bluuebunny/crossref_metadata_2025_split huggingface dataset:
The NHS breast screening programme (pathology) EQA: experience in recent years relating to issues involved in individual performance appraisal
Authors: Parham D M , Coleman D , Kodikara S , Moss S , Ellis I O , Al-sam S , Anderson N , Bobrow L , Buley I , Connolly C E , Dallimore N S , Hales S , Hanby A , Humphreys S , Knox F , Lowe J , Macartney J , Nash R , Patnick J , Pinder S E , Quinn C M , Robertson A J , Shrimankar J , Walker R A , Wells C , Winder R , Patel N 
Published: January 2006

Background:The original role of the National Health Service breast screening programme (pathology) external quality assessment (EQA) scheme was educational; it aimed to raise standards, reinforce use of common terminology, and assess the consistency of pathology reporting of breast disease in the UK.Aims/Methods:To examine the performance (scores) of pathologists participating in the scheme in recent years. The scheme has evolved to help identify poor performers, reliant upon setting an acceptable cutpoint. Therefore, the effects of different cutpoint strategies were evaluated and implications discussed.Results/Conclusions:Pathologists who joined the scheme improved over time, particularly those who did less well initially. There was no obvious association between performance and the number of breast cancer cases reported each year. This is not unexpected because the EQA does not measure expertise, but was established to demonstrate a common level of performance (conformity to consensus) for routine cases, rather than the ability to diagnose unusual/difficult cases. A new method of establishing cutpoints using interquartile ranges is proposed. The findings also suggest that EQA can alter a pathologist’s practice: those who leave the scheme (for whatever reason) have, on average, marginally lower scores. Consequently, with the cutpoint methodology currently used (which is common to several EQA schemes) there is the potential for the cutpoint to drift upwards. In future, individuals previously deemed competent could subsequently be erroneously labelled as poor performers. Due consideration should be given to this issue with future development of schemes.
Colocalisation of intraplaque C reactive protein, complement, oxidised low density lipoprotein, and macrophages in stable and unstable angina and acute myocardial infarction
Authors: Meuwissen M , van der Wal A C , Niessen H W M , Koch K T , de Winter R J , van der Loos C M , Rittersma S Z H , Chamuleau S A J , Tijssen J G P , Becker A E , Piek J J 
Published: January 2006

Background:C reactive protein (CRP), an important serum marker of atherosclerotic vascular disease, has recently been reported to be active inside human atherosclerotic plaques.Aims:To investigate the simultaneous presence of macrophages, CRP, membrane attack complex C5b–9 (MAC), and oxidised low density lipoprotein (oxLDL) in atherectomy specimens from patients with different coronary syndromes.Methods:In total, 54 patients with stable angina (SA; n = 21), unstable angina (UA; n = 15), and myocardial infarction (MI; n = 18) underwent directional coronary atherectomy for coronary lesions. Cryostat sections of atherosclerotic plaques were immunohistochemically stained with monoclonal antibodies: anti-CD68 (macrophages), anti-5G4 (CRP), aE11 (MAC), and 12E7 (oxLDL). Immunopositive areas were evaluated in relation to fibrous and neointima tissues, atheroma, and media. Quantitative analysis was performed using image cytometry with systematic random sampling (percentage immunopositive/total tissue area).Results:Macrophages, CRP, MAC, and oxLDL were simultaneously present in a higher proportion of fibrous tissue and atheroma of atherectomy specimens from patients with UA and MI compared with SA (p<0.05). Quantitative analysis showed significantly higher mean percentages of macrophages in plaques from patients with MI (44%) than UA (30%; p<0.01) and SA (20%; p<0.001). Significantly higher mean percentages of CRP were also seen in MI (25%) and UA (25%) compared with SA (12%; p<0.05).Conclusions:The presence of CRP, complement, and oxLDL in a high proportion of plaque tissue from patients with unstable coronary artery disease implies that these surrogate markers have important proinflammatory effects inside atherosclerotic plaques. This may increase vulnerability to plaque rupture and thrombosis, with subsequent clinical sequelae.
Epstein-Barr virus nuclear antigen 2 induces FcRH5 expression through CBF1
Authors: Mohan Joanne , Dement-Brown Jessica , Maier Sabine , Ise Tomoko , Kempkes Bettina , Tolnay Mate 
Published: January 2006

