Coreference resolution in clinical discharge summaries, progress notes, surgical and pathology reports: a unified lexical approach

We developed a lexical rule-based system that uses a unified approach to resolving coreference across a wide variety of clinical records comprising discharge summaries, progress notes, pathology, radiology and surgical reports from two corpora (Ontology Development and Information Extraction (ODIE) and i2b2/VA) provided for the fifth i2b2/VA shared task. Taking the unweighted mean between 4 coreference metrics, validation of the system against the i2b2/VA corpus attained an overall F-score of 87.7% across all mention classes, with a maximum of 93.1% for coreference of persons, and a minimum of 77.2% for coreference of tests. For the ODIE corpus the overall F-score across all mention classes was 79.4%, with a maximum of 82.0% for coreference of persons and a minimum of 13.1% for coreference of diagnostic reagents. For the ODIE corpus our results are comparable to the mean reported inter-annotator agreement with the gold standard. We discuss the four categories of errors we identified, and how these might be addressed. The system uses a number of reusable modules and techniques that may be of benefit to the research community

A tool for enhancing MetaMap performance when annotating clinical guideline documents with UMLS concepts

We developed a tool that integrates the National Library of Medicine's MetaMap software with GATE, an open-source text an- alytics framework. The tool allows non-ASCII encoded documents of numerous formats to be annotated with UMLS concepts. We created a GATE pipeline to chunk cardiovascular disease guideline text into default segments (blank-line delimited), XML element content, sentences and phrases, which were sequentially submitted to MetaMap for annotation. XML element, sentence and phrase chunking allowed term extraction and mapping to be completed in around 1/3 of the time taken with de- fault chunking, although with slight loss of accuracy (F1.0s=0.94-0.99). However, phrase chunking allows more complex input to be processed in real time, which is not possible with the other approaches. We discuss the results in relation to use of MetaMap's --term processing option for generating pre- and post-coordinated mappings from composite phrases

Automated recognition and post-coordination of complex clinical terms

One of the key tasks in integrating guideline-based decision support systems with the electronic patient record is the mapping of clinical terms contained in both guidelines and patient notes to a common, controlled terminology. However, a vocabulary of pre-coordinated terms cannot cover every possible variation - clinical terms are often highly compositional and complex. We present a rule-based approach for automated recognition and post-coordination of clinical terms using minimal, morpheme-based thesauri, neoclassical combining forms and part-of-speech analysis. The process integrates MetaMap with the open-source GATE framework

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

What are the potential emissions from engine-generation sets?

Biogas is generated from anaerobic digestion of manure and organic wastes. It primarily consists of methane (50-70%), carbon dioxide (25-50%) and water vapor (1-5%). Depending on the feedstock and anaerobic digester conditions, biogas may also contain nitrogen gas (0-5%), hydrogen sulfide (0-7,500 ppm), and ammonia (0-500 ppm). Others volatiles and particulates are trace-level components of biogas

Greenhouse gas reduction and other benefits of biogas upgrading

Biogas obtained from anaerobic digestion of livestock manure is a complex mixture containing ~60% methane (CH4) and other less valuable gases. Upgrading the biogas to reduce contaminants and increase the CH4 concentration is advantageous for several reasons

Pressure effects on magnetic ground states in cobalt doped multiferroic Mn1−x_{1-x}Cox_{x}WO4_4

Using ambient pressure x-ray and high pressure neutron diffraction, we studied the pressure effect on structural and magnetic properties of multiferroic Mn$_{1-x}$Co$_x$WO$_4$ single crystals ($x=0, 0.05, 0.135$ and $0.17$), and compared it with the effects of doping. Both Co doping and pressure stretch the Mn-Mn chain along the $c$~direction. At high doping level ($x=0.135$ and $0.17$), pressure and Co doping drive the system in a similar way and induce a spin-flop transition for the $x=0.135$ compound. In contrast, magnetic ground states at lower doping level ($x=0$ and $0.05$) are robust against pressure but experience a pronounced change upon Co substitution. As Co introduces both chemical pressure and magnetic anisotropy into the frustrated magnetic system, our results suggest the magnetic anisotropy is the main driving force for the Co induced phase transitions at low doping level, and chemical pressure plays a more significant role at higher Co concentrations.Comment: 6 pages, 4 figures, to be published in Physical Rev.

Pressure shift of the superconducting T_c of LiFeAs

The effect of hydrostatic pressure on the superconductivity in LiFeAs is investigated up to 1.8 GPa. The superconducting transition temperature, T_c, decreases linearly with pressure at a rate of 1.5 K/GPa. The negative pressure coefficient of T_c and the high ambient pressure T_c indicate that LiFeAs is the high-pressure analogue of the isoelectronic SrFe_2As_2 and BaFe_2As_2.Comment: 3 pages, 2 figure