Parameterized Domination in Circle Graphs

A circle graph is the intersection graph of a set of chords in a circle. Keil [Discrete Applied Mathematics, 42(1):51-63, 1993] proved that Dominating Set, Connected Dominating Set, and Total Dominating Set are NP-complete in circle graphs. To the best of our knowledge, nothing was known about the parameterized complexity of these problems in circle graphs. In this paper we prove the following results, which contribute in this direction: Dominating Set, Independent Dominating Set, Connected Dominating Set, Total Dominating Set, and Acyclic Dominating Set are W[1]-hard in circle graphs, parameterized by the size of the solution. Whereas both Connected Dominating Set and Acyclic Dominating Set are W[1]-hard in circle graphs, it turns out that Connected Acyclic Dominating Set is polynomial-time solvable in circle graphs. If T is a given tree, deciding whether a circle graph has a dominating set isomorphic to T is NP-complete when T is in the input, and FPT when parameterized by |V(T)|. We prove that the FPT algorithm is subexponential

The Farthest Known Supernova: Support for an Accelerating Universe and a Glimpse of the Epoch of Deceleration

We present photometric observations of an apparent Type Ia supernova (SN Ia) at a redshift of ~1.7, the farthest SN observed to date. SN 1997ff, was discovered in a repeat observation by the HST of the HDF-), and serendipitously monitored with NICMOS on HST throughout the GTO campaign. The SN type can be determined from the host galaxy type:an evolved, red elliptical lacking enough recent star formation to provide a significant population of core-collapse SNe. The class- ification is further supported by diagnostics available from the observed colors and temporal behavior of the SN, both of which match a typical SN