bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can the laboratory affect the investigation and diagnosis of primary biliary cirrhosis?: Table 1
Authors: Sinclair D , Spedding A , Young R 
Published: February 2006

Background:Primary biliary cirrhosis (PBC) is an autoimmune liver disease characterised by the presence of various laboratory abnormalities but the precise role of laboratory staff in initiating clinical referral and subsequent biopsy is not clear.Objective:To examine the impact of laboratory abnormalities in the investigation of PBC.Methods:In a retrospective study of laboratory results over nine years from 1996, computer records were reviewed to identify how many referrals for biopsy were initiated and subsequent diagnoses made as a result of clinical signs, raised serum alkaline phosphatase activity (ALP), raised IgM concentration, or positive mitochondrial antibodies accompanied by a clinical comment from the laboratory suggesting further action.Results:22 diagnoses of PBC were confirmed by histopathology. Eleven had high ALP activity which had follow up tests initiated by the laboratory (mitochondrial antibodies or IgM or both) and a comment added suggesting further investigation into the possibility of PBC. Seven had abnormal liver antibodies and one had a high polyclonal IgM concentration which prompted the relevant follow on testing and comments. One had an earlier diagnosis made on serological/clinical grounds and the biopsy was a confirmatory measure. One had no liver related antibodies. One had a request by laboratory staff for follow on tests but these were not asked for in subsequent samples by the requesting clinician.Conclusions:There is a positive role for laboratory staff in the diagnosis of PBC. Unexplained rises in ALP activity, positive mitochondrial antibodies, or raised IgM concentrations should be investigated more fully by laboratory staff and advice given to prompt a clinical referral for review and biopsy.
Serum HER-2 concentration in patients with primary breast cancer
Authors: Kong S-Y , Kang J H , Kwon Y , Kang H-S , Chung K-W , Kang S H , Lee D H , Ro J , Lee E S 
Published: February 2006

Objective:To evaluate whether serum HER-2/neu (HER-2) concentration is a valid index of HER-2 status in women with primary breast cancer, and to establish a normal reference range for serum HER-2 concentration in Korean women.Methods:Serum HER-2 concentration was measured and immunohistochemistry (IHC) and fluorescence in situ hybridisation (FISH) carried out on tissue samples from 86 consecutive female patients. The results of the three datasets were compared. The cut off value of HER-2 concentration was determined from the mean +2SD values derived from the serum of 93 healthy volunteers.Results:The IHC and FISH data were significantly correlated (p<0.01), but neither showed significant correlation with the serum HER-2 data. The cut off value of serum HER-2 was 10.2 μg/l, and the serum HER-2 concentration of patients with primary breast cancer ranged from 5.0 to 17.5 μg/l. Only five patients had a serum HER-2 value above the cut off value.Conclusions:Serum HER-2 concentration cannot be substituted for IHC or FISH to evaluate HER-2 status, nor can it be used as a diagnostic tumour marker in primary breast cancer, considering the low prevalence of serum HER-2 elevation.
Biblical Interpretation in the Patristic Era, A 'Handbook of Patristic Exegesis' and Some Other Recent Books and Related Projects
Authors: van Oort Johannes 
Published: February 2006

AbstractDuring the past ten years several books in the field of patristic exegesis have been published and some major projects have started. The aim of this article is to provide an introduction to this noticeably new trend of research and to evaluate some results.
"The Puzzle of the Last Four Books of Augustine's Confessions": An Illegitimate Issue?
Authors: Kotzé Annemaré 
Published: February 2006

AbstractThe most important point this article wants to make is that the expectations of the ancient reader, Augustine's contemporary, of a work like the Confessions may have been diametrically opposite to the expectations with which the work has been read for the past number of centuries. I contend that, even though they too would no doubt have recognized the novel and creative devices that characterize the work, ancient readers would not have been perplexed by the presence of the last four books of the Confessions. The whole issue surrounding the presence of these books is a problem created by the illegitimate assumptions later readers carried into their reading.
Determination of the cation exchange capacity of clays with copper complexes revisited
Authors: Ammann L. , Bergaya F. , Lagaly G. 
Published: February 2006

