites, genes implicated in lipid and homocysteine metabolism, thrombosis, leukocyte adhesion, and blood pressure regulation. For most of the candidate markers within lipid metabolism genes, the less frequent alleles were more common in the Chinese population compared with the French population, while the less frequent alleles of the majority of the other markers were detected only or more commonly in the French population. In conclusion, polymorphisms in 13 genes exhibited statistically significant differences in allelic frequencies between the two populations. Since the two populations were selected as examples of successful ageing, we could hypothesise that genetic factors that could play a role in a successful ageing process may be different between the two populations.
Development, validation and evaluation of a homogenous one-step reverse transcriptase-initiated PCR assay with competitive internal control for the detection of hepatitis C virus RNA
Authors: Mueller Jens , Gessner Matthias , Remberg Anja , Hoch Jochen , Zerlauth Gerold , Hanfland Peter 
Published: August 2005

AbstractNucleic acid amplification testing for hepatitis C virus (HCV) RNA has become an essential tool for the prevention and clinical management of hepatitis C. We describe the development, validation and evaluation of a homogenous reverse transcriptase-initiated HCV-PCR assay with competitive internal control that is applicable to both the quantitative detection of HCV genomes in single patient samples and the screening of blood donations by mini-pool testing. For the implementation of a positive run control, a HCV RNA-positive plasma sample was calibrated against an international HCV RNA standard preparation. For quantification purposes, an in vitro-transcribed RNA calibrator sequence was used. The detection limit of the assay (95% positive cut-off) was determined by probit analysis and was calculated as 114IU/mL. Comparable sensitivity to different HCV template sequences was verified for HCV genotypes 1–5. Quantitative test results correlated well with viral loads that had been previously determined by the Bayer VERSANT HCV RNA 3.0 bDNA assay (n=53, R=0.943, p<0.001). During more than 5years of blood donation testing, the specificity of the assay was found to be 99.51%. All assay components showed constant performance during this time period. In conclusion, we introduce a well-proven method that allows fast and reliable quantification of HCV genomes.
Preliminary evaluation of the performance of a new, highly sensitive commercial immunoassay for serum ferritin determination
Authors: Signò Paolo , Barassi Alessandra , Novario Raffaele , Melzi d'Eril Gian Vico 
Published: August 2005

AbstractWe evaluated the analytical performance of a new, commercial, fully automated immunoturbidimetric assay for the determination of ferritin [FER-Latex(X2)CN SEIKEN, Denka Seiken, Japan] in serum on the Olympus AU2700 analyzer. The new assay is a latex-enhanced turbidimetric immunoassay with an analysis time of 10min. The linearity of the assay was confirmed up to 2505pmol/L (R