bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural basis for platelet collagen responses by the immune-type receptor glycoprotein VI
Authors: Horii Katsunori , Kahn Mark L. , Herr Andrew B. 
Published: April 2006

Abstract
Activation of circulating platelets by exposed vessel wall collagen is a primary step in the pathogenesis of heart attack and stroke, and drugs to block platelet activation have successfully reduced cardiovascular morbidity and mortality. In humans and mice, collagen activation of platelets is mediated by glycoprotein VI (GPVI), a receptor that is homologous to immune receptors but bears little sequence similarity to known matrix protein adhesion receptors. Here we present the crystal structure of the collagen-binding domain of human GPVI and characterize its interaction with a collagen-related peptide. Like related immune receptors, GPVI contains 2 immunoglobulin-like domains arranged in a perpendicular orientation. Significantly, GPVI forms a back-to-back dimer in the crystal, an arrangement that could explain data previously obtained from cell-surface GPVI inhibition studies. Docking algorithms identify 2 parallel grooves on the GPVI dimer surface as collagen-binding sites, and the orientation and spacing of these grooves precisely match the dimensions of an intact collagen fiber. These findings provide a structural basis for the ability of an immunetype receptor to generate signaling responses to collagen and for the development of GPVI inhibitors as new therapies for human cardiovascular disease.
Intravenous administration of activated protein C in Pseudomonas-induced lung injury: impact on lung fluid balance and the inflammatory response
Authors: Robriquet Laurent , Collet François , Tournoys Antoine , Prangère Thierry , Nevière Rémi , Fourrier François , Guery Benoît P 
Published: April 2006

Abstract

Background
Acute lung injury (ALI) induces a coagulation/fibrinolysis imbalance and leads to fibrin deposition. The protein C pathway is an important regulator of the coagulation system and reduces the inflammatory response. The aim of the study was to examine the effects of recombinant human activated protein C (rhAPC) in the early phase of Pseudomonas aeruginosa (Pa)-induced lung injury.

Methods
The study was conducted in vivo on a rat model of Pa-induced ALI. Continuous intravenous (IV) rhAPC was administrated simultaneously with intratracheal (IT) Pa. We instilled into the airspaces a 5% bovine albumin solution with 1 μ(Ci of 125 I-albumin and injected IV 1 μ(Ci of 111In-albumin to measure lung liquid clearance (LLC) and endothelial injury. Cytokines levels (TNFα and IL-6) and thrombin-antithrombin (TAT) complexes were measured in blood and bronchoalveolar lavage fluid (BALF) at 4 hours. Four groups were compared: control (CTR), pneumonia (PNP) receiving IT Pa (0.5 ml/kg of 1 × 109 cfu), APC: IV rhAPC (300 μg/kg/h), A-PNP: IT Pa /IV rhAPC.

Results
Alveolar-capillary permeability was increased in the PNP versus the CTR group (0.28 ± 0.08 vs. 0.03 ± 0.01, p < 0.05). IV rhAPC in Pa-induced ALI led to further injury (0.47 ± 0.17 vs. 0.28 ± 0.08, p = 0.2). The LLC was significantly decreased in the A-PNP group compared to PNP group (9.1 ± (4.3% vs. 33.4 ± 2.6%, p < 0.05). The lung wet to dry weight ratio was significantly increased in the PNP group (4.62 ± 0.31) compared to the CTR group (3.87 ± 0.22, p < 0.05). IV rhAPC administration tends to increase this parameter in Pa-induced ALI (5.80 ± 0.66, p = 0.07). These findings were associated with a loss of inflammatory response compartmentalization measured by TNFα and IL-6 systemic levels. TAT complexes in BALF were increased in the A-PNP group (23.17 ± 2.89 ng/ml) compared to the CTR group (0.92 ± 0.17 ng/ml, p < 0.05) and the PNP group (11.06 ± 2.76 ng/ml, p < 0.05).

