Hierarchical multi-class segmentation of glioma images using networks with multi-level activation function

For many segmentation tasks, especially for the biomedical image, the topological prior is vital information which is useful to exploit. The containment/nesting is a typical inter-class geometric relationship. In the MICCAI Brain tumor segmentation challenge, with its three hierarchically nested classes 'whole tumor', 'tumor core', 'active tumor', the nested classes relationship is introduced into the 3D-residual-Unet architecture. The network comprises a context aggregation pathway and a localization pathway, which encodes increasingly abstract representation of the input as going deeper into the network, and then recombines these representations with shallower features to precisely localize the interest domain via a localization path. The nested-class-prior is combined by proposing the multi-class activation function and its corresponding loss function. The model is trained on the training dataset of Brats2018, and 20% of the dataset is regarded as the validation dataset to determine parameters. When the parameters are fixed, we retrain the model on the whole training dataset. The performance achieved on the validation leaderboard is 86%, 77% and 72% Dice scores for the whole tumor, enhancing tumor and tumor core classes without relying on ensembles or complicated post-processing steps. Based on the same start-of-the-art network architecture, the accuracy of nested-class (enhancing tumor) is reasonably improved from 69% to 72% compared with the traditional Softmax-based method which blind to topological prior.Comment: 12pages first versio

Patterns of care in older patients with squamous cell carcinoma of the head and neck: A Surveillance, Epidemiology, and End Results-Medicare analysis

There is growing evidence in the literature that older patients may not benefit from more intensive therapy for Head and Neck Squamous Cell Carcinoma (HNSCC). A growing number of patients with Head and Neck Squamous Cell Carcinoma (HNSCC) are age 65 and older; however, much of the evidence base informing treatment decisions is based on substantially younger and healthier clinical trial populations. The purpose of this study was to assess the patterns of care of older HNSCC patients to better understand how age is associated with treatment decision

Characteristics and Impact of Drug Detailing for Gabapentin

BACKGROUND: Sales visits by pharmaceutical representatives (“drug detailing”) are common, but little is known about the content of these visits or about the impact of visit characteristics on prescribing behavior. In this study, we evaluated the content and impact of detail visits for gabapentin by analyzing market research forms completed by physicians after receiving a detail visit for this drug. METHODS AND FINDINGS: Market research forms that describe detail visits for gabapentin became available through litigation that alleged that gabapentin was promoted for “off-label” uses. Forms were available for 97 physicians reporting on 116 detail visits between 1995 and 1999. Three-quarters of recorded visits (91/116) occurred in 1996. Two-thirds of visits (72/107) were 5 minutes or less in duration, 65% (73/113) were rated of high informational value, and 39% (42/107) were accompanied by the delivery or promise of samples. During the period of this study, gabapentin was approved by the US Food and Drug Administration only for the adjunctive treatment of partial seizures, but in 38% of visits (44/115) the “main message” of the visit involved at least one off-label use. After receiving the detail visit, 46% (50/108) of physicians reported the intention to increase their prescribing or recommending of gabapentin in the future. In multivariable analysis, intent to increase future use or recommendation of gabapentin was associated with receiving the detail in a small group (versus one-on-one) setting and with low or absent baseline use of the drug, but not with other factors such as visit duration, discussion of “on-label” versus “off-label” content, and the perceived informational value of the presentation. CONCLUSIONS: Detail visits for gabapentin were of high perceived informational value and often involved messages about unapproved uses. Despite their short duration, detail visits were frequently followed by physician intentions to increase their future recommending or prescribing of the drug

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

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

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

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

Intelligence, reason of state and the art of governing risk and opportunity in early modern Europe

Drawing upon primary and secondary historical material, this paper explores the role of intelligence in early modern government. It focuses upon developments in seventeenth- and early-eighteenth-century England, a site-specific genealogical moment in the broader history of state power/knowledges. Addressing a tendency in Foucauldian work to neglect pre-eighteenth-century governance, the analysis reveals a set of interrelated processes which gave rise to an innovative technique for anticipating hazard and opportunity for the state. At the intersection of raison d’État, the evolving art of government, widespread routines of secrecy and a post-Westphalia field of European competition and exchange, intelligence was imagined as a fundamental solution to the concurrent problems of ensuring peace and stability while improving state forces. In the administrative offices of the English Secretary of State, an assemblage of complex and interrelated procedures sought to produce and manipulate information in ways which exposed both possible risks to the state and potential opportunities for expansion and gain. As this suggests, the art of intelligence played an important if largely unacknowledged role in the formation and growth of the early modern state. Ensuring strategic advantage over rivals, intelligence also limited the ability of England's neighbours to dominate trade, control the seas and master the colonies, functioning as a constitutive feature of European balance and equilibrium. As the analysis concludes, understanding intelligence as a form of governmental technique – a way of doing something – reveals an entirely novel way of thinking about and investigating its myriad (historical and contemporary) formations

Hepatitis C Virus Infection Suppresses the Interferon Response in the Liver of the Human Hepatocyte Chimeric Mouse

BACKGROUND AND AIMS: Recent studies indicate that hepatitis C virus (HCV) can modulate the expression of various genes including those involved in interferon signaling, and up-regulation of interferon-stimulated genes by HCV was reported to be strongly associated with treatment outcome. To expand our understanding of the molecular mechanism underlying treatment resistance, we analyzed the direct effects of interferon and/or HCV infection under immunodeficient conditions using cDNA microarray analysis of human hepatocyte chimeric mice. METHODS: Human serum containing HCV genotype 1b was injected into human hepatocyte chimeric mice. IFN-α was administered 8 weeks after inoculation, and 6 hours later human hepatocytes in the mouse livers were collected for microarray analysis. RESULTS: HCV infection induced a more than 3-fold change in the expression of 181 genes, especially genes related to Organismal Injury and Abnormalities, such as fibrosis or injury of the liver (P = 5.90E-16∼3.66E-03). IFN administration induced more than 3-fold up-regulation in the expression of 152 genes. Marked induction was observed in the anti-fibrotic chemokines such as CXCL9, suggesting that IFN treatment might lead not only to HCV eradication but also prevention and repair of liver fibrosis. HCV infection appeared to suppress interferon signaling via significant reduction in interferon-induced gene expression in several genes of the IFN signaling pathway, including Mx1, STAT1, and several members of the CXCL and IFI families (P = 6.0E-12). Genes associated with Antimicrobial Response and Inflammatory Response were also significantly repressed (P = 5.22×10(-10)∼1.95×10(-2)). CONCLUSIONS: These results provide molecular insights into possible mechanisms used by HCV to evade innate immune responses, as well as novel therapeutic targets and a potential new indication for interferon therapy