A reappraisal of sentence and token splitting for life sciences documents.

Natural language processing of real-world documents requires several low-level tasks such as splitting a piece of text into its constituent sentences, and splitting each sentence into its constituent tokens to be performed by some preprocessor (prior to linguistic analysis). While this task is often considered as unsophisticated clerical work, in the life sciences domain it poses enormous problems due to complex naming conventions. In this paper, we first introduce an annotation framework for sentence and token splitting underlying a newly constructed sentence- and token-tagged biomedical text corpus.

Large-scale evaluation of a medical cross-language information retrieval system.

We propose an approach to multilingual medical document retrieval in which complex word forms are segmented according to medically relevant morpho-semantic criteria. At its core lies a multilingual dictionary, in which entries are equivalence classes of subwords, i.e.

Kinetics of TmHU binding to DNA as observed by optical tweezers.

The kinetics of binding for the histone-like protein TmHU (from Thermotoga maritima) to DNA is analyzed on a single molecule level by use of optical tweezers. For the reaction rate a pronounced concentration-dependence is found with an "all or nothing"-limit which suggests the cooperative nature of the binding-reaction. By analyzing the statistics of mechanically induced dissociation-events of TmHU from DNA multiple reaction sites are observed to become more likely with increasing TmHU concentration.

The rationality of informal argumentation: a Bayesian approach to reasoning fallacies.

Classical informal reasoning "fallacies," for example, begging the question or arguing from ignorance, while ubiquitous in everyday argumentation, have been subject to little systematic investigation in cognitive psychology. In this article it is argued that these "fallacies" provide a rich taxonomy of argument forms that can be differentially strong, dependent on their content. A Bayesian theory of content-dependent argument strength is presented.

Spatial location and its relevance for terminological inferences in bio-ontologies.

Background: An adequate and expressive ontological representation of biological organisms and their parts requires formal reasoning mechanisms for their relations of physical aggregation and containment.

Results: We demonstrate that the proposed formalism allows to deal consistently with "role propagation along non-taxonomic hierarchies", a problem which had repeatedly been identified as an intricate reasoning problem in biomedical ontologies.

Conclusion: The proposed approach seems to be suitable for the redesign of compositional hierarchies in (bio)medical terminology systems which are embedded into the framework of the OBO (Open Biological Ontologies) Relation Ontology and are using knowledge representation languages developed by the Semantic Web community.

Pharmacokinetic and pharmacodynamic comparison of enteric-coated mycophenolate sodium and mycophenolate mofetil in maintenance renal transplant patients.

The aim of this single-center crossover substudy was to assess pharmacokinetics and pharmacodynamics [inosine 5'-monophosphate dehydrogenase (IMPDH) activity] of enteric-coated mycophenolate sodium (EC-MPS) and mycophenolate mofetil (MMF) at steady-state conditions. Stable maintenance renal transplant patients on 1 g MMF b.i.

Towards the ontological foundations of symbolic biological theories.

Objective: Support for the symbolic representation of the physical structure of living organisms by an ontologically solid and logically sound foundation as a basis for formal reasoning.

Methods: A set of canonical relations and attributes necessary for empirically adequate descriptions of biological entities is proposed.

Results: It is shown how a broad range of biological organisms and their parts can be represented by cascading theories which are ordered by the dimensions of granularity, development, species, and canonicity.

Monitoring of ELISA-reactive antibodies against anthrax protective antigen (PA), lethal factor (LF), and toxin-neutralising antibodies in serum of individuals vaccinated against anthrax with the PA-based UK anthrax vaccine.

The human anthrax vaccines currently licensed contain the protective antigen (PA) of Bacillus anthracis as main antigen together with traces of some other bacillus components, e.g. lethal factor (LF).

Self-assembly of fullerene-rich nanostructures with a stannoxane core.

Fullerene derivatives bearing a carboxylic acid function undergo self-assembly with n-butylstannonic acid (nBuSn(O)OH) to produce fullerene-rich nanostructures with a stannoxane core in almost quantitative yields.

Towards an upper level ontology for molecular biology.

