bluuebunny/crossref_metadata_2025_split huggingface dataset:
LcrV Plague Vaccine with Altered Immunomodulatory Properties
Authors: Overheim Katie A. , DePaolo R. William , DeBord Kristin L. , Morrin Elizabeth M. , Anderson Debra M. , Green Nathaniel M. , Brubaker Robert R. , Jabri Bana , Schneewind Olaf 
Published: July 2005

ABSTRACTYersinia pestis, the causative agent of plague, secretes LcrV (low-calcium-response V or V antigen) during infection. LcrV triggers the release of interleukin 10 (IL-10) by host immune cells and suppresses proinflammatory cytokines such as tumor necrosis factor alpha and gamma interferon as well as innate defense mechanisms required to combat the pathogenesis of plague. Although immunization of animals with LcrV elicits protective immunity, the associated suppression of host defense mechanisms may preclude the use of LcrV as a human vaccine. Here we show that short deletions within LcrV can reduce its immune modulatory properties. An LcrV variant lacking amino acid residues 271 to 300 (rV10) elicited immune responses that protected mice against a lethal challenge withY. pestis. Compared to full-length LcrV, rV10 displayed a reduced ability to release IL-10 from mouse and human macrophages. Furthermore, the lipopolysaccharide-stimulated release of proinflammatory cytokines by human or mouse macrophages was inhibited by full-length LcrV but not by the rV10 variant. Thus, it appears that LcrV variants with reduced immune modulatory properties could be used as a human vaccine to generate protective immunity against plague.
Cytokine and Chemokine Responses Associated with Clearance of a Primary
Salmonella enterica
Serovar Typhimurium Infection in the Chicken and in Protective Immunity to Rechallenge
Authors: Withanage G. S. K. , Wigley Paul , Kaiser Pete , Mastroeni Pietro , Brooks Heather , Powers Claire , Beal Richard , Barrow Paul , Maskell Duncan , McConnell Ian 
Published: July 2005

ABSTRACT

Infection of poultry with
Salmonella enterica
serovar Typhimurium poses a significant risk to public health through contamination of meat from infected animals. Vaccination has been proposed to control infections in chickens. However, the vaccines are currently largely empirical, and our understanding of the mechanisms that underpin immune clearance and protection in avian salmonellosis is not complete. In this study we describe the cytokine, chemokine, and antibody responses and cellular changes in primary and secondary infections of chickens with
Salmonella
serovar Typhimurium. Infection of 1-week-old chickens induced early expression of a macrophage inflammatory protein (MIP) family chemokine in the spleen and liver, followed by increased expression of gamma interferon accompanied by increased numbers of both CD4
+
and CD8
+
T cells and the formation of granuloma-like follicular lesions. This response correlated with a Th1-mediated clearance of the systemic infection. Primary infection also induced specific immunoglobulin M (IgM), IgG, and IgA antibody responses. In contrast to previously published studies performed with newly hatched chicks, the expression levels of proinflammatory cytokines in the gastrointestinal tract were not greatly increased following infection. However, significant expression of the anti-inflammatory cytokine transforming growth factor β4 was detected in the gut early in infection. Following secondary challenge, the birds were fully protected against systemic infection and showed a high level of protection against gastrointestinal colonization. Rapid expression of the MIP family chemokine and interleukin-6 was detected in the guts of these birds and was accompanied by an influx of lymphocytes. Increased levels of serum IgA-specific antibodies were also found following rechallenge. These findings suggest that cellular responses, particularly Th1 responses, play a crucial role in immune clearance in avian salmonellosis and that protection against rechallenge involves the rapid recruitment of cells to the gastrointestinal tract. Additionally, the high levels of inflammatory response found following
Salmonella
serovar Typhimurium infection of newly hatched chicks were not observed following infection of older birds (1 week old), in which the expression of regulatory cytokines appeared to limit inflammation.
Staphylococcus aureusPeptidoglycan Is a Toll-Like Receptor 2 Activator: a Reevaluation
Authors: Dziarski Roman , Gupta Dipika 
Published: July 2005

