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1.  Concept annotation in the CRAFT corpus 
BMC Bioinformatics  2012;13:161.
Background
Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.
Results
This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement.
Conclusions
As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.
doi:10.1186/1471-2105-13-161
PMCID: PMC3476437  PMID: 22776079
2.  Structure and Function of Eukaryotic Ribonuclease P RNA 
Molecular cell  2006;24(3):445-456.
Summary
Ribonuclease P (RNase P) is the ribonucleoprotein endonuclease that processes the 5′-ends of precursor-tRNAs. Bacterial and eukaryal RNase P RNAs had the same primordial ancestor, however, they were molded differently by evolution. RNase P RNAs of eukaryotes, in contrast to bacterial RNAs, are not catalytically active in vitro without proteins. By comparing the bacterial and eukaryal RNAs we can begin to understand the transitions made between the RNA and protein-dominated worlds. We report based on crosslinking studies that eukaryal RNAs, although catalytically inactive alone, fold into functional forms and specifically bind tRNA even in the absence of proteins. Based on the crosslinking results and crystal structures of bacterial RNAs we develop a tertiary structure model of the eukaryal RNase P RNA. The eukaryal RNA contains a core structure similar to the bacterial RNA, but lacks specific features, that in bacterial RNAs contributes to catalysis and global stability of tertiary structure.
doi:10.1016/j.molcel.2006.09.011
PMCID: PMC1716732  PMID: 17081993
3.  Recovery of Streptococcus iniae from Diseased Fish Previously Vaccinated with a Streptococcus Vaccine 
Streptococcus iniae was recovered from diseased rainbow trout (Oncorhynchus mykiss, Walbaum) previously vaccinated against streptococcosis. PCR and serological methods indicate the presence of a new serotype in the diseased fish.
doi:10.1128/AEM.67.8.3756-3758.2001
PMCID: PMC93086  PMID: 11472962
4.  trans Splicing of Polycistronic Caenorhabditis elegans Pre-mRNAs: Analysis of the SL2 RNA 
Molecular and Cellular Biology  2000;20(18):6659-6667.
Genes in Caenorhabditis elegans operons are transcribed as polycistronic pre-mRNAs in which downstream gene products are trans spliced to a specialized spliced leader, SL2. SL2 is donated by a 110-nucleotide RNA, SL2 RNA, present in the cell as an Sm-bound snRNP. SL2 RNA can be conceptually folded into a phylogenetically conserved three-stem-loop secondary structure. Here we report an in vivo mutational analysis of the SL2 RNA. Some sequences can be changed without consequence, while other changes result in a substantial loss of trans splicing. Interestingly, the spliced leader itself can be dramatically altered, such that the first stem-loop cannot form, with only a relatively small loss in trans-splicing efficiency. However, the primary sequence of stem II is crucial for SL2 trans splicing. Similarly, the conserved primary sequence of the third stem-loop plays a key role in trans splicing. While mutations in stem-loop III allow snRNP formation, a single nucleotide substitution in the loop prevents trans splicing. In contrast, the analogous region of SL1 RNA is not highly conserved, and its mutation does not abrogate function. Thus, stem-loop III appears to confer a specific function to SL2 RNA. Finally, an upstream sequence, previously predicted to be a proximal sequence element, is shown to be required for SL2 RNA expression.
PMCID: PMC86170  PMID: 10958663
5.  Covert video surveillance -- a response to Professor Southall and Dr. Samuels. 
Journal of Medical Ethics  1996;22(1):29-31.
In their reply to my recent paper on Munchausen's syndrome by proxy, Professor Southall and Dr. Samuels concede that some things may be learned from my observations. They do not attend to the main argument of the paper, however, that the proportion of research interest in their use of covert video surveillance merits consideration of the research protocol by an independent research ethics committee. It will not do simply to assert that the use of this technology for the purposes outlined in their accounts is not research. I formulated arguments based on facts divulged in those published accounts for regarding their work as containing a considerable proportion of research activity. Unfortunately their reply did not address these arguments. Until such points are adequately answered the protection of patients calls for satisfactory judgments to be made on certain important issues which any research ethics committee would be obliged to consider in an evaluation of their activities. I suggest that some of these features will create more difficulties for approval of such a protocol than others.
PMCID: PMC1376855  PMID: 11644878
7.  Correlation of Immunological Responsiveness with Lymphocyte Changes in Chickens Infected with Marek's Disease 
Infection and Immunity  1971;4(5):567-574.
Several immunological, hematological, and pathological responses associated with Marek's disease were determined. Four-week-old Marek's disease-infected and control chickens were injected with Salmonella pullorum antigen. About one-half of all infected chickens tested were unresponsive to antigenic challenge. Antibody titers in responsive infected chickens were significantly depressed at 1 and 2 weeks post-inoculation when compared to controls. Total white blood cell counts of control and control-antigen chickens were significantly lower than counts in infected chickens. Based on response to antigenic challenge, 24% of the responsive group had leukemia compared to 54% of the unresponsive chickens. The predominant cell populations in these two groups responsible for the mononuclear cell leukemia were large lymphocytes and blast cells. These cell increases were significantly greater in unresponsive chickens. Also, transient increases in the granulocytic elements were observed in some infected chickens. Large fluctuations in hematocrit values were observed in Marek's disease-infected chickens. As many as 30% of the infected chickens were anemic throughout the testing periods. Infected chickens which did not receive antigen had lower incidences of mortality and gross lesions than similarly treated chickens which did receive antigen. In addition, those chickens which were unresponsive to antigenic challenge had a higher mortality rate and increased percentages of gross lesions when compared with responsive chickens.
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PMCID: PMC416354  PMID: 5292890

Results 1-7 (7)