AbstractThe determination of the cation exchange capacity (CEC) of clays by exchange with the cationic copper complexes [Cu(en)2]2+ and [Cu(trien)]2+ is revisited. The procedures reported by Bergaya & Vayer (1997) and Meier & Kahr (1999) are modified slightly. The concentration of the copper complexes in the equilibrium solutions is measured by spectral photometry. Correct CEC values of the [Cu(en)2]2+ exchange are only obtained when a buffer (‘tris’, tris (hydroxymethyl) aminomethane, pH = 8) is added to the equilibrium solution after separation of the clay, because the molar extinction coefficient of this complex depends on the pH of the solution. A standard procedure is recommended as a reference method. In most cases, tris addition is not needed for the determination with [Cu(trien)]2+ cations. Nevertheless, tris addition is recommended in the standard procedure. Determination of CEC for 40 samples (kaolins, ‘common clays’, bentonites, montmorillonites and beidellite) shows a good agreement between measurements using [Cu(en)2]2+ and [Cu(trien)]2+ cations and with results by the ammonium acetate method.
Bentonites from Cabo de Gata, Almería, Spain: a mineralogical and geochemical overview
Authors: Caballero E. , Jiménez de Cisneros C. , Huertas F. J. , Huertas F. , Pozzuoli A. , Linares J. 
Published: February 2006

AbstractThe Neogene volcanic region of Cabo de Gata, Almería, SE Spain, is dotted with many outcrops of bentonite, some of them of significant economic interest. The bentonites have their origin in the hydrothermal alteration of pyroclastic rocks (15-7 Ma). The deposits are usually associated with fractures. The major mineral is a dioctahedral Fe- and Mg-smectite (89-75%) and this is accompanied by minor amounts of feldspars, quartz, amphiboles, pyroxenes, biotite, zeolites, disordered tridymite, calcite, etc. This paper describes the geological background, the general characteristics of the bentonites and major aspects of their formation, e.g. type of low-temperature hydrothermal solutions, mass balance, chemical evolutions of the smectites and geochemistry of trace elements. Finally, the characteristics of three of the most important deposits are described.
Hydraulic conductivity and imbibition speed of solid clay aggregates: two different approaches involving the tortuosity of pathways
Authors: Konta J. 
Published: February 2006

Abstract:Two different approaches used to express the tortuosity of water pathways in a solid clay body are known: (1) a static approach based on microscopic measurement in thin sections; and (2) a dynamic approach based on ‘imbibition’ speed. Each is expressed by a corresponding equation. The second method has the following advantages over the first: (a) it enables the testing of a much larger volume than that observed in a common thin section; (b) it measures the effects of all particles, including the finest fragments barely visible under optical microscope which also have influence on hydraulic conductivity or the imbibition speed of water; (c) in the case of expansible clays, the magnitude ofk(tortuosity of pathways including the shape of particles) can be compared withkfor non-expansible clays using a non-polar liquid, e.g. tetraline; (d) the measurement of the imbibition speed into the clay aggregate through a constant area is automated. Specific properties and processes important for sealing clays are discussed in the connection with the dynamic approach.
The relationship between zeolite (heulandite-clinoptilolite) content and the ammonium-exchange capacity of pyroclastic rocks in Gördes, Turkey
Authors: Esenli F. , Sirkecioğlu A. 
Published: February 2006

