Identification of T-cell antigens specific for latent mycobacterium tuberculosis infection.

BACKGROUND: T-cell responses against dormancy-, resuscitation-, and reactivation-associated antigens of Mycobacterium tuberculosis are candidate biomarkers of latent infection in humans. METHODOLOGY/PRINCIPAL FINDINGS: We established an assay based on two rounds of in vitro restimulation and intracellular cytokine analysis that detects T-cell responses to antigens expressed during latent M. tuberculosis infection. Comparison between active pulmonary tuberculosis (TB) patients and healthy latently M. tuberculosis-infected donors (LTBI) revealed significantly higher T-cell responses against 7 of 35 tested M. tuberculosis latency-associated antigens in LTBI. Notably, T cells specific for Rv3407 were exclusively detected in LTBI but not in TB patients. The T-cell IFNgamma response against Rv3407 in individual donors was the most influential factor in discrimination analysis that classified TB patients and LTBI with 83% accuracy using cross-validation. Rv3407 peptide pool stimulations revealed distinct candidate epitopes in four LTBI. CONCLUSIONS: Our findings further support the hypothesis that the latency-associated antigens can be exploited as biomarkers for LTBI

Interobserver Agreement in the Diagnosis of Stroke Type

Interobserver Agreement is Essential to the Reliability of Clinical Data from Cooperative Studies and Provides the Foundation for Applying Research Results to Clinical Practice. in the Stroke Data Bank, a Large Cooperative Study of Stroke, We Sought to Establish the Reliability of a Key Aspect of Stroke Diagnosis: The Mechanism of Stroke. Seventeen Patients Were Evaluated by Six Neurologists. Interobserver Agreement Was Measured When Diagnosis Was based on Patient History and Neurologic Examination Only, as Well as When It Was based on Results of a Completed Workup, Including a Computed Tomographic Scan. Initial Clinical Impressions, based Solely on History and One Neurologic Examination, Were Fairly Reliable in Establishing the Mechanism of Stroke (Ie, Distinguishing among Infarcts, Subarachnoid Hemorrhages, and Parenchymatous Hemorrhages). Classification into One of Nine Stroke Subtypes Was Substantially Reliable When Diagnoses Were based on a Completed Workup. Compared with Previous Findings for the Same Physicians and Patients, the Diagnosis of Stroke Type Was Generally More Reliable Than Individual Signs and Symptoms. These Results Suggest that Multicentered Studies Can Rely on the Independent Diagnostic Choices of Several Physicians When Common Definitions Are Employed and Data from a Completed Workup Are Available. Furthermore, Reliability May Be Less for Individual Measurements Such as Signs or Symptoms Than for More-Complex Judgments Such as Diagnoses. © 1986, American Medical Association. All Rights Reserved

Interobserver Reliability in the Interpretation of Computed Tomographic Scans of Stroke Patients

Interobserver Reliability in Interpretation of Computed Tomographic Images Was Studied by Six Senior Neurologists Who Independently Evaluated on a Standardized Stroke Data Bank Form the Brain Lesions of 17 Patients. the Results Analyzed with K Statistics Yielded Moderate to Substantial Agreement on Most Items of Interest Including the Stroke Pathology and Anatomy. in General, the Levels of Agreement Were as High as Previously Reported for the Diagnosis of the Mechanism of the Stroke, and Much Higher Than on Many Stroke History Items and Items of Neurologic Examination. Excellent Agreement Was Obtained for the Detection of Infarcts and Intracerebral Hemorrhage, and Substantial Agreement Was Obtained on Whether the Computed Tomographic Images Were Normal or Indicative of Small Deep Infarcts, Superficial and Deep Infarcts, and Aneurysms. the Level of Agreement on Anatomy of the Lesions Was Best for the Frontal, Parietal, and Temporal Lobes, Putamen, Cerebellum, and Subarachnoid Space. Implications for Clinical Research and Diagnosis Are Discussed. © 1987 American Medical Association All Rights Reserved

Interobserver Variability in the Assessment of Neurologic History and Examination in the Stroke Data Bank

Interobserver Reliability in Obtaining Neurologic Histories and Examinations Was Investigated among Neurologists Collaborating in the Stroke Data Bank (SDB). Seventeen In-Hospital Stroke Patients Were Examined by Six Neurologists Experienced in Stroke over the Course of Three Days. Patients Were Examined Twice a Day for Two Successive Days, with Each Patient Seen by Four Different Neurologists. Data Were Recorded on SDB Forms, According to Definitions and Procedures Established for the SDB. Percent Agreement and Κ Coefficients Were Calculated to Assess the Levels of Agreement for Each Item. Important Differences in Levels of Agreement Were Found among Items on Both Neurologic History and Examination. Agreement among Neurologists Was Higher for Neurologic Examination Than for History. Patterns of Agreement for Items with Low Prevalence or with Numerous Unknown Ratings Are Discussed. Improvement in Interobserver Agreement Due to Data Editing for Intra-Observer Consistency Was Shown. © 1985, American Medical Association. All Rights Reserved

Lipid-Based Passivation in Nanofluidics

Stretching DNA in nanochannels is a useful tool for direct, visual studies of genomic DNA at the single molecule level. To facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We demonstrate virtually complete long-term passivation of nanochannel surfaces to a range of relevant reagents, including streptavidin-coated quantum dots, RecA proteins, and RecA-DNA complexes. We show that the performance of the lipid bilayer is significantly better than that of standard bovine serum albumin-based passivation. Finally, we show how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation by DNase I. We expect that our approach will open up for detailed, systematic studies of a wide range of protein-DNA interactions with high spatial and temporal resolution

The DINGO dataset: a comprehensive set of data for the SAMPL challenge

Part of the latest SAMPL challenge was to predict how a small fragment library of 500 commercially available compounds would bind to a protein target. In order to assess the modellers’ work, a reasonably comprehensive set of data was collected using a number of techniques. These included surface plasmon resonance, isothermal titration calorimetry, protein crystallization and protein crystallography. Using these techniques we could determine the kinetics of fragment binding, the energy of binding, how this affects the ability of the target to crystallize, and when the fragment did bind, the pose or orientation of binding. Both the final data set and all of the raw images have been made available to the community for scrutiny and further work. This overview sets out to give the parameters of the experiments done and what might be done differently for future studies