Renal Cell Carcinoma Metastatic to the Scalp.

Because of the asymptomatic natural history of renal cell carcinoma (RCC), by the time a diagnosis is made, metastatic disease is present in about one third of the cases. Thus, the overall survival of patients with RCC remains poor. Ultimately up to 50% of patients with RCC will develop metastases.

Systematic characterizations of text similarity in full text biomedical publications.

Background: Computational methods have been used to find duplicate biomedical publications in MEDLINE. Full text articles are becoming increasingly available, yet the similarities among them have not been systematically studied. Here, we quantitatively investigated the full text similarity of biomedical publications in PubMed Central.

Carbamazepine alone and in combination with doxycycline attenuates isoproterenol-induced cardiac hypertrophy.

β-adrenergic signaling is involved in the development of cardiac hypertrophy (CH), justifying the use of β-blockers as a therapy to minimize and postpone the consequences of this disease. Evidence suggests that adenylate cyclase, a downstream effector of the β-adrenergic pathway, might be a therapeutic target. We examined the effects of the anti-epileptic drug carbamazepine (CBZ), an inhibitor of adenylate cyclase.

Identifying duplicate content using statistically improbable phrases.

Motivation: Document similarity metrics such as PubMed's 'Find related articles' feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability.

Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure.

Background: Isoproterenol-induced cardiac hypertrophy in mice has been used in a number of studies to model human cardiac disease. In this study, we compared the transcriptional response of the heart in this model to other animal models of heart failure, as well as to the transcriptional response of human hearts suffering heart failure.

Results: We performed microarray analyses on RNA from mice with isoproterenol-induced cardiac hypertrophy and mice with exercise-induced physiological hypertrophy and identified 865 and 2,534 genes that were significantly altered in pathological and physiological cardiac hypertrophy models, respectively.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

Background: Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genomic variation and can cause phenotypic differences between individuals, including diseases. Bases are subject to various levels of selection pressure, reflected in their inter-species conservation.

Results: We propose a method that is not dependant on transcription information to score each coding base in the human genome reflecting the disease probability associated with its mutation.

Deja vu: a database of highly similar citations in the scientific literature.

In the scientific research community, plagiarism and covert multiple publications of the same data are considered unacceptable because they undermine the public confidence in the scientific integrity. Yet, little has been done to help authors and editors to identify highly similar citations, which sometimes may represent cases of unethical duplication. For this reason, we have made available Déjà vu, a publicly available database of highly similar Medline citations identified by the text similarity search engine eTBLAST.

Doxycycline attenuates isoproterenol- and transverse aortic banding-induced cardiac hypertrophy in mice.

The United States Food and Drug Administration-approved antibiotic doxycycline (DOX) inhibits matrix metalloproteases, which contribute to the development of cardiac hypertrophy (CH). We hypothesized that DOX might serve as a treatment for CH. The efficacy of DOX was tested in two mouse models of CH: induced by the beta-adrenergic agonist isoproterenol (ISO) and induced by transverse aortic banding.

Déjà vu--a study of duplicate citations in Medline.

Motivation: Duplicate publication impacts the quality of the scientific corpus, has been difficult to detect, and studies this far have been limited in scope and size. Using text similarity searches, we were able to identify signatures of duplicate citations among a body of abstracts.

Results: A sample of 62,213 Medline citations was examined and a database of manually verified duplicate citations was created to study author publication behavior.

eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications.

Authors, editors and reviewers alike use the biomedical literature to identify appropriate journals in which to publish, potential reviewers for papers or grants, and collaborators (or competitors) with similar interests. Traditionally, this process has either relied upon personal expertise and knowledge or upon a somewhat unsystematic and laborious process of manually searching through the literature for trends. To help with these tasks, we report three utilities that parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.

Text similarity: an alternative way to search MEDLINE.

Motivation: The most widely used literature search techniques, such as those offered by NCBI's PubMed system, require significant effort on the part of the searcher, and inexperienced searchers do not use these systems as effectively as experienced users. Improved literature search engines can save researchers time and effort by making it easier to locate the most important and relevant literature.

Results: We have created and optimized a new, hybrid search system for Medline that takes natural text as input and then delivers results with high precision and recall.

Friend, an integrated analytical front-end application for bioinformatics.

Unlabelled: Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities, such as structure visualization, with different rendering and coloring, sequence alignment and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions and protein super-families. It is also useful for functional annotation of proteins, protein modeling and protein folding studies.

Conservation of amino acids into multiple alignments involved in pairwise interactions in three-dimensional protein structures.

We present an original strategy, that involves a bioinformatic software structure, in order to perform an exhaustive and objective statistical analysis of three-dimensional structures of proteins. We establish the relationship between multiple sequences alignments and various structural features of proteins. We show that amino acids implied in disulfide bonds, salt bridges and hydrophobic interactions have been studied.

Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures.

Motivation: Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist between them.