AbstractDiagenetic alteration in two tuff horizons (the lower and upper tuff units) in the GoÈrdes region of Turkey led to the formation of mainly heulandite-clinoptilolite-type zeolites and also clay and silica minerals and K-feldspar. Possible variations in the climate and geological environment followed by variations in the hydrological system and the composition of the Miocene lake water and groundwater at that time resulted in the mineralogical facies. The lower tuffs are unaltered or slightly altered in the northern part and are more altered, particularly to zeolite (clinoptilolite) in the southern part of the study area. Heulandite and K-feldspar are mainly authigenic minerals in the upper tuff unit. The ammonium-exchange capacities of the 16 samples were investigated to understand the effects of the mineralogical composition on their ion-exchange capacities, which vary in the range 0.19-2.00 mEq/g. It is observed that the ion-exchange capacities are strongly dependent on the zeolite contents of the rocks. The correlation coefficient of this linear relation is 0.86. The most significant increase in ammonium-exchange capacity (from 0.2 to ~1.0 mEq/g) was observed when the zeolite contents increased from 0 to 30 wt.%. The second increase in exchange capacity was observed for samples containing >80 wt.% zeolite. Although there is no significant effect from the other authigenic minerals, smectite has a positive effect, and K-feldspar and opal-CT have almost no effect on the ion exchange capacities.
EM703 improves bleomycin-induced pulmonary fibrosis in mice by the inhibition of TGF-β signaling in lung fibroblasts
Authors: Li Ying Ji , Azuma Arata , Usuki Jiro , Abe Shinji , Matsuda Kuniko , Sunazuka Toshiaki , Shimizu Takako , Hirata Yukiyo , Inagaki Hirofumi , Kawada Tomoyuki , Takahashi Satoru , Kudoh Shoji , Omura Satoshi 
Published: February 2006

AbstractBackgroundFourteen-membered ring macrolides have been effective in reducing chronic airway inflammation and also preventing lung injury and fibrosis in bleomycin-challenged mice via anti-inflammatory effects. EM703 is a new derivative of erythromycin (EM) without the bactericidal effects. We investigated the anti-inflammatory and antifibrotic effects of EM703 in an experimental model of bleomycin-induced lung injury and subsequent fibrosis in mice.MethodsSeven-week-old male ICR mice were used. All experiments used eight mice/group, unless otherwise noted in the figure legends. Bleomycin was administered intravenously to the mice on day 0. EM703 was orally administered daily to mice. All groups were examined for cell populations in the bronchoalveolar lavage (BAL) fluid and for induction of messenger RNA (mRNA) of Smad3 and Smad4 in the lung tissues by reverse transcriptase (RT)-polymerase chainreaction (PCR) on day 7. Fibroblastic foci were assessed histologically, and the hydroxyproline content was chemically determined in the lung tissues on day 28. We performed assay of proliferation and soluble collagen production, and examined the induction of mRNA of Smad3 and Smad4 by RT-PCR in murine lung fibroblast cell line MLg2908. We also examined Smad3, Smad4 and phosphorylated Smad2/3 (p-Smad2/3) protein assay by western blotting in MLg2908.ResultsBleomycin-induced lung fibrosis, and the infiltration of macrophages and neutrophils into the airspace were inhibited by EM703. The expression of Smad3 and Smad4 mRNA was clearly attenuated by bleomycin, but was recovered by EM703. EM703 also inhibited fibroblast proliferation and the collagen production in lung fibroblasts induced by Transforming growth factor-beta (TGF-β). The expression of Smad3 and Smad4 mRNA in murine lung fibroblasts disappeared due to TGF-β, but was recovered by EM703. EM703 inhibited the expression of p-Smad2/3 and Smad4 protein in murine lung fibroblasts induced by TGF-β.ConclusionThese findings suggest that EM703 improves bleomycin-induced pulmonary fibrosis in mice by actions of anti-inflammation and regulation of TGF-β signaling in lung fibroblasts.
Discovering semantic features in the literature: a foundation for building functional associations
Authors: Chagoyen Monica , Carmona-Saez Pedro , Shatkay Hagit , Carazo Jose M , Pascual-Montano Alberto 
Published: February 2006