AbstractFc-receptor homolog 5 (FcRH5) is a recently identified B-cell membrane protein of unknown function. In Burkitt lymphoma cell lines with chromosome 1q21 abnormalities, FcRH5 expression is deregulated, implicating FcRH5 in lymphomagenesis. Epstein-Barr virus infects and immortalizes B cells, and is implicated in the etiology of several tumors of B-cell origin. Overexpression of genes located on 1q21-25 has been proposed as a surrogate for Epstein-Barr virus in Burkitt lymphoma. We now report that Epstein-Barr virus nuclear antigen 2 (EBNA2) markedly induces the expression of the FcRH5 gene, encoded on chromosome 1q21. Induction occurred in the absence of other viral proteins and did not require de novo protein synthesis. EBNA2 lacks a DNA-binding domain and can target responsive genes through the host DNA binding protein CBF1. We show that induction of FcRH5 by EBNA2 is strictly CBF1 dependent, as it was abolished in CBF1-deficient cells. Accordingly, EBNA2 targeted CBF1 binding sites present in the FcRH5 promoter in vivo, as detected by chromatin immunoprecipitation. These results identify FcRH5 as a novel, direct target of EBNA2 that may contribute to the development of Epstein-Barr virus–associated tumors.
Selective regulation of MAP kinases and Chemokine expression after ligation of ICAM-1 on human airway epithelial cells
Authors: Krunkosky Thomas M , Jarrett Carla L 
Published: January 2006

AbstractBackgroundIntercellular adhesion molecule 1 (ICAM-1) is an immunoglobulin-like cell adhesion molecule expressed on the surface of multiple cell types, including airway epithelial cells. It has been documented that cross-linking ICAM-1 on the surface of leukocytes results in changes in cellular function through outside-inside signaling; however, the effect of cross-linking ICAM-1 on the surface of airway epithelial cells is currently unknown. The objective of this study was to investigate whether or not cross-linking ICAM-1 on the surface of airway epithelial cells phosphorylated MAP kinases or stimulated chemokine expression and secretion.MethodsThe human lung adenocarcinoma (A549) cells and primary cultures of normal human bronchial epithelial (NHBE) cells were used in these studies. To increase ICAM-1 surface expression, cultures were stimulated with TNFα to enhance ICAM-1 surface expression. Following ICAM-1 upregulation, ICAM-1 was ligated with a murine anti-human ICAM-1 antibody and subsequently cross-linked with a secondary antibody (anti-mouse IgG(ab')2) in the presence or absence of the MAP kinase inhibitors. Following treatments, cultures were assessed for MAPK activation and chemokine gene expression and secretion. Control cultures were treated with murine IgG1 antibody or murine IgG1 antibody and anti-mouse IgG(ab')2to illustrate specificity. Data were analyzed for significance using a one-way analysis of variance (ANOVA) with Bonferroni post-test correction for multiple comparisons, and relative gene expression was analyzed using the 2-ΔΔCT method.ResultsICAM-1 cross-linking selectively phosphorylated both ERK and JNK MAP kinases as detected by western blot analysis. In addition, cross-linking resulted in differential regulation of chemokine expression. Specifically, IL-8 mRNA and protein secretion was not altered by ICAM-1 cross-linking, in contrast, RANTES mRNA and protein secretion was induced in both epithelial cultures. These events were specifically inhibited by the ERK inhibitor PD98059. Data indicates that ICAM-1 cross-linking stimulates a synergistic increase in TNFα-mediated RANTES production involving activation of ERK in airway epithelial cells.ConclusionResults demonstrate that cytokine induced ICAM-1 on the surface of airway epithelial cells induce outside-inside signaling through cross-linking ICAM-1, selectively altering intracellular pathways and cytokine production. These results suggest that ICAM-1 cross-linking can contribute to inflammation in the lung via production of the chemokine RANTES.
On the effects of cycloheximide on cell motility and polarisation in Dictyostelium discoideum
Authors: Clotworthy Margaret , Traynor David 
Published: January 2006