ABSTRACTSince the ability of peptidoglycan (PGN) to activate Toll-like receptor 2 (TLR2) was recently questioned, we reevaluated activation of TLR2 by PGN. Polymeric soluble or insolubleStaphylococcus aureusPGN, repurified by sodium dodecyl sulfate or phenol extraction, activated TLR2 at 0.1 to 1 or 10 μg/ml, respectively, and induced tumor necrosis factor alpha production. The TLR2 activation by PGN, but not by lipoteichoic acid, was abolished by muramidase digestion. We conclude that polymericS. aureusPGN is a TLR2 activator.
Selective Capture ofSalmonella entericaSerovar Typhi Genes Expressed in Macrophages That Are Absent from theSalmonella entericaSerovar Typhimurium Genome
Authors: Faucher Sébastien P. , Curtiss Roy , Daigle France 
Published: July 2005

ABSTRACTThirty-sixSalmonella entericaserovar Typhi-specific genes, absent from theSalmonella entericaserovar Typhimurium genome, that were expressed in human macrophages were identified by selective capture of transcribed sequences. These genes are located on 15 unique loci of the serovar Typhi genome, includingSalmonellapathogenicity islands (SPI-7, SPI-8, and SPI-10) and bacteriophages (ST15, ST18, and ST35).
Investigation of Oxidative Stress Defenses of
Neisseria gonorrhoeae
by Using a Human Polymorphonuclear Leukocyte Survival Assay
Authors: Seib Kate L. , Simons Mark P. , Wu Hsing-Ju , McEwan Alastair G. , Nauseef William M. , Apicella Michael A. , Jennings Michael P. 
Published: July 2005

ABSTRACT

Neisseria gonorrhoeae
has well-characterized oxidative stress defense systems that protect against oxidative killing in in vitro assays. In contrast, mutant strains of
N. gonorrhoeae
lacking oxidative stress defenses are identical to the wild type when tested in an ex vivo survival assay using human polymorphonuclear leukocytes.
The Retrieval of Ice-Cloud Properties from Cloud Radar and Lidar Synergy
Authors: Tinel Claire , Testud Jacques , Pelon Jacques , Hogan Robin J. , Protat Alain , Delanoë Julien , Bouniol Dominique 
Published: July 2005

Abstract
Clouds are an important component of the earth’s climate system. A better description of their microphysical properties is needed to improve radiative transfer calculations. In the framework of the Earth, Clouds, Aerosols, and Radiation Explorer (EarthCARE) mission preparation, the radar–lidar (RALI) airborne system, developed at L’Institut Pierre Simon Laplace (France), can be used as an airborne demonstrator. This paper presents an original method that combines cloud radar (94–95 GHz) and lidar data to derive the radiative and microphysical properties of clouds. It combines the apparent backscatter reflectivity from the radar and the apparent backscatter coefficient from the lidar. The principle of this algorithm relies on the use of a relationship between the extinction coefficient and the radar specific attenuation, derived from airborne microphysical data and Mie scattering calculations. To solve radar and lidar equations in the cloud region where signals can be obtained from both instruments, the extinction coefficients at some reference range z0 must be known. Because the algorithms are stable for inversion performed from range z0 toward the emitter, z0 is chosen at the farther cloud boundary as observed by the lidar. Then, making an assumption of a relationship between extinction coefficient and backscattering coefficient, the whole extinction coefficient, the apparent reflectivity, cloud physical parameters, the effective radius, and ice water content profiles are derived. This algorithm is applied to a blind test for downward-looking instruments where the original profiles are derived from in situ measurements. It is also applied to real lidar and radar data, obtained during the 1998 Cloud Lidar and Radar Experiment (CLARE’98) field project when a prototype airborne RALI system was flown pointing at nadir. The results from the synergetic algorithm agree reasonably well with the in situ measurements.
Evaluation of Microphysical Retrievals from Polarimetric Radar with Wind Profiler Data
Authors: May Peter T. , Keenan Thomas D. 
Published: July 2005

Abstract
Polarimetric radar data have been used to produce microphysical classifications. This kind of analysis is run in a real-time mode from several research radars, including the C-band polarimetric (C-Pol) radar in Darwin, Australia. However, these classifications have had very little systematic evaluation with independent data. Using surface data is often difficult because of sampling issues, particularly for hail. The approach taken here is to use a combination of 50- and 920-MHz wind profiler estimates of rain and hail to provide validation data for the radar pixels over the profiler. The profilers also observe signals associated with lightning, and some comparisons are made between lightning occurrence and the radar measurements of graupel. The retrievals of hail–rain mixtures are remarkably robust; there are some issues regarding other microphysical classes, however, including difficulties in detecting melting snow layers in stratiform rain. These difficulties are largely due to the resampling of the radar volume data onto a grid and to poor separation of the snow classes.
Quantitative trait analysis of the development of pulmonary tolerance to inhaled zinc oxide in mice
Authors: Wesselkamper Scott C , Chen Lung Chi , Gordon Terry 
Published: July 2005

