Bayesian minimax estimation of the normal model with incomplete prior covariance matrix specification

This work addresses the issue of Bayesian robustness in the multivariate normal model when the prior covariance matrix is not completely specified, but rather is described in terms of positive semi-definite bounds. This occurs in situations where, for example, the only prior information available is the bound on the diagonal of the covariance matrix derived from some physical constraints, and that the covariance matrix is positive semi-definite, but otherwise arbitrary. Under the conditional Gamma-minimax principle, previous work by DasGupta and Studden shows that an analytically exact solution is readily available for a special case where the bound difference is a scaled identity. The goal in this work is to consider this problem for general positive definite matrices. The contribution in this paper is a theoretical study of the geometry of the minimax problem. Extension of previous results to a more general case is shown and a practical algorithm that relies on semi-definite programming and the convexity of the minimax formulation is derived. Although the algorithm is numerically exact for up to the bivariate case, its exactness for other cases remains open. Numerical studies demonstrate the accuracy of the proposed algorithm and the robustness of the minimax solution relative to standard and recently proposed methods

Electrical conductivity beyond linear response in layered superconductors under magnetic field

The time-dependent Ginzburg-Landau approach is used to investigate nonlinear response of a strongly type-II superconductor. The dissipation takes a form of the flux flow which is quantitatively studied beyond linear response. Thermal fluctuations, represented by the Langevin white noise, are assumed to be strong enough to melt the Abrikosov vortex lattice created by the magnetic field into a moving vortex liquid and marginalize the effects of the vortex pinning by inhomogeneities. The layered structure of the superconductor is accounted for by means of the Lawrence-Doniach model. The nonlinear interaction term in dynamics is treated within Gaussian approximation and we go beyond the often used lowest Landau level approximation to treat arbitrary magnetic fields. The I-V curve is calculated for arbitrary temperature and the results are compared to experimental data on high-$T_{c}$ superconductor YBa$_{2}$Cu$_{3}$O$$.Comment: 8 pages, 3 figure

A case of hepatic cyst-induced internal jugular venous thrombosis

• Echocardiography can demonstrate hepatic cyst–induced right atrial compression. • Hepatic cyst–induced blood flow stasis can cause internal jugular venous thrombus. • Laparoscopic deroofing of hepatic cysts is a safe and effective treatment

A New Approach and Tool in Verifying Asynchronous Circuits

Research in asynchronous circuit approach has been carried out recently when asynchronous circuits are presented more widely in electronic systems. As they are more important in human life, their correctness should be considered carefully. Although there are some EDA tools for design and synthesis of asynchronous circuits, they are lack of methods for verifying the correctness of the produced circuits. In this work, we are about to propose a verification method and apply it in making a new version of the PAiD tool that can enable engineers to design, synthesize and verify asynchronous circuits. Experiments in verifying circuits have been also provided in this work

HIV-Associated TB in An Giang Province, Vietnam, 2001–2004: Epidemiology and TB Treatment Outcomes

BACKGROUND: Mortality is high in HIV-infected TB patients, but few studies from Southeast Asia have documented the benefits of interventions, such as co-trimoxazole (CTX), in reducing mortality during TB treatment. To help guide policy in Vietnam, we studied the epidemiology of HIV-associated TB in one province and examined factors associated with outcomes, including the impact of CTX use. METHODOLOGY/PRINCIPAL FINDINGS: We retrospectively abstracted data for all HIV-infected persons diagnosed with TB from 2001-2004 in An Giang, a province in southern Vietnam in which TB patients receive HIV counseling and testing. We used standard WHO definitions to classify TB treatment outcomes. We conducted multivariate analysis to identify risk factors for the composite outcome of death, default, or treatment failure during TB treatment. From 2001-2004, 637 HIV-infected TB patients were diagnosed in An Giang. Of these, 501 (79%) were male, 321 (50%) were aged 25-34 years, and the most common self-reported HIV risk factor was sex with a commercial sex worker in 221 (35%). TB was classified as smear-positive in 531 (83%). During TB treatment, 167 (26%) patients died, 9 (1%) defaulted, and 6 (1%) failed treatment. Of 454 patients who took CTX, 116 (26%) had an unsuccessful outcome compared with 33 (70%) of 47 patients who did not take CTX (relative risk, 0.4; 95% confidence interval [CI], 0.3-0.5). Adjusting for male sex, rural residence, TB smear status and disease location, and the occurrence of adverse events during TB treatment in multivariate analysis, the benefit of CTX persisted (adjusted odds ratio for unsuccessful outcome 0.1; CI, 0.1-0.3). CONCLUSIONS/SIGNIFICANCE: In An Giang, Vietnam, HIV-associated TB was associated with poor TB treatment outcomes. Outcomes were significantly better in those taking CTX. This finding suggests that Vietnam should consider applying WHO recommendations to prescribe CTX to all HIV-infected TB patients

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

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

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