Conclusion
rhAPC reduces LLC following Pa-induced ALI and may influence pulmonary edema formation. The early massive fibrin formation is probably beneficial in ALI limiting both the extent of injury and permeability disorders.
Expression of S100A8 correlates with inflammatory lung disease in congenic mice deficient of the cystic fibrosis transmembrane conductance regulator
Authors: Tirkos Sam , Newbigging Susan , Nguyen Van , Keet Mary , Ackerley Cameron , Kent Geraldine , Rozmahel Richard F 
Published: April 2006

AbstractBackgroundLung disease in cystic fibrosis (CF) patients is dominated by chronic inflammation with an early and inappropriate influx of neutrophils causing airway destruction. Congenic C57BL/6 CF mice develop lung inflammatory disease similar to that of patients. In contrast, lungs of congenic BALB/c CF mice remain unaffected. The basis of the neutrophil influx to the airways of CF patients and C57BL/6 mice, and its precipitating factor(s) (spontaneous or infection induced) remains unclear.MethodsThe lungs of 20-day old congenic C57BL/6 (before any overt signs of inflammation) and BALB/c CF mouse lines maintained in sterile environments were investigated for distinctions in the neutrophil chemokines S100A8 and S100A9 by quantitative RT-PCR and RNA in situ hybridization, that were then correlated to neutrophil numbers.ResultsThe lungs of C57BL/6 CF mice had spontaneous and significant elevation of both neutrophil chemokines S100A8 and S100A9 and a corresponding increase in neutrophils, in the absence of detectable pathogens. In contrast, BALB/c CF mouse lungs maintained under identical conditions, had similar elevations of S100A9 expression and resident neutrophil numbers, but diverged in having normal levels of S100A8.ConclusionThe results indicate early and spontaneous lung inflammation in CF mice, whose progression corresponds to increased expression of both S100A8 and S100A9, but not S100A9 alone. Moreover, since both C57BL/6 and BALB/c CF lungs were maintained under identical conditions and had similar elevations in S100A9 and neutrophils, the higher S100A8 expression in the former (or suppression in latter) is a result of secondary genetic influences rather than environment or differential infection.
Empirical validation of the S-Score algorithm in the analysis of gene expression data
Authors: Kennedy Richard E , Archer Kellie J , Miles Michael F 
Published: April 2006

Abstract

Background
Current methods of analyzing Affymetrix GeneChip® microarray data require the estimation of probe set expression summaries, followed by application of statistical tests to determine which genes are differentially expressed. The S-Score algorithm described by Zhang and colleagues is an alternative method that allows tests of hypotheses directly from probe level data. It is based on an error model in which the detected signal is proportional to the probe pair signal for highly expressed genes, but approaches a background level (rather than 0) for genes with low levels of expression. This model is used to calculate relative change in probe pair intensities that converts probe signals into multiple measurements with equalized errors, which are summed over a probe set to form the S-Score. Assuming no expression differences between chips, the S-Score follows a standard normal distribution, allowing direct tests of hypotheses to be made. Using spike-in and dilution datasets, we validated the S-Score method against comparisons of gene expression utilizing the more recently developed methods RMA, dChip, and MAS5.

Results
The S-score showed excellent sensitivity and specificity in detecting low-level gene expression changes. Rank ordering of S-Score values more accurately reflected known fold-change values compared to other algorithms.

Conclusion
The S-score method, utilizing probe level data directly, offers significant advantages over comparisons using only probe set expression summaries.
Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases
Authors: Schneider Georg , Neuberger Georg , Wildpaner Michael , Tian Sun , Berezovsky Igor , Eisenhaber Frank 
Published: April 2006

Abstract

Background
Manually finding subtle yet statistically significant links to distantly related homologues becomes practically impossible for very populated protein families due to the sheer number of similarity searches to be invoked and analyzed. The unclear evolutionary relationship between classical mammalian lipases and the recently discovered human adipose triglyceride lipase (ATGL; a patatin family member) is an exemplary case for such a problem.

Results
We describe an unsupervised, sensitive sequence segment collection heuristic suitable for assembling very large protein families. It is based on fan-like expanding, iterative database searches. To prevent inclusion of unrelated hits, additional criteria are introduced: minimal alignment length and overlap with starting sequence segments, finding starting sequences in reciprocal searches, automated filtering for compositional bias and repetitive patterns. This heuristic was implemented as FAMILYSEARCHER in the ANNIE sequence analysis environment and applied to search for protein links between the classical lipase family and the patatin-like group.