AbstractBackgroundCycloheximide is a protein synthesis inhibitor that acts specifically on the 60S subunit of eukaryotic ribosomes. It has previously been shown that a short incubation ofDictyostelium discoideumamoebae in cycloheximide eliminates fluid phase endocytosis.ResultsWe found that treatment with cycloheximide also causes the amoebae to retract their pseudopodia, round up and cease movement. Furthermore, fluid phase endocytosis, phagocytosis and capping cease in the presence of 2 mM cycloheximide, although membrane uptake, as measured using FM1-43, is unaffected. In the presence of cycloheximide, aggregation-competent amoebae sensitive to cAMP, although round, can still localise CRAC, ABP120, PI3K and actin polymerisation in response to a micropipette filled with cAMP. The behaviour of wild-type amoebae in the presence of cycloheximide is surprisingly similar to that of amoebae having a temperature-sensitive version of NSF at the restrictive temperature.ConclusionOur results may suggest that, upon cycloheximide treatment, either a labile protein required for polarised membrane recycling is lost, or a control mechanism linking protein synthesis to membrane recycling is activated.
PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease
Authors: Vouk Katja , Strmecki Lana , Stekrova Jitka , Reiterova Jana , Bidovec Matjaz , Hudler Petra , Kenig Anton , Jereb Simona , Zupanic-Pajnic Irena , Balazic Joze , Haarpaintner Guido , Leskovar Bostjan , Adamlje Anton , Skoflic Antun , Dovc Reina , Hojs Radovan , Komel Radovan 
Published: January 2006

Abstract

Background
Autosomal dominant polycystic kidney disease (ADPKD) is a genetically heterogeneous disorder caused by mutations in at least two different loci. Prior to performing mutation screening, if DNA samples of sufficient number of family members are available, it is worthwhile to assign the gene involved in disease progression by the genetic linkage analysis.

Methods
We collected samples from 36 Slovene ADPKD families and performed linkage analysis in 16 of them. Linkage was assessed by the use of microsatellite polymorphic markers, four in the case of PKD1 (KG8, AC2.5, CW3 and CW2) and five for PKD2 (D4S1534, D4S2929, D4S1542, D4S1563 and D4S423). Partial PKD1 mutation screening was undertaken by analysing exons 23 and 31–46 and PKD2 .

Results
Lod scores indicated linkage to PKD1 in six families and to PKD2 in two families. One family was linked to none and in seven families linkage to both genes was possible. Partial PKD1 mutation screening was performed in 33 patients (including 20 patients from the families where linkage analysis could not be performed). We analysed PKD2 in 2 patients where lod scores indicated linkage to PKD2 and in 7 families where linkage to both genes was possible. We detected six mutations and eight polymorphisms in PKD1 and one mutation and three polymorphisms in PKD2.

Conclusion
In our study group of ADPKD patients we detected seven mutations: three frameshift, one missense, two nonsense and one putative splicing mutation. Three have been described previously and 4 are novel. Three newly described framesfift mutations in PKD1 seem to be associated with more severe clinical course of ADPKD. Previously described nonsense mutation in PKD2 seems to be associated with cysts in liver and milder clinical course.
Abulia following penetrating brain injury during endoscopic sinus surgery with disruption of the anterior cingulate circuit: Case report
Authors: Grunsfeld Alexander A , Login Ivan S 
Published: January 2006

AbstractBackgroundIt is common knowledge that the frontal lobes mediate complex human behavior and that damage to these regions can cause executive dysfunction, apathy, disinhibition and personality changes. However, it is less well known that subcortical structures such as the caudate and thalamus are part of functionally segregated fronto-subcortical circuits, that can also alter behavior after injury.Case presentationWe present a 57 year old woman who suffered penetrating brain injury during endoscopic sinus surgery causing right basal ganglia injury which resulted in an abulic syndrome.ConclusionAbulia does not result solely from cortical injury but can occur after disruption anywhere in the anterior cingulate circuit – in the case of our patient, most prominently at the right caudate.
BACH1 Ser919Pro variant and breast cancer risk
Authors: Vahteristo Pia , Yliannala Kristiina , Tamminen Anitta , Eerola Hannaleena , Blomqvist Carl , Nevanlinna Heli 
Published: January 2006