There is a growing need for the general-purpose description of the basic conceptual entities in the life sciences. Up until now, upper level models have mainly been purpose-driven, such as the GENIA ontology, originally devised as a vocabulary for corpus annotation. As an alternative,we here present BioTop, a description-logic-based top level ontology for molecular biology, which we consider as an ontologically conscious redesign of the GENIA ontology.

Cross-lingual alignment of biomedical acronyms and their expansions.

We propose a method that aligns biomedical acronyms and their definitions across different languages. The approach is based upon a freely available tool for the extraction of abbreviations together with their expansions, and the subsequent normalization of language-specific variants, synonyms, and translations of the extracted acronym definitions. In this step, acronym expansions are mapped onto a language-independent concept-layer on which intra- as well as interlingual comparisons are drawn.

A language classifier that automatically divides medical documents for experts and health care consumers.

We propose a pipelined system for the automatic classification of medical documents according to their language (English, Spanish and German) and their target user group (medical experts vs. health care consumers). We use a simple n-gram based categorization model and present experimental results for both classification tasks.

[Lecture disasters - and how to prevent them].

Presentations at medical conferences can sometimes confuse or compromise understanding of current topics. Although considerable time and financial costs may be taken to be present at such events, all too often one must go through inferior presentations that are poorly structured and do not contribute to one's understanding of the topic at hand. A good presentation is distinguishable by the clear intentions of the speaker to give a good lecture.

The semantics of procedures and diseases in SNOMED CT.

Objectives: SNOMED CT is emerging as a reference terminology for the entire health care process. It claims to be founded on logic-based modelling principles. In this article, we analyze a special encoding scheme for diseases and procedures in SNOMED CT, the so-called relationship groups (RGs), which had been devised to avoid ambiguities in definitions.

Disseminated mucormycosis in haematological patients: CT and MRI findings with pathological correlation.

Disseminated mucormycosis is a rare, mostly fatal infectious complication in immunocompromised haematological patients. The purpose of our study was to describe the multiorgan manifestations of disseminated mucormycosis documented at CT and MRI in four patients and correlate these with the pathological findings and patient outcome. Irrespective of the site of infection, infarction or haemorrhage are the constant features of invasive mycosis.

Electrospray mass spectrometry analysis of dendritic branches bearing peripheral fullerene subunits.

The electrospray mass spectrometric characterization of neutral dendrons with a carboxylic acid function or a t-butyl ester moiety at the central point and up to eight peripheral C60 subunits has been performed and is described in detail. Molecules bearing a carboxylic acid group at the center turned out to be preferentially ionized by deprotonation, whereas those with a t-butyl ester head group were ionized by reduction of the C60 units in the infusion capillary of the electrospray source.

Automatic lexeme acquisition for a multilingual medical subword thesaurus.

Purpose: We present a method for the automated acquisition of a multilingual medical lexicon (for Spanish, French and Swedish) to be used within the framework of a medical cross-language text retrieval system.

Methods: For the lexical acquisition process, we incorporate seed lexicons and lists of trusted term translations derived from the UMLS Metathesaurus. The seed lexicons for Spanish, French and Swedish are automatically generated from (previously manually constructed) Portuguese, German and English sources by simple string transformations.

Effective grading of termhood in biomedical literature.

The ever-increasing amount of textual information in biomedicine calls for effective procedures for automatic terminology extraction which assist biomedical researchers and professionals in gathering and organizing terminological knowledge encoded in text documents. In this study, we propose a new, linguistically grounded measure for automatically identifying multi-word terms from the biomedical literature. Our approach is based on the limited paradigmatic modifiability of terms and is tested on bigram, trigram and quadgram noun phrases extracted from a 104-million-word text corpus comprised of Medline abstracts.

How to distinguish parthood from location in bioontologies.

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organism reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular may often be controversial.

Binding of TmHU to single dsDNA as observed by optical tweezers.

Optical tweezers are employed to study the action of the histone-like protein from Thermotoga maritima (TmHU) on DNA at a single molecule level. Binding and disruption of TmHU to and from DNA are found to take place in discrete steps of 4-5 nm length and a net binding enthalpy of about 16kBT. This is in reasonable agreement with a microscopic model that estimates the extension of the binding sites of the protein and evaluates the energetics mainly for bending of the DNA in the course of interaction.