Assessment of Advanced Diagnostic Bronchoscopy Outcomes for Peripheral Lung Lesions: A Delphi Consensus Definition of Diagnostic Yield and Recommendations for Patient-centered Study Designs. An Official American Thoracic Society/American College of Chest Physicians Research Statement.

Advanced diagnostic bronchoscopy targeting the lung periphery has developed at an accelerated pace over the last two decades, whereas evidence to support introduction of innovative technologies has been variable and deficient. A major gap relates to variable reporting of diagnostic yield, in addition to limited comparative studies. To develop a research framework to standardize the evaluation of advanced diagnostic bronchoscopy techniques for peripheral lung lesions.

Proteomic profiling of human plasma identifies apolipoprotein E as being associated with smoking and a marker for squamous metaplasia of the lung.

Biomarkers to identify subjects at high-risk for developing lung cancer will revolutionize the disease outlook. Most biomarker studies have focused on patients already diagnosed with lung cancer and in most cases the disease is often advanced and incurable. The objective of this study was to use proteomics to identify a plasma biomarker for early detection of lung lesions that may subsequently be the harbinger for cancer.

Correlation of ultrasound findings with the Bethesda cytopathology classification for thyroid nodule fine-needle aspiration: a primer for radiologists.

Objective: Ultrasound and ultrasound-guided fine-needle aspiration play a critical role in the evaluation of thyroid nodules. The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC) was developed to facilitate communication among cytopathologists, radiologists, and referring physicians. The reporting scheme has rapidly become one of the most important contributions to thyroid nodule management.

Training perspective: the impact of starting an endobronchial ultrasound program at a major academic center on fellows training of transbronchial needle aspiration.

The proliferation of endobronchial ultrasound as the standard of care in lymph node sampling has significantly impacted the way fellows are trained in transbronchial needle aspiration (TBNA). To assess the impact of starting an endobronchial ultrasound (EBUS) program on fellows training of conventional TBNA (cTBNA), we reviewed all TBNAs performed at the Johns Hopkins Hospital from September 2006 until December of 2009. The number of nodes sampled, specimen adequacy, diagnostic yield, and fellow involvement were recorded.

Observation of nanosecond laser induced fluorescence of in vitro seawater phytoplankton.

Seawater has been irradiated using a train of 70 ns flashes from a 440 nm laser source. This wavelength is on resonance with the blue absorption peak of Chlorophyll pigment associated with the photosystem of in vitro phytoplankton. The resulting fluorescence at 685 nm is instantaneously recorded during each laser pulse using a streak camera.

RNA immunoprecipitation for determining RNA-protein associations in vivo.

Similar to chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP) can be used to detect the association of individual proteins with specific nucleic acid regions, in this case on RNA. Live cells are treated with formaldehyde to generate protein-RNA cross-links between molecules that are in close proximity in vivo. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the formaldehyde cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR.

Multiple approaches to study S. cerevisiae Rad9, a prototypical checkpoint protein.

The Saccharomyces cerevisiae RAD9 checkpoint gene is the prototypical checkpoint gene and is required for efficient checkpoint regulation in late G1, S, and at the G2/M cell cycle transition following DNA damage. Rad9 is required for the activation of Rad53 after damage and has been proposed to have roles in lesion recognition as well as DNA repair and the maintenance of genome stability. Here we describe methodology suitable for the study of G1, intra-S, and G2/M checkpoints in budding yeast, the analysis of Rad9/Rad53 phospho-forms, the biochemical analysis of Rad9 and Rad53, the fractionation of soluble and chromatin associated proteins, including Rad9, and the live cell imaging of GFP tagged Rad9.

A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage.

Eukaryotic cells use multiple, highly conserved mechanisms to contend with ultraviolet-light-induced DNA damage. One important response mechanism is transcription-coupled repair (TCR), during which DNA lesions in the transcribed strand of an active gene are repaired much faster than in the genome overall. In mammalian cells, defective TCR gives rise to the severe human disorder Cockayne's syndrome (CS).