Abstract

Background
BACH1 (BRCA1-associated C-terminal helicase 1; also known as BRCA1-interacting protein 1, BRIP1) is a helicase protein that interacts in vivo with BRCA1, the protein product of one of the major genes for hereditary predisposition to breast cancer. Previously, two BACH1 germ line missense mutations have been identified in early-onset breast cancer patients with and without family history of breast and ovarian cancer.
In this study, we aimed to evaluate whether there are BACH1 genetic variants that contribute to breast cancer risk in Finland.

Methods
The BACH1 gene was screened for germ line alterations among probands from 43 Finnish BRCA1/2 negative breast cancer families. Recently, one of the observed common variants, Ser-allele of the Ser919Pro polymorphism, was suggested to associate with an increased breast cancer risk, and was here evaluated in an independent, large series of 888 unselected breast cancer patients and in 736 healthy controls.

Results
Six BACH1 germ line alterations were observed in the mutation analysis, but none of these were found to associate with the cancer phenotype. The Val193Ile variant that was seen in only one family was further screened in an independent series of 346 familial breast cancer cases and 183 healthy controls, but no additional carriers were observed. Individuals with the BACH1 Ser919-allele were not found to have an increased breast cancer risk when the Pro/Ser heterozygotes (OR 0.90; 95% CI 0.70–1.16; p = 0.427) or Ser/Ser homozygotes (OR 1.02; 95% CI 0.76–1.35; p = 0.91) were compared to Pro/Pro homozygotes, and there was no association of the variant with any breast tumor characteristics, age at cancer diagnosis, family history of cancer, or survival.

Conclusion
Our results suggest that the BACH1 Ser919 is not a breast cancer predisposition allele in the Finnish study population. Together with previous studies, our results also indicate that although some rare germ line variants in BACH1 may contribute to breast cancer development, the contribution of BACH1 germline alterations to familial breast cancer seems marginal.
P-Selectin- and CD63-Exposing Platelet Microparticles Reflect Platelet Activation in Peripheral Arterial Disease and Myocardial Infarction
Authors: van der Zee P Marc , Biró Éva , Ko Yung , de Winter Robbert J , Hack C Erik , Sturk Augueste , Nieuwland Rienk 
Published: January 2006

Abstract
Background: Platelet-derived microparticles (PMPs) are generally considered a marker of platelet activation in cardiovascular disease. We studied the extent to which PMP subpopulations parallel platelet activation in vitro and in vivo.
Methods: Using flow cytometry, we analyzed PMP subpopulations from resting and activated platelets in vitro (n = 6) as well as from plasma samples of patients with stable angina, peripheral arterial disease, or myocardial infarction [non-ST-elevation (NSTEMI) and ST-elevation (STEMI)] and from older, age- and sex-matched and young healthy individuals [n = 10 for all groups except NSTEMI (n = 11)]. Coagulation markers prothrombin fragment F1 + 2 and thrombin-antithrombin complexes were determined by ELISA. The PMP-associated fraction of soluble (s)P-selectin was estimated by ELISA.
Results: In vitro, stimulation of platelets with thrombin receptor–activating peptide (15 μmol/L) or the calcium ionophore A23187 (2.5 μmol/L) increased fractions of both platelets and PMPs exposing P-selectin or CD63 (P &lt;0.001 for all). Whereas the number of PMPs released by A23187-stimulated platelets increased significantly (P &lt;0.001), the number of PMPs released from thrombin receptor-activating peptide–stimulated platelets remained constant (P &gt;0.05). Ex vivo, numbers of circulating PMPs were comparable in all groups. Compared with young persons, P-selectin–exposing PMPs were increased in older persons (P = 0.02) and were further increased in patients with NSTEMI (P = 0.007) and STEMI (P = 0.045). CD63-exposing PMPs were increased in patients with peripheral arterial disease (P = 0.041), NSTEMI (P = 0.001), and STEMI (P = 0.049). Subpopulations exposing P-selectin or CD63 correlated with each other (r = 0.581; P &lt;0.001), but neither correlated with the plasma concentrations of F1 + 2 or thrombin–antithrombin complexes. The PMP-associated fraction of sP-selectin constituted only 2.2 (4.7)% [mean (SD)] of total sP-selectin.
Conclusions: PMP subpopulations reflect platelet activation status better than the total number of PMPs. Increased concentrations of circulating PMP subpopulations are found in aging, and further increases are encountered in peripheral arterial disease and myocardial infarction.
The MGED Ontology: a resource for semantics-based description of microarray experiments
Authors: Whetzel Patricia L. , Parkinson Helen , Causton Helen C. , Fan Liju , Fostel Jennifer , Fragoso Gilberto , Game Laurence , Heiskanen Mervi , Morrison Norman , Rocca-Serra Philippe , Sansone Susanna-Assunta , Taylor Chris , White Joseph , Stoeckert Christian J. 
Published: January 2006

