Categorical and thematic knowledge representation in the brain: neural correlates of taxonomic and thematic conceptual relations.

Most current models of knowledge organization in the brain are based on hierarchical or taxonomic categories (animals, tools). Another important organizational pattern is thematic categorization, i.e.

Expression and characterization of full-length human heme oxygenase-1: the presence of intact membrane-binding region leads to increased binding affinity for NADPH cytochrome P450 reductase.

Heme oxygenase-1 (HO-1) is the chief regulatory enzyme in the oxidative degradation of heme to biliverdin. In the process of heme degradation, HO-1 receives the electrons necessary for catalysis from the flavoprotein NADPH cytochrome P450 reductase (CPR), releasing free iron and carbon monoxide. Much of the recent research involving heme oxygenase has been done using a 30 kDa soluble form of the enzyme, which lacks the membrane binding region (C-terminal 23 amino acids).

Graphs in molecular biology.

Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network.

Coverage and error models of protein-protein interaction data by directed graph analysis.

Using a directed graph model for bait to prey systems and a multinomial error model, we assessed the error statistics in all published large-scale datasets for Saccharomyces cerevisiae and characterized them by three traits: the set of tested interactions, artifacts that lead to false-positive or false-negative observations, and estimates of the stochastic error rates that affect the data. These traits provide a prerequisite for the estimation of the protein interactome and its modules.

Delayed recovery and late development of complex regional pain syndrome in patients with an isolated fracture of the distal radius: prediction of a regional inflammatory response by early signs.

We studied prospectively the regional inflammatory response to a unilateral distal radial fracture in 114 patients at eight to nine weeks after injury and again at one year. Our aim was to identify patients at risk for a delayed recovery and particularly those likely to develop complex regional pain syndrome. In order to quantify clinically the inflammatory response, a regional inflammatory score was developed.

Correction of tailor's bunion with the Boesch technique: a retrospective study.

Background: The Boesch technique(1,2) is a minimally-invasive and time-saving subcutaneous subcapital metatarsal osteotomy. Since 1984, we have been using this osteotomy technique for patients with a symptomatic tailor's bunion in whom conservative treatment has failed. This distal osteotomy is stabilized by a combination of a Kirschner wire and a special dressing.

Thiols and the chemoprevention of cancer.

Thiols such as glutathione interfere with the complex carcinogenic process. Under stress conditions, they scavenge harmful molecules: Glutathione conjugation of electrophilic carcinogens may prevent tumor initiation, and reduced thiols may defend against oxidative stress. Thus, associated chemopreventive strategies involve enhancement of antioxidant or conjugating capacity by increasing the levels of, particularly, glutathione through precursor application or synthesis stimulation and by inducing the corresponding enzymes.

Naphthalen-1-yl-(4-pentyloxynaphthalen-1-yl)methanone: a potent, orally bioavailable human CB1/CB2 dual agonist with antihyperalgesic properties and restricted central nervous system penetration.

Selective activation of peripheral cannabinoid CB1 receptors has the potential to become a valuable therapy for chronic pain conditions as long as central nervous system effects are attenuated. A new class of cannabinoid ligands was rationally designed from known aminoalkylindole agonists and showed good binding and functional activities at human CB1 and CB2 receptors. This has led to the discovery of a novel CB1/CB2 dual agonist, naphthalen-1-yl-(4-pentyloxynaphthalen-1-yl)methanone (13), which displays good oral bioavailability, potent antihyperalgesic activity in animal models, and limited brain penetration.

Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts.

Background: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is a high-throughput assay for DNA-protein-binding or post-translational chromatin/histone modifications. However, the raw microarray intensity readings themselves are not immediately useful to researchers, but require a number of bioinformatic analysis steps. Identified enriched regions need to be bioinformatically annotated and compared to related datasets by statistical methods.

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.

Background: Non-coding RNAs (ncRNAs) are an emerging focus for both computational analysis and experimental research, resulting in a growing number of novel, non-protein coding transcripts with often unknown functions. Whole genome screens in higher eukaryotes, for example, provided evidence for a surprisingly large number of ncRNAs. To supplement these searches, we performed a computational analysis of seven yeast species and searched for new ncRNAs and RNA motifs.

