Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal.

Background: The continued advance of antibiotic resistance threatens the treatment and control of many infectious diseases. This is exemplified by the largest global outbreak of extensively drug-resistant (XDR) tuberculosis (TB) identified in Tugela Ferry, KwaZulu-Natal, South Africa, in 2005 that continues today. It is unclear whether the emergence of XDR-TB in KwaZulu-Natal was due to recent inadequacies in TB control in conjunction with HIV or other factors.

Approaches to Fungal Genome Annotation.

Fungal genome annotation is the starting point for analysis of genome content. This generally involves the application of diverse methods to identify features on a genome assembly such as protein-coding and non-coding genes, repeats and transposable elements, and pseudogenes. Here we describe tools and methods leveraged for eukaryotic genome annotation with a focus on the annotation of fungal nuclear and mitochondrial genomes.

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C.

Cross-kingdom patterns of alternative splicing and splice recognition.

Background: Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are often caused by variable recognition of splice junctions by the exon definition (ED) mechanism. We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized.

Androgen deficiency in the aging male: a guide to diagnosis and testosterone replacement therapy.

A steady decline in androgen levels occurs in males as they age. Evidence suggests that this decline may be at least partially responsible for a variety of physical and mental changes associated with the aging process. For instance, abnormally low levels of androgens can lead to profound changes in bone density, body composition, as well as sexual and cognitive function.

Conrad: gene prediction using conditional random fields.

We present Conrad, the first comparative gene predictor based on semi-Markov conditional random fields (SMCRFs). Unlike the best standalone gene predictors, which are based on generalized hidden Markov models (GHMMs) and trained by maximum likelihood, Conrad is discriminatively trained to maximize annotation accuracy. In addition, unlike the best annotation pipelines, which rely on heuristic and ad hoc decision rules to combine standalone gene predictors with additional information such as ESTs and protein homology, Conrad encodes all sources of information as features and treats all features equally in the training and inference algorithms.

Clinical predictors and characteristics of patients with chronic liver disease and intrapulmonary shunts.

Background: Intrapulmonary shunting (IPS) is a well-described phenomenon in chronic liver disease but its significance is not known.

Hypothesis: The study was undertaken to enhance our understanding of the characteristics and prevalence of IPS.

Methods: We retrospectively studied 204 consecutive patients with end-stage chronic liver disease who underwent a dobutamine stress echocardiogram, along with a saline contrast bubble study, as part of their pretransplant evaluation.