The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data.

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being 'good' or 'bad.' Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to 'bad' quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer's Disease Neuroimaging Initiative (ADNI). LONI-QC's functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community

Contemporary Art and Transitional Justice in Northern Ireland: The Consolation of Form

Abstract Contemporary artworks in Northern Ireland are explored here as critical constellations, in Walter Benjamin’s sense, that engage the cultural processes of transition through their problematisation of it. It is argued that the artworks become sites in which the assumptions of transition are opened up for critical reflection, requesting attention to the foreclosing of the meanings of memory, of past-and-future, of community. A mode of critical questioning of the present renders the present problematic not in terms of exclusions nor with reference to a past that cannot or will not be erased, but in terms of the present’s inability to be conceived through a linear conception of time. That is, the past and its relation to both the present and to the future are set in oscillation as artworks explore the complex temporalities of a present self-consciously attempting to narrate itself away from the past. The artworks, ‘without the bigotry of conviction’ as Seamus Deane put it, suggest that the task of dealing with the past is flawed wherever the past is conceived as a history that can be rendered present to be judged by subjects who are thereby placed beyond it. That is the illusion of a present ‘no-time’ that dovetails with the desires of commercial enterprise and neo-liberal conceptions of freedom. If this suggests an unceasing restlessness, the consolation is that this questioning does take a form, not as judgement or political decision but as artworks which by definition, remain open to reinterpretation and new understandings. These issues are discussed with reference to the work of four artists in Northern Ireland: the paintings of Rita Duffy, the photography and installation work of Anthony Haughey, and the sculptural works of Philip Napier and Mike Hogg

Visually assessed breast density, breast cancer risk and the importance of the craniocaudal view

Contains fulltext : 69403.pdf (publisher's version ) (Open Access)INTRODUCTION: Mammographic density is known to be a strong risk factor for breast cancer. A particularly strong association with risk has been observed when density is measured using interactive threshold software. This, however, is a labour-intensive process for large-scale studies. METHODS: Our aim was to determine the performance of visually assessed percent breast density as an indicator of breast cancer risk. We compared the effect on risk of density as measured with the mediolateral oblique view only versus that estimated as the average density from the mediolateral oblique view and the craniocaudal view. Density was assessed using a visual analogue scale in 10,048 screening mammograms, including 311 breast cancer cases diagnosed at that screening episode or within the following 6 years. RESULTS: Where only the mediolateral oblique view was available, there was a modest effect of breast density on risk with an odds ratio for the 76% to 100% density relative to 0% to 25% of 1.51 (95% confidence interval 0.71 to 3.18). When two views were available, there was a considerably stronger association, with the corresponding odds ratio being 6.77 (95% confidence interval 2.75 to 16.67). CONCLUSION: This indicates that a substantial amount of information on risk from percentage breast density is contained in the second view. It also suggests that visually assessed breast density has predictive potential for breast cancer risk comparable to that of density measured using the interactive threshold software when two views are available. This observation needs to be confirmed by studies applying the different measurement methods to the same individuals

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Keeping vigil over the profession: a grounded theory of the context of nurse anaesthesia practice

<p>Abstract</p> <p>Background</p> <p>Nurse anaesthetists in the US have faced continued, repeated challenges to their profession. Regardless, they have met these challenges and have established themselves as major anaesthesia care providers. In this paper we address the research question: How do certified registered nurse anaesthetists (CRNAs) manage the socio-political context in which they provide care for their patients?</p> <p>Methods</p> <p>Grounded theory was used to explore how nurse anaesthetists protect and promote their profession. Purposive, snowball, and theoretical sampling was used and data were collected through participant observation and interviews conducted at a conference of the professional association, an educational program, by telephone, email exchanges, and time spent in operating rooms and an outpatient surgical clinic. Analysis included coding at increasingly abstract levels and constant comparison.</p> <p>Results</p> <p>The basic social process identified was Keeping Vigil Over the Profession, which explains how nurse anaesthetists protect and promote their profession. It is comprised of three contextual categories: Establishing Public Credibility through regulatory and educational standards, Political Vigilance and taking action in governmental and policy arenas, and Tending the Flock through a continuous information loop between local and administrative/political levels.</p> <p>Conclusions</p> <p>From our study of the context of nurse anaesthesia practice, it is clear that CRNAs are dedicated to protecting their ability to provide high quality patient care by maintaining constant vigilance over their profession.</p

Quantum confinement-induced semimetal-to-semiconductor evolution in large-area ultra-thin PtSe2 films grown at 400 °C

In this work, we present a comprehensive theoretical and experimental study of quantum confinement in layered platinum diselenide (PtSe2) films as a function of film thickness. Our electrical measurements, in combination with density functional theory calculations, show distinct layer-dependent semimetal-to-semiconductor evolution in PtSe2 films, and highlight the importance of including van der Waals interactions, Green’s function calibration, and screened Coulomb interactions in the determination of the thickness-dependent PtSe2 energy gap. Large-area PtSe2 films of varying thickness (2.5–6.5 nm) were formed at 400 °C by thermally assisted conversion of ultra-thin platinum films on Si/SiO2 substrates. The PtSe2 films exhibit p-type semiconducting behavior with hole mobility values up to 13 cm2/V·s. Metal-oxide-semiconductor field-effect transistors have been fabricated using the grown PtSe2 films and a gate field-controlled switching performance with an ION/IOFF ratio of >230 has been measured at room temperature for a 2.5–3 nm PtSe2 film, while the ratio drops to <2 for 5–6.5 nm-thick PtSe2 films, consistent with a semiconducting-to-semimetallic transition with increasing PtSe2 film thickness. These experimental observations indicate that the low-temperature growth of semimetallic or semiconducting PtSe2 could be integrated into the back-end-of-line of a silicon complementary metal-oxide-semiconductor process

Real-Time PCR in HIV/Trypanosoma cruzi Coinfection with and without Chagas Disease Reactivation: Association with HIV Viral Load and CD4+ Level

Chagas disease is endemic in Latin America and is caused by the flagellate protozoan T. cruzi. The acute phase is asymptomatic in the majority of the cases and rarely causes inflammation of the heart or the central nervous system. Most infected patients progress to a chronic phase, characterized by cardiac or digestive involvement when not asymptomatic. However, when patients are also exposed to an immunosuppressant (such as chemotherapy), neoplasia, or other infections such as HIV, T. cruzi infection may develop into a severe disease (Chagas disease reactivation) involving the heart and central nervous system. The current microscopic methods for diagnosing Chagas disease reactivation are not sensitive enough to prevent the high rate of death observed in these cases. Therefore, we propose a quantitative method to monitor blood levels of the parasite, which will allow therapy to be administered as early as possible, even if the patient has not yet presented symptoms