Practical advance in obtaining an emergency airway via cricothyroidotomy.

By the time a cricothyroidotomy is deemed necessary, the patient is in critical need of an emergency airway before anoxic damage ensues. Two things are necessary for the delivery of the requisite oxygen. First, an airway must be rapidly established.

High-throughput flow cytometry-based assay to identify apoptosis-inducing proteins.

After sequencing the human genome, the challenge ahead is to systematically analyze the functions and disease relation of the proteins encoded. Here the authors describe the application of a flow cytometry-based high-throughput assay to screen for apoptosis-activating proteins in transiently transfected cells. The assay is based on the detection of activated caspase-3 with a specific antibody, in cells overexpressing proteins tagged C- or N-terminally with yellow fluorescent protein.

Coma as a presenting symptom of primary HIV infection.

Primary HIV infection (PHI) is symptomatic in 50-90% of patients. The diagnosis, however, is seldom made at first presentation. This is probably because of the multifaceted and unspecific manifestations, the omission to perform adequate diagnostic testing and the failure to assess risks for PHI.

Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality.

In studies of their transcriptional activity, genomes have shown a high order of organization. We assessed the question of how genomically neighboring genes are transcriptionally coupled across tissues and what could be the driving force behind their coupling. We focused our analysis on the transcriptome information for 13 tissues of Mus musculus and 79 tissues of Homo sapiens.

Thermodynamic studies on the interaction of antibodies with beta-amyloid peptide.

Antibodies against beta-amyloid peptides (Abetas) are considered an important therapeutic opportunity in Alzheimer's disease. Despite the vast interest in Abeta no thermodynamic data on the interaction of antibodies with Abeta are available as yet. In the present study we use isothermal titration calorimetry (ITC) and surface plasmon resonance to provide a quantitative thermodynamic analysis of the interaction between soluble monomeric Abeta(1-40) and mouse monoclonal antibodies (mAb).

CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data.

Motivation: CoCo, ChIP-on-Chip online, is an open-source web application that supports the annotation and curation of regulatory regions and associated target genes discovered in ChIP-on-chip experiments. CoCo integrates ChIP-on-chip results with diverse types of gene expression data (expression profiling, in situ hybridization) and displays them within a genomic context. Regulatory relationships between the transcription factor-bound regions and putative target genes can be stored and expanded throughout different sessions.

Hemodynamics after endoscopic submucosal injection of epinephrine in patients with nonvariceal upper gastrointestinal bleeding: a matter of concern.

We report about detailed hemodynamic changes and one major cardiac complication occurring after submucosal injection of epinephrine (1 : 10 000) for management of upper gastrointestinal bleeding in a series of four consecutive patients. Cardiac contractility and afterload, determined by the cardiac index and the systemic vascular resistence index (SVRI), were assessed by transpulmonary thermodilution using the Pulse Contour Cardiac Output monitoring system (PiCCO; Pulsion Medical Systems, Munich, Germany), and the mean arterial pressure and heart rate were recorded. We observed a distinct rise in both mean arterial pressure and heart rate, and this effect was pronounced in the three patients with esophageal lesions.

Hydrologic regionalisation impacts on wet-weather control selection.

Continuous simulation is performed using the US Environmental Protection Agency (USEPA) Storm Water Management Model (SWMM) to evaluate regional differences around the United States in hydrologic and water quality performance of wet-weather controls. Controls are characterised as being limited by peak inflow rate (i.e.

The scope of integrated modelling: system boundaries, sub-systems, scales and disciplines.

Integrated modelling has become an urgent issue of urban drainage and wastewater treatment planning. The scope of integrated modelling, system boundaries and disciplines to be involved are addressed in view of future developments and new paradigms in urban drainage, demanding the inclusion of the full urban water cycle. A system analysis is demonstrated to identify relevant sub-systems and components, processes and interactions within the urban water system.

Biomolecular interaction analysis in drug discovery using surface plasmon resonance technology.

The review gives first an introduction into the basics of surface plasmon resonance technology. The physical principle is shortly discussed followed by a discussion of the experimental details to be considered when using this technology for biomolecular interaction analysis. Based on recent publications it is demonstrated that the technology has widespread applications in many fields of the drug discovery process.