AbstractBackgroundIndividuals may develop tolerance to the induction of adverse pulmonary effects following repeated exposures to inhaled toxicants. Previously, we demonstrated that genetic background plays an important role in the development of pulmonary tolerance to inhaled zinc oxide (ZnO) in inbred mouse strains, as assessed by polymorphonuclear leukocytes (PMNs), macrophages, and total protein in bronchoalveolar lavage (BAL) phenotypes. The BALB/cByJ (CBy) and DBA/2J (D2) strains were identified as tolerant and non-tolerant, respectively. The present study was designed to identify candidate genes that control the development of pulmonary tolerance to inhaled ZnO.MethodsGenome-wide linkage analyses were performed on a CByD2F2 mouse cohort phenotyped for BAL protein, PMNs, and macrophages following 5 consecutive days of exposure to 1.0 mg/m3inhaled ZnO for 3 hours/day. A haplotype analysis was carried out to determine the contribution of each quantitative trait locus (QTL) and QTL combination to the overall BAL protein phenotype. Candidate genes were identified within each QTL interval using the positional candidate gene approach.ResultsA significant quantitative trait locus (QTL) on chromosome 1, as well as suggestive QTLs on chromosomes 4 and 5, for the BAL protein phenotype, was established. Suggestive QTLs for the BAL PMN and macrophage phenotypes were also identified on chromosomes 1 and 5, respectively. Analysis of specific haplotypes supports the combined effect of three QTLs in the overall protein phenotype. Toll-like receptor 5 (Tlr5) was identified as an interesting candidate gene within the significant QTL for BAL protein on chromosome 1. Wild-derivedTlr5-mutant MOLF/Ei mice were tolerant to BAL protein following repeated ZnO exposure.ConclusionGenetic background is an important influence in the acquisition of pulmonary tolerance to BAL protein, PMNs, and macrophages following ZnO exposure. Promising candidate genes exist within the identified QTL intervals that would be good targets for additional studies, includingTlr5. The implications of tolerance to health risks in humans are numerous, and this study furthers the understanding of gene-environment interactions that are likely to be important factors from person-to-person in regulating the development of pulmonary tolerance to inhaled toxicants.
Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi
Authors: Nilsson R Henrik , Kristiansson Erik , Ryberg Martin , Larsson Karl-Henrik 
Published: July 2005

Abstract
Background
During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed.

Results
A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service http://emerencia.math.chalmers.se, users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available.

Discussion
The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases contain a thorough sampling of taxonomically well-annotated sequences. Taxonomy, held by some to be an old-fashioned trade, has accordingly never been more important. emerencia does not automate the taxonomic process, but it does allow researchers to focus their efforts elsewhere than countless manual BLAST runs and arduous sieving of BLAST hit lists. The emerencia system is available on an open source basis for local installation with any organism and gene group as targets.
Processing methods for differential analysis of LC/MS profile data
Authors: Katajamaa Mikko , Orešič Matej 
Published: July 2005

Abstract
Background
Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data.

Results
We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of Catharanthus roseus cell cultures.

Conclusion
The software is freely available under the GNU General Public License and it can be obtained from the project web page at: http://mzmine.sourceforge.net/.
Communication and re-use of chemical information in bioscience
Authors: Murray-Rust Peter , Mitchell John BO , Rzepa Henry S 
Published: July 2005

AbstractThe current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.
The missense mutation in Abcg5 gene in spontaneously hypertensive rats (SHR) segregates with phytosterolemia but not hypertension
Authors: Chen Jianliang , Batta Ashok , Zheng Shuqin , Fitzgibbon Wayne R , Ullian Michael E , Yu Hongwei , Tso Patrick , Salen Gerald , Patel Shailendra B 
Published: July 2005

Abstract

Background
Sitosterolemia is a recessively inherited disorder in humans that is associated with premature atherosclerotic disease. Mutations in ABCG5 or ABCG8, comprising the sitosterolemia locus, STSL, are now known to cause this disease. Three in-bred strains of rats, WKY, SHR and SHRSP, are known to be sitosterolemic, hypertensive and they carry a missense 'mutation' in a conserved residue of Abcg5, Gly583Cys. Since these rat strains are also know to carry mutations at other genetic loci and the extent of phytosterolemia is only moderate, it is important to verify that the mutations in Abcg5 are causative for phytosterolemia and whether they contribute to hypertension.