Abstract
Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards.
Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation.
Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at . Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System ().
Contact: Stoeckrt@pcbi.upenn.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches
Authors: Pellegrini-Calace Marialuisa , Tramontano Anna 
Published: January 2006

Abstract
Summary: Down syndrome (DS) is the most frequent form of mental retardation and is caused by chromosome 21 (HSA21) trisomy. Despite the number of known genes involved in DS and its high therapeutic interest, biological mechanisms leading to the DS phenotype are not fully clear. We present a functional hypothesis based on fold recognition and hidden Markov model techniques for four HSA21 genes located in the DS Candidate Region (DSCR). More specifically, we propose that they are members of a novel mitogen-activated protein kinase pathway with DYRK1A, SNF1LK and RIPK4 gene products being elements of the kinase cascade and the DSCR3 acting as structural scaffold for their interaction. This hypothesis finds support in various biochemical studies concerning the biological behavior and features of the involved HSA21 proteins. Our analysis calls for specifically designed experiments to validate our prediction and establish its relevance in terms of therapeutic approaches to the disease.
Contact: anna.tramontano@uniroma1.it
Suplementary information: Supplementary data are available at Bioinformatics online.
Genetic test bed for feature selection
Authors: Choudhary Ashish , Brun Marcel , Hua Jianping , Lowey James , Suh Ed , Dougherty Edward R. 
Published: January 2006

Abstract
Motivation: Given a large set of potential features, such as the set of all gene-expression values from a microarray, it is necessary to find a small subset with which to classify. The task of finding an optimal feature set of a given size is inherently combinatoric because to assure optimality all feature sets of a given size must be checked. Thus, numerous suboptimal feature-selection algorithms have been proposed. There are strong impediments to evaluate feature-selection algorithms using real data when data are limited, a common situation in genetic classification. The difficulty is compound. First, there are no class-conditional distributions from which to draw data points, only a single small labeled sample. Second, there are no test data with which to estimate the feature-set errors, and one must depend on a training-data-based error estimator. Finally, there is no optimal feature set with which to compare the feature sets found by the algorithms.
Results: This paper describes a genetic test bed for the evaluation of feature-selection algorithms. It begins with a large biological feature-label dataset that is used as an empirical distribution and, using massively parallel computation, finds the top feature sets of various sizes based on a given sample size and classification rule. The user can draw random samples from the data, apply a proposed algorithm, and evaluate the proficiency of the proposed algorithm via three different measures (code provided). A key feature of the test bed is that, once a dataset is input, a single command creates the entire test bed relative to the dataset. The particular dataset used for the first version of the test bed comes from a microarray-based classification study that analyzes a large number of microarrays, prepared with RNA from breast tumor samples from each of 295 patients.
Availability: The software and supplementary material are available at
Contact: edward@ece.tamu.edu