Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that is distinctly characterized by granuloma formation within infected tissues. Granulomas are dynamic and organized immune cell aggregates that limit dissemination, but can also hinder bacterial clearance. Consequently, outcome in TB is influenced by how granuloma structure and composition shift the balance between these two functions. To date, our understanding of what factors drive granuloma function in humans is limited. With this in mind, we used Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF) to profile 37 proteins in tissues from thirteen patients with active TB disease from the U.S. and South Africa. With this dataset, we constructed a comprehensive tissue atlas where the lineage, functional state, and spatial distribution of 19 unique cell subsets were mapped onto eight phenotypically-distinct granuloma microenvironments. This work revealed an immunosuppressed microenvironment specific to TB granulomas with spatially coordinated co-expression of IDO1 and PD-L1 by myeloid cells and proliferating regulatory T cells. Interestingly, this microenvironment lacked markers consistent with T-cell activation, supporting a myeloid-mediated mechanism of immune suppression. We observed similar trends in gene expression of immunoregulatory proteins in a confirmatory transcriptomic analysis of peripheral blood collected from over 1500 individuals with latent or active TB infection and healthy controls across 29 cohorts spanning 14 countries. Notably, PD-L1 gene expression was found to correlate with TB progression and treatment response, supporting its potential use as a blood-based biomarker. Taken together, this study serves as a framework for leveraging independent cohorts and complementary methodologies to understand how local and systemic immune responses are linked in human health and disease

Multiplexed imaging of human tuberculosis granulomas uncovers immunoregulatory features conserved across tissue and blood

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that is distinctly characterized by granuloma formation within infected tissues. Granulomas are dynamic and organized immune cell aggregates that limit dissemination, but can also hinder bacterial clearance. Consequently, outcome in TB is influenced by how granuloma structure and composition shift the balance between these two functions. To date, our understanding of what factors drive granuloma function in humans is limited. With this in mind, we used Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF) to profile 37 proteins in tissues from thirteen patients with active TB disease from the U.S. and South Africa. With this dataset, we constructed a comprehensive tissue atlas where the lineage, functional state, and spatial distribution of 19 unique cell subsets were mapped onto eight phenotypically-distinct granuloma microenvironments. This work revealed an immunosuppressed microenvironment specific to TB granulomas with spatially coordinated co-expression of IDO1 and PD-L1 by myeloid cells and proliferating regulatory T cells. Interestingly, this microenvironment lacked markers consistent with T-cell activation, supporting a myeloid-mediated mechanism of immune suppression. We observed similar trends in gene expression of immunoregulatory proteins in a confirmatory transcriptomic analysis of peripheral blood collected from over 1500 individuals with latent or active TB infection and healthy controls across 29 cohorts spanning 14 countries. Notably, PD-L1 gene expression was found to correlate with TB progression and treatment response, supporting its potential use as a blood-based biomarker. Taken together, this study serves as a framework for leveraging independent cohorts and complementary methodologies to understand how local and systemic immune responses are linked in human health and disease

The immunoregulatory landscape of human tuberculosis granulomas.

Tuberculosis (TB) in humans is characterized by formation of immune-rich granulomas in infected tissues, the architecture and composition of which are thought to affect disease outcome. However, our understanding of the spatial relationships that control human granulomas is limited. Here, we used multiplexed ion beam imaging by time of flight (MIBI-TOF) to image 37 proteins in tissues from patients with active TB. We constructed a comprehensive atlas that maps 19 cell subsets across 8 spatial microenvironments. This atlas shows an IFN-γ-depleted microenvironment enriched for TGF-β, regulatory T cells and IDO

The Woody Guthrie Centennial Bibliography

This bibliography updates two extensive works designed to include comprehensively all significant works by and about Woody Guthrie. Richard A. Reuss published A Woody Guthrie Bibliography, 1912–1967 in 1968 and Jeffrey N. Gatten\u27s article “Woody Guthrie: A Bibliographic Update, 1968–1986” appeared in 1988. With this current article, researchers need only utilize these three bibliographies to identify all English-language items of relevance related to, or written by, Guthrie