Conclusion
The FAMILYSEARCHER is an efficient tool for tracing distant evolutionary relationships involving large protein families. Although classical lipases and ATGL have no obvious sequence similarity and differ with regard to fold and catalytic mechanism, homology links detected with FAMILYSEARCHER show that they are evolutionarily related. The conserved sequence parts can be narrowed down to an ancestral core module consisting of three β-strands, one α-helix and a turn containing the typical nucleophilic serine. Moreover, this ancestral module also appears in numerous enzymes with various substrate specificities, but that critically rely on nucleophilic attack mechanisms.
Smad7 and protein phosphatase 1α are critical determinants in the duration of TGF-β/ALK1 signaling in endothelial cells
Authors: Valdimarsdottir Gudrun , Goumans Marie-José , Itoh Fumiko , Itoh Susumu , Heldin Carl-Henrik , Dijke Peter ten 
Published: April 2006

Abstract

Background
In endothelial cells (EC), transforming growth factor-β (TGF-β) can bind to and transduce signals through ALK1 and ALK5. The TGF-β/ALK5 and TGF-β/ALK1 pathways have opposite effects on EC behaviour. Besides differential receptor binding, the duration of TGF-β signaling is an important specificity determinant for signaling responses. TGF-β/ALK1-induced Smad1/5 phosphorylation in ECs occurs transiently.

Results
The temporal activation of TGF-β-induced Smad1/5 phosphorylation in ECs was found to be affected by de novo protein synthesis, and ALK1 and Smad5 expression levels determined signal strength of TGF-β/ALK1 signaling pathway. Smad7 and protein phosphatase 1α (PP1α) mRNA expression levels were found to be specifically upregulated by TGF-β/ALK1. Ectopic expression of Smad7 or PP1α potently inhibited TGF-β/ALK1-induced Smad1/5 phosphorylation in ECs. Conversely, siRNA-mediated knockdown of Smad7 or PP1α enhanced TGF-β/ALK1-induced signaling responses. PP1α interacted with ALK1 and this association was further potentiated by Smad7. Dephosphorylation of the ALK1, immunoprecipitated from cell lysates, was attenuated by a specific PP1 inhibitor.

Conclusion
Our results suggest that upon its induction by the TGF-β/ALK1 pathway, Smad7 may recruit PP1α to ALK1, and thereby control TGF-β/ALK1-induced Smad1/5 phosphorylation.
Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements
Authors: Tobes Raquel , Pareja Eduardo 
Published: April 2006

Abstract

Background
Mobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. The insertion of some specific Insertion Sequences had been associated with repetitive extragenic palindromic (REP) elements. Considering that there are a sufficient number of available genomes with described REPs, and exploiting the advantage of the traceability of transposition events in genomes, we decided to exhaustively analyze the relationship between REP sequences and mobile elements.

Results
This global multigenome study highlights the importance of repetitive extragenic palindromic elements as target sequences for transposases. The study is based on the analysis of the DNA regions surrounding the 981 instances of Insertion Sequence elements with respect to the positioning of REP sequences in the 19 available annotated microbial genomes corresponding to species of bacteria with reported REP sequences. This analysis has allowed the detection of the specific insertion into REP sequences for ISPsy8 in Pseudomonas syringae DC3000, ISPa11 in P. aeruginosa PA01, ISPpu9 and ISPpu10 in P. putida KT2440, and ISRm22 and ISRm19 in Sinorhizobium meliloti 1021 genome. Preference for insertion in extragenic spaces with REP sequences has also been detected for ISPsy7 in P. syringae DC3000, ISRm5 in S. meliloti and ISNm1106 in Neisseria meningitidis MC58 and Z2491 genomes. Probably, the association with REP elements that we have detected analyzing genomes is only the tip of the iceberg, and this association could be even more frequent in natural isolates.