AbstractBackgroundExperimental techniques such as DNA microarray, serial analysis of gene expression (SAGE) and mass spectrometry proteomics, among others, are generating large amounts of data related to genes and proteins at different levels. As in any other experimental approach, it is necessary to analyze these data in the context of previously known information about the biological entities under study. The literature is a particularly valuable source of information for experiment validation and interpretation. Therefore, the development of automated text mining tools to assist in such interpretation is one of the main challenges in current bioinformatics research.ResultsWe present a method to create literature profiles for large sets of genes or proteins based on common semantic features extracted from a corpus of relevant documents. These profiles can be used to establish pair-wise similarities among genes, utilized in gene/protein classification or can be even combined with experimental measurements. Semantic features can be used by researchers to facilitate the understanding of the commonalities indicated by experimental results. Our approach is based onnon-negative matrix factorization(NMF), a machine-learning algorithm for data analysis, capable of identifying local patterns that characterize a subset of the data. The literature is thus used to establish putative relationships among subsets of genes or proteins and to provide coherent justification for this clustering into subsets. We demonstrate the utility of the method by applying it to two independent and vastly different sets of genes.ConclusionThe presented method can create literature profiles from documents relevant to sets of genes. The representation of genes as additive linear combinations of semantic features allows for the exploration of functional associations as well as for clustering, suggesting a valuable methodology for the validation and interpretation of high-throughput experimental data.
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
Authors: Barsnes Harald , Mikalsen Svein-Ole , Eidhammer Ingvar 
Published: February 2006

Abstract

Background
Proteomics is the study of the proteome, and is critical to the understanding of cellular processes. Two central and related tasks of proteomics are protein identification and protein characterization. Many small laboratories are interested in the characterization of a small number of proteins, e.g., how posttranslational modifications change under different conditions.

Results
We have developed a software tool called MassSorter for administrating and analyzing data from peptide mass fingerprinting experiments on proteins with known amino acid sequences. It is meant for small scale mass spectrometry laboratories that are interested in posttranslational modifications of known proteins. Several experiments can be compared simultaneously, and the matched and unmatched peak values are clearly indicated. The hits can be sorted according to m/z values (default) or according to the sequence of the protein. Filters defined by the user can mark autolytic protease peaks and other contaminating peaks (keratins, proteins co-migrating with the protein of interest, etc.). Unmatched peaks can be further analyzed for unexpected modifications by searches against a local version of the UniMod database. They can also be analyzed for unexpected cleavages, a highly useful feature for proteins that undergo maturation by proteolytic cleavage, creating new N- or C-terminals. Additional tools exist for visualization of the results, like sequence coverage, accuracy plots, different types of statistics, 3D models, etc. The program and a tutorial are freely available for academic users at http://www.bioinfo.no/software/massSorter.

Conclusion
MassSorter has a number of useful features that can promote the analysis and administration of MS-data.
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms
Authors: Van den Bulcke Tim , Van Leemput Koenraad , Naudts Bart , van Remortel Piet , Ma Hongwu , Verschoren Alain , De Moor Bart , Marchal Kathleen 
Published: February 2006

AbstractBackgroundThe development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark data sets for which the underlying network is known. Since experimental data sets of the appropriate size and design are usually not available, there is a clear need to generate well-characterized synthetic data sets that allow thorough testing of learning algorithms in a fast and reproducible manner.ResultsIn this paper we describe a network generator that creates synthetic transcriptional regulatory networks and produces simulated gene expression data that approximates experimental data. Network topologies are generated by selecting subnetworks from previously described regulatory networks. Interaction kinetics are modeled by equations based on Michaelis-Menten and Hill kinetics. Our results show that the statistical properties of these topologies more closely approximate those of genuine biological networks than do those of different types of random graph models. Several user-definable parameters adjust the complexity of the resulting data set with respect to the structure learning algorithms.ConclusionThis network generation technique offers a valid alternative to existing methods. The topological characteristics of the generated networks more closely resemble the characteristics of real transcriptional networks. Simulation of the network scales well to large networks. The generator models different types of biological interactions and produces biologically plausible synthetic gene expression data.
Querying the public databases for sequences using complex keywords contained in the feature lines
Authors: Croce Olivier , Lamarre Michaël , Christen Richard 
Published: February 2006

Abstract

Background
High throughput technologies often require the retrieval of large data sets of sequences. Retrieval of EMBL or GenBank entries using keywords is easy using tools such as ACNUC, Entrez or SRS, but has some limitations, in particular when querying with complex keywords.