The Post-traumatic Confusional State: A Case Definition and Diagnostic Criteria

In response to the need to better define the natural history of emerging consciousness after traumatic brain injury (TBI) and to better describe the characteristics of the condition commonly labeled Post-traumatic Amnesia, a case definition and diagnostic criteria for the Post- traumatic Confusional State (PTCS) were developed. This project was completed by the Confusion Workgroup of the American Congress of Rehabilitation Medicine Brain Injury Interdisciplinary Special Interest group. The case definition was informed by an exhaustive literature review and expert opinion of workgroup members from multiple disciplines. The workgroup reviewed 2,466 abstracts and extracted evidence from 44 articles. Consensus was reached through teleconferences, face-to-face meetings, and three rounds of modified Delphi voting. The case definition provides detailed description of PTCS (1) core neurobehavioral features, (2) associated neurobehavioral features, (3) functional implications, (4) exclusion criteria, (5) lower boundary, and (6) criteria for emergence. Core neurobehavioral features include disturbances of attention, orientation, and memory as well as excessive fluctuation. Associated neurobehavioral features include emotional and behavioral disturbances, sleep-wake cycle disturbance, delusions, perceptual disturbances and confabulation. The lower boundary distinguishes PTCS from the minimally conscious state while upper boundary is marked by significant improvement in the four core and five associated features. Key research goals are establishment of cut-offs on assessment instruments and determination of levels of behavioral function that distinguish persons in PTCS from those who have emerged to the period of continued recovery

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

New Security Paradigms Workshop

The 2010 New Security Paradigms Workshop began with a reception and dinner on September 20 and ended at noon on September 23. The highly interactive workshop has its participation limited to about 35 people. NSPW encourages authors "to present ideas that might be considered risky in some other forum, and all participants are charged with providing feedback in a constructive manner. The resulting intensive brainstorming has proven to be an excellent medium for furthering the development of these ideas.

Quis Custodiet ipsos Custodes? A New Paradigm for Analyzing Security Paradigms

Do you believe that more than one single security paradigm exists? We do.We also believe that we have a major problem because of all these security paradigms: until we find a way to identify and understand how these paradigms restrict our analyses we will never have the ability to do a good job identifying risks and threats, let alone protect ourselves from them.We also believe that the majority of people working in the security community use only one paradigm without recognizing that self-imposed constraint. The paradigm they use may change or even expand based on new data and experiences, but it still continues to limit their approaches and analyses, and therefore limit their effectiveness.At NSPW 2009 we presented a panel simulation using four analysts in order to demonstrate how security paradigms constrain perceptions and points of view, and how the combination of the different paradigms confuses the analysts' conclusions. Our panel used real-time, interactive exploration to investigate how individuals in the security community work together within their different paradigms and how they often lack awareness of their particular paradigms while working in the same way that a fish does not notice the water in which it swims.We presented a provocative, live scenario followed by an intensive analysis with NSPW audience participation. We hoped that this would illustrate the misunderstandings and erroneous conclusions that can emerge from the inadvertent and often faulty composition of differing universes of discourse.Ultimately this led to a new paradigm for dealing with the compositions of the paradigms held by various individuals that we call "Multi-Paradigm Composition Analysis.

Quis Custodiet ipsos Custodes? A New Paradigm for Analyzing Security Paradigms

Do you believe that more than one single security paradigm exists? We do.We also believe that we have a major problem because of all these security paradigms: until we find a way to identify and understand how these paradigms restrict our analyses we will never have the ability to do a good job identifying risks and threats, let alone protect ourselves from them.We also believe that the majority of people working in the security community use only one paradigm without recognizing that self-imposed constraint. The paradigm they use may change or even expand based on new data and experiences, but it still continues to limit their approaches and analyses, and therefore limit their effectiveness.At NSPW 2009 we presented a panel simulation using four analysts in order to demonstrate how security paradigms constrain perceptions and points of view, and how the combination of the different paradigms confuses the analysts' conclusions. Our panel used real-time, interactive exploration to investigate how individuals in the security community work together within their different paradigms and how they often lack awareness of their particular paradigms while working in the same way that a fish does not notice the water in which it swims.We presented a provocative, live scenario followed by an intensive analysis with NSPW audience participation. We hoped that this would illustrate the misunderstandings and erroneous conclusions that can emerge from the inadvertent and often faulty composition of differing universes of discourse.Ultimately this led to a new paradigm for dealing with the compositions of the paradigms held by various individuals that we call "Multi-Paradigm Composition Analysis.