Methods
To investigate whether the missense change in Abcg5 is responsible for the sitosterolemia we performed a segregation analysis in 103 F2 rats from a SHR × SD cross. Additionally, we measured tail-cuff blood pressure and measured intestinal lipid transport to identify possible mechanisms whereby this mutation causes sitosterolemia.

Results
Segregation analysis showed that the inheritance of the Gly583Cys mutation Abcg5 segregated with elevated plant sterols and this pattern was recessive, proving that this genetic change is responsible for the sitosterolemia in these rat strains. Tail-cuff monitoring of blood pressure in conscious animals showed no significant differences between wild-type, heterozygous and homozygous mutant F2 rats, suggesting that this alteration may not be a significant determinant of hypertension in these rats on a chow diet.

Conclusion
This study shows that the previously identified Gly583Cys change in Abcg5 in three hypertension-susceptible rats is responsible for the sitosterolemia, but may not be a major determinant of blood pressure in these rats.
Impact of cryopreservation on tetramer, cytokine flow cytometry, and ELISPOT
Authors: Maecker Holden T , Moon James , Bhatia Sonny , Ghanekar Smita A , Maino Vernon C , Payne Janice K , Kuus-Reichel Kristine , Chang Jennie C , Summers Amanda , Clay Timothy M , Morse Michael A , Lyerly H Kim , DeLaRosa Corazon , Ankerst Donna P , Disis Mary L 
Published: July 2005

AbstractBackgroundCryopreservation of PBMC and/or overnight shipping of samples are required for many clinical trials, despite their potentially adverse effects upon immune monitoring assays such as MHC-peptide tetramer staining, cytokine flow cytometry (CFC), and ELISPOT. In this study, we compared the performance of these assays on leukapheresed PBMC shipped overnight in medium versus cryopreserved PBMC from matched donors.ResultsUsing CMV pp65 peptide pool stimulation or pp65 HLA-A2 tetramer staining, there was significant correlation between shipped and cryopreserved samples for each assay (p ≤ 0.001). The differences in response magnitude between cryopreserved and shipped PBMC specimens were not significant for most antigens and assays. There was significant correlation between CFC and ELISPOT assay using pp65 peptide pool stimulation, in both shipped and cryopreserved samples (p ≤ 0.001). Strong correlation was observed between CFC (using HLA-A2-restricted pp65 peptide stimulation) and tetramer staining (p < 0.001). Roughly similar sensitivity and specificity were observed between the three assays and between shipped and cryopreserved samples for each assay.ConclusionWe conclude that all three assays show concordant results on shipped versus cryopreserved specimens, when using a peptide-based readout. The assays are also concordant with each other in pair wise comparisons using equivalent antigen systems.
Inhibition of chemokine expression in rat inflamed paws by systemic use of the antihyperalgesic oxidized ATP
Authors: Fulgenzi Alessandro , Dell'Antonio Giacomo , Foglieni Chiara , Cin Elena Dal , Ticozzi Paolo , Franzone Josè S , Ferrero Maria Elena 
Published: July 2005

Abstract

Background
We previously showed that local use of periodate oxidized ATP (oATP, a selective inhibitor of P2X7 receptors for ATP) in rat paw treated with Freund's adjuvant induced a significant reduction of hyperalgesia Herein we investigate the role of oATP, in the rat paws inflamed by carrageenan, which mimics acute inflammation in humans.

Results
Local, oral or intravenous administration of a single dose of oATP significantly reduced thermal hyperalgesia in hind paws of rats for 24 hours, and such effect was greater than that induced by diclofenac or indomethacin. Following oATP treatment, the expression of the pro-inflammatory chemokines interferon-gamma-inducible protein-10 (IP-10), mon ocyte chemoattractant protein-1 (MCP-1) and interleukin-8 (IL-8) within the inflamed tissues markedly decreased on vessels and infiltrated cells. In parallel, the immunohistochemical findings showed an impairment, with respect to the untreated rats, in P2X7 expression, mainly on nerves and vessels close to the site of inflammation. Finally, oATP treatment significantly reduced the presence of infiltrating inflammatory macrophages in the paw tissue.

Conclusion
Taken together these results clearly show that oATP reduces carrageenan-induced inflammation in rats.