Results
We show that Entrez has severe limitations with respect to retrieving subsequences. SRS works well with simple keywords but not with keywords composed of several terms, and has problems with complex queries. ACNUC works well, but does not allow precise queries in the Feature qualifiers. We developed specific Perl scripts to precisely retrieve subsequences as defined by complex descriptors in the Features qualifiers of the EMBL entries. We improved parts of the bioPerl library to allow parsing of large data files, and we embedded these scripts in a user friendly interface (OS independent) for easy use.

Conclusion
Although not as fast as the public tools that use prebuilt indexes, parsing the complete entries using a script is often necessary in order to retrieve the exact data searched for. Embedding in a user friendly interface allows biologists to use the scripts, which can easily be modified, if necessary, by bioinformaticians for unforeseen needs.
Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network
Authors: Chung Wen-Yu , Albert Reka , Albert Istvan , Nekrutenko Anton , Makova Kateryna D 
Published: February 2006

Abstract

Background
While gene duplication is known to be one of the most common mechanisms of genome evolution, the fates of genes after duplication are still being debated. In particular, it is presently unknown whether most duplicate genes preserve (or subdivide) the functions of the parental gene or acquire new functions. One aspect of gene function, that is the expression profile in gene coexpression network, has been largely unexplored for duplicate genes.

Results
Here we build a human gene coexpression network using human tissue-specific microarray data and investigate the divergence of duplicate genes in it. The topology of this network is scale-free. Interestingly, our analysis indicates that duplicate genes rapidly lose shared coexpressed partners: after approximately 50 million years since duplication, the two duplicate genes in a pair have only slightly higher number of shared partners as compared with two random singletons. We also show that duplicate gene pairs quickly acquire new coexpressed partners: the average number of partners for a duplicate gene pair is significantly greater than that for a singleton (the latter number can be used as a proxy of the number of partners for a parental singleton gene before duplication). The divergence in gene expression between two duplicates in a pair occurs asymmetrically: one gene usually has more partners than the other one. The network is resilient to both random and degree-based in silico removal of either singletons or duplicate genes. In contrast, the network is especially vulnerable to the removal of highly connected genes when duplicate genes and singletons are considered together.

Conclusion
Duplicate genes rapidly diverge in their expression profiles in the network and play similar role in maintaining the network robustness as compared with singletons.

Contact:kdm16@psu.edu

Supplementary information: Please see additional files.
Protein kinases associated with the yeast phosphoproteome
Authors: Brinkworth Ross I , Munn Alan L , Kobe Boštjan 
Published: February 2006

Abstract

Background
Protein phosphorylation is an extremely important mechanism of cellular regulation. A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphorylation sites in 216 peptide sequences. However, the protein kinases responsible for the phosphorylation of the identified proteins have not previously been assigned.

Results
We used Predikin in combination with other bioinformatic tools, to predict which of 116 unique protein kinases in yeast phosphorylates each experimentally determined site in the phosphoproteome. The prediction was based on the match between the phosphorylated 7-residue sequence and the predicted substrate specificity of each kinase, with the highest weight applied to the residues or positions that contribute most to the substrate specificity. We estimated the reliability of the predictions by performing a parallel prediction on phosphopeptides for which the kinase has been experimentally determined.

Conclusion
The results reveal that the functions of the protein kinases and their predicted phosphoprotein substrates are often correlated, for example in endocytosis, cytokinesis, transcription, replication, carbohydrate metabolism and stress response. The predictions link phosphoproteins of unknown function with protein kinases with known functions and vice versa, suggesting functions for the uncharacterized proteins. The study indicates that the phosphoproteins and the associated protein kinases represented in our dataset have housekeeping cellular roles; certain kinases are not represented because they may only be activated during specific cellular responses. Our results demonstrate the utility of our previously reported protein kinase substrate prediction approach (Predikin) as a tool for establishing links between kinases and phosphoproteins that can subsequently be tested experimentally.