A novel technique for post-pyloric feeding tube placement in critically ill patients: A pilot study

Publisher's copy made available with the permission of the publisher © Australian Society of AnaesthetistsDelivery of enteral nutrition in critically ill patients is often hampered by gastric stasis necessitating direct feeding into the small intestine. Current techniques for placement of post-pyloric feeding catheters are complex, time consuming or both, and improvements in feeding tube placement techniques are required. The Cathlocator™ is a novel device that permits real time localisation of the end of feeding tubes via detection of a magnetic field generated by a small electric current in a coil incorporated in the tip of the tube. We performed a pilot study evaluating the feasibility of the Cathlocator™ system to guide and evaluate the placement of (1) nasoduodenal feeding tubes, and (2) nasogastric drainage tubes in critically ill patients with feed intolerance due to slow gastric emptying. A prospective study of eight critically ill patients was undertaken in the intensive care unit of a tertiary hospital. The Cathlocator™ was used to (1) guide the positioning of the tubes post-pylorically and (2) determine whether nasogastric and nasoduodenal tubes were placed correctly. Tube tip position was compared with data obtained by radiology. Data are expressed as median (range). Duodenal tube placement was successful in 7 of 8 patients (insertion time 12.6 min (5.3-34.4)). All nasogastric tube placements were successful (insertion time 3.4 min (0.6-10.0)). The Cathlocator™ accurately determined the position of both tubes without complication in all cases. The Cathlocator™ allows placement and location of an enteral feeding tube in real time in critically ill patients with slow gastric emptying. These findings warrant further studies into the application of this technique for placement of post-pyloric feeding tubes.R. J. Young, M. J. Chapman, R. Fraser, R. Vozzo, D. P. Chorley, S. Creedhttp://www.aaic.net.au/Article.asp?D=200430

The Sequence Ontology: a tool for the unification of genome annotations

The Sequence Ontology ( SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators

Transcriptomic profiling reveals extraordinary diversity of venom peptides in unexplored predatory gastropods of the genus Clavus

Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis, and two specimens of Cv. davidgilmouri were analyzed, leading to the identification of a total of 1,176 putative venom peptide toxins ( drillipeptides ). Based on the combined evidence of secretion signal sequence identity, entire precursor similarity search (BLAST), and the orthology inference, putative Clavus toxins were assigned to 158 different gene families. The majority of identified transcripts comprise signal, pro-, mature peptide, and post- regions, with a typically short ( \u3c 50 amino acids) and cysteine-rich mature peptide region. Thus drillipeptides are structurally similar to conotoxins. However, convincing homology with known groups of Conus toxins was only detected for very few toxin families. Among these are Clavus counterparts of Conus venom insulins (drillinsulins), porins (drilliporins), highly diversified lectins (drillilectins). The short size of most drillipeptpides and structural similarity to conotoxins was unexpected, given that most related conoidean gastropod families (Terebridae and Turridae) possess longer mature peptide regions. Our findings indicate that, similar to conotoxins, drillipeptides may represent a valuable resource for future pharmacological exploration

Spontaneous apoptosis in ovarian carcinomas: a positive association with p53 gene mutation is dependent on growth fraction

Changes in cell survival contribute to tumour development, influence tumour biology and its response to chemotherapy. p53 gene alterations should negatively affect apoptosis by impaired p53-dependent apoptotic response. We looked for associations between spontaneous apoptosis, p53 gene mutation, p53 protein accumulation, growth fraction, bcl-2 expression and histological parameters in 64 ovarian, four tubal and three peritoneal carcinomas. Apoptotic cells were detected with the TUNEL method. p53 gene variants were detected by the single-strand conformation polymorphism and were sequenced directly. P53, Ki-67 and bcl-2 protein expressions were detected immunohistochemically. A weighed multiple logistic regression model was applied. Apoptotic index (Al) ranged 0.02–0.18 (mean 0.11); proliferation index (PI) ranged 3–90% (mean 54%). p53 gene mutations were present in 51, p53 protein accumulation in 46, and diffuse bcl-2 expression in 29 of 71 tumours. The AI was positively associated with the presence of p53 gene mutation (P = 0.011). However, the PI included into the analysis did positively influence the AI (P = 0.02) and diminished the association with p53 gene mutation (P = 0.082). The AI was negatively associated with good histological differentiation (P = 0.0006), the serous tumour type (P = 0.002), and diffuse bcl-2 expression (P = 0.025). Strong bcl-2 expression was associated with endometrioid tumour type (P = 0.002). FIGO stage and p53 protein accumulation were the only parameters that influenced overall survival time. Thus, our results suggest that histological tumour type and grade are major determinants of spontaneous apoptosis in ovarian carcinomas;p53 alterations do not adversely but rather positively affect spontaneous apoptosis by increasing growth fraction. This, in turn, suggests p53-independency of spontaneous apoptosis in ovarian carcinomas. © 2000 Cancer Research Campaig

Logics, rhetoric and 'the blob': populist logic in the Conservative reforms to English schooling

A lot has been written about the lasting implications of the Conservative reforms to English schooling, particularly changes made by Michael Gove as Education Secretary (2010–2014). There is a lot less work, however, on studying the role that language, strategy and the broader political framework played in the process of instituting and winning consent for these reforms. Studying these factors is important for ensuring that any changes to education and schooling are not read in isolation from their political context. Speeches particularly capture moments where intellectual and strategic political traditions meet, helping us to form a richer understanding of the motives behind specific reform goals and where they fit into a political landscape. This article analyses speeches and policy documents from prominent politicians who led the Conservative education agenda between 2010–2014 to illustrate how politicians mobilised a deliberate populist strategy and argumentation to achieve specific educational goals, but which have had broader social and political implications. Concepts from interpretive political studies are used to develop a case analysis of changes to teacher training provision and curriculum reform, illustrating how politicians constructed a frontier between ‘the people’ (commonly teachers or parents) and an illegitimate ‘elite’ (an educational establishment) that opposed change. This anti‐elite populist rhetoric, arguably first tested in the Department for Education, has now become instituted more widely in our current British politics

Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs

The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct annotation is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3-prime untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3-prime polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental dataComment: 44 pages, 9 figure

A scalable machine-learning approach to recognize chemical names within large text databases

MOTIVATION: The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. RESULTS: A first-order Markov Model (MM) was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing

<p>Abstract</p> <p>Background</p> <p>Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a state-of-the-art Natural Language Processing system that creates computer-readable networks of regulatory interactions directly from different collections of abstracts and full-text papers. Our major aim is to understand how automatic annotation using Text-Mining techniques can complement manual curation of biological databases. We implemented a rule-based system to generate networks from different sets of documents dealing with regulation in <it>Escherichia coli </it>K-12.</p> <p>Results</p> <p>Performance evaluation is based on the most comprehensive transcriptional regulation database for any organism, the manually-curated RegulonDB, 45% of which we were able to recreate automatically. From our automated analysis we were also able to find some new interactions from papers not already curated, or that were missed in the manual filtering and review of the literature. We also put forward a novel Regulatory Interaction Markup Language better suited than SBML for simultaneously representing data of interest for biologists and text miners.</p> <p>Conclusion</p> <p>Manual curation of the output of automatic processing of text is a good way to complement a more detailed review of the literature, either for validating the results of what has been already annotated, or for discovering facts and information that might have been overlooked at the triage or curation stages.</p