Conclusion
Our findings characterize REP elements as hot spots for transposition and reinforce the relationship between REP sequences and genomic plasticity mediated by mobile elements. In addition, this study defines a subset of REP-recognizer transposases with high target selectivity that can be useful in the development of new tools for genome manipulation.
Similarities in the immunoglobulin response and VH gene usage in rhesus monkeys and humans exposed to porcine hepatocytes
Authors: Zahorsky-Reeves Joanne L , Gregory Clare R , Cramer Donald V , Patanwala Insiyyah Y , Kyles Andrew E , Borie Dominic C , Kearns-Jonker Mary K 
Published: April 2006

AbstractBackgroundThe use of porcine cells and organs as a source of xenografts for human patients would vastly increase the donor pool; however, both humans and Old World primates vigorously reject pig tissues due to xenoantibodies that react with the polysaccharide galactose α (1,3) galactose (αGal) present on the surface of many porcine cells. We previously examined the xenoantibody response in patients exposed to porcine hepatocytes via treatment(s) with bioartficial liver devices (BALs), composed of porcine cells in a support matrix. We determined that xenoantibodies in BAL-treated patients are predominantly directed at porcine αGal carbohydrate epitopes, and are encoded by a small number of germline heavy chain variable region (VH) immunoglobulin genes. The studies described in this manuscript were designed to identify whether the xenoantibody responses and the IgVHgenes encoding antibodies to porcine hepatocytes in non-human primates used as preclinical models are similar to those in humans. Adult non-immunosuppressed rhesus monkeys (Macaca mulatta) were injected intra-portally with porcine hepatocytes or heterotopically transplanted with a porcine liver lobe. Peripheral blood leukocytes and serum were obtained prior to and at multiple time points after exposure, and the immune response was characterized, using ELISA to evaluate the levels and specificities of circulating xenoantibodies, and the production of cDNA libraries to determine the genes used by B cells to encode those antibodies.ResultsXenoantibodies produced following exposure to isolated hepatocytes and solid organ liver grafts were predominantly encoded by genes in the VH3 family, with a minor contribution from the VH4 family. Immunoglobulin heavy-chain gene (VH) cDNA library screening and gene sequencing of IgM libraries identified the genes as most closely-related to the IGHV3-11 and IGHV4-59 germline progenitors. One of the genes most similar to IGHV3-11, VH3-11cyno, has not been previously identified, and encodes xenoantibodies at later time points post-transplant. Sequencing of IgG clones revealed increased usage of the monkey germline progenitor most similar to human IGHV3-11 and the onset of mutations.ConclusionThe small number of IGVHgenes encoding xenoantibodies to porcine hepatocytes in non-human primates and humans is highly conserved. Rhesus monkeys are an appropriate preclinical model for testing novel reagents such as those developed using structure-based drug design to target and deplete antibodies to porcine xenografts.
Detection of human and rodent 5-HT3Breceptor subunits by anti-peptide polyclonal antibodies
Authors: Reeves David C , Lummis Sarah CR 
Published: April 2006

Abstract

Background
The 5-HT3 receptor is a member of a neurotransmitter-gated ion channel family which includes nicotinic acetylcholine, GABAA, and glycine receptors. While antibodies specific for the 5-HT3A receptor subunit are plentiful, and have revealed a wealth of structural and functional information, few antisera exist for the detection of 5-HT3B receptor subunits. Here we describe the generation and characterisation of a rabbit polyclonal antiserum that specifically recognises 5-HT3B receptor subunits

Results
Immunization of a rabbit with a 20-mer peptide, corresponding to the N-terminus of the human 5-HT3B receptor subunit, generated serum with polyclonal antibodies from which an IgG fraction was purified, yielding pAb77. The antibodies were shown to label 5-HT3B receptor subunits in transfected human embryonic kidney cells and rodent tissues using Western blots. Immunocytochemistry using pAb77 on these cells showed that 5-HT3B receptor subunits do not reach the plasma membrane in the absence of 5-HT3A receptor subunits. Immunohistochemical analysis of rat brain sections showed pAb77 immunoreactivity in distinct populations of cells in the hippocampus.

Conclusion
We have demonstrated that pAb77 antibodies specifically label native and recombinant 5-HT3B receptor subunits with high affinity and specificity. The antibody was shown to be useful for the determination of both receptor trafficking and also mapping 5-HT3B receptor subunit expression in the CNS.
Reproducibility of the STARD checklist: an instrument to assess the quality of reporting of diagnostic accuracy studies
Authors: Smidt Nynke , Rutjes Anne WS , van der Windt Daniëlle AWM , Ostelo Raymond WJG , Bossuyt Patrick M , Reitsma Johannes B , Bouter Lex M , de Vet Henrica CW 
Published: April 2006

Abstract

Background
In January 2003, STAndards for the Reporting of Diagnostic accuracy studies (STARD) were published in a number of journals, to improve the quality of reporting in diagnostic accuracy studies. We designed a study to investigate the inter-assessment reproducibility, and intra- and inter-observer reproducibility of the items in the STARD statement.

Methods
Thirty-two diagnostic accuracy studies published in 2000 in medical journals with an impact factor of at least 4 were included. Two reviewers independently evaluated the quality of reporting of these studies using the 25 items of the STARD statement. A consensus evaluation was obtained by discussing and resolving disagreements between reviewers. Almost two years later, the same studies were evaluated by the same reviewers. For each item, percentages agreement and Cohen's kappa between first and second consensus assessments (inter-assessment) were calculated. Intraclass Correlation coefficients (ICC) were calculated to evaluate its reliability.

Results
The overall inter-assessment agreement for all items of the STARD statement was 85% (Cohen's kappa 0.70) and varied from 63% to 100% for individual items. The largest differences between the two assessments were found for the reporting of the rationale of the reference standard (kappa 0.37), number of included participants that underwent tests (kappa 0.28), distribution of the severity of the disease (kappa 0.23), a cross tabulation of the results of the index test by the results of the reference standard (kappa 0.33) and how indeterminate results, missing data and outliers were handled (kappa 0.25). Within and between reviewers, also large differences were observed for these items. The inter-assessment reliability of the STARD checklist was satisfactory (ICC = 0.79 [95% CI: 0.62 to 0.89]).

Conclusion
Although the overall reproducibility of the quality of reporting on diagnostic accuracy studies using the STARD statement was found to be good, substantial disagreements were found for specific items. These disagreements were not so much caused by differences in interpretation of the items by the reviewers but rather by difficulties in assessing the reporting of these items due to lack of clarity within the articles. Including a flow diagram in all reports on diagnostic accuracy studies would be very helpful in reducing confusion between readers and among reviewers.
How good is probabilistic record linkage to reconstruct reproductive histories? Results from the Aberdeen children of the 1950s study
Authors: Nitsch Dorothea , Morton Susan , DeStavola Bianca L , Clark Heather , Leon David A 
Published: April 2006

Abstract

Background
Probabilistic record linkage is widely used in epidemiology, but studies of its validity are rare. Our aim was to validate its use to identify births to a cohort of women, being drawn from a large cohort of people born in Scotland in the early 1950s.

Methods
The Children of the 1950s cohort includes 5868 females born in Aberdeen 1950–56 who were in primary schools in the city in 1962. In 2001 a postal questionnaire was sent to the cohort members resident in the UK requesting information on offspring. Probabilistic record linkage (based on surname, maiden name, initials, date of birth and postcode) was used to link the females in the cohort to birth records held by the Scottish Maternity Record System (SMR 2).

Results
We attempted to mail a total of 5540 women; 3752 (68%) returned a completed questionnaire. Of these 86% reported having had at least one birth. Linkage to SMR 2 was attempted for 5634 women, one or more maternity records were found for 3743. There were 2604 women who reported at least one birth in the questionnaire and who were linked to one or more SMR 2 records. When judged against the questionnaire information, the linkage correctly identified 4930 births and missed 601 others. These mostly occurred outside of Scotland (147) or prior to full coverage by SMR 2 (454). There were 134 births incorrectly linked to SMR 2.

Conclusion
Probabilistic record linkage to routine maternity records applied to population-based cohort, using name, date of birth and place of residence, can have high specificity, and as such may be reliably used in epidemiological research.