OBJECTIVE To evaluate HIV-1 transmission trends and the impact of highly active antiretroviral therapy (HAART) on newly diagnosed HIV infections in Geneva, Switzerland. DESIGN Retrospective molecular epidemiology analysis of all newly HIV-diagnosed individuals between 2008 and 2010. METHODS Phylogenetic analyses were performed using pol sequences of 780 newly HIV-1 diagnosed individuals bet...

Herpes Simplex virus (HSV) is responsible for a number of diseases which range in severity from subclinical infection to lethal encephalitis. The most common human illnesses caused by HSV are the recurrent common cold sore and genital herpes. Following infection of human individuals with HSV the virus replicates lytically in peripheral epithelial cells causing mucocutaneous lesions before infec...

Open Information Extraction (OIE) systems extract relational tuples from text without requiring to specify in advance the relations of interest. Systems perform well on widely used metrics such as precision and yield, but a close look at systems output shows a general lack of informativeness in facts deemed correct. We propose a new evaluation protocol, based on question answering, that is clos...

Open IE methods extract structured propositions from text. However, these propositions are neither consolidated nor generalized, and querying them may lead to insufficient or redundant information. This work suggests an approach to organize open IE propositions using entailment graphs. The entailment relation unifies equivalent propositions and induces a specific-to-general structure. We create...

This paper presents a novel algorithm for the acquisition of Information Extraction patterns. The approach makes the assumption that useful patterns will have similar meanings to those already identified as relevant. Patterns are compared using a variation of the standard vector space model in which information from an ontology is used to capture semantic similarity. Evaluation shows this algor...

SUMMARY IE-Kb (Intron Exon-Knowledge base) illustrates the intron-exon dynamics in eukaryotic genes. We have developed three different knowledge sets, namely 'Non-redundant ExInt', 'Non-redundant Pfam-ExInt complement' and 'Non-redundant GenBank eukaryotic subdivisional sets' to understand this phenomenon. Statistical analysis is performed on each knowledge set and the results are made availabl...

With 133 million individuals infected with human immunodeficiency virus type 1 (HIV-1) worldwide, and with 12 million more individuals infected every year [1], the need for an effective HIV-1 vaccine has never been greater. With the recent failure of a T cell immunity vaccine to prevent HIV-1 infection, and with the suggestion that the vaccine actually increased the risk of HIV-1 infection in i...

BACKGROUND AND OBJECTIVES Idiopathic erythrocytosis (IE) is characterized by erythrocytosis in the absence of megakaryocytic or granulocytic hyperplasia, and is associated with variable serum erythropoietin (Epo) levels. Most patients with IE lack the JAK2 V617F mutation that occurs in the majority of polycythemia vera patients. Four novel JAK2 mutant alleles have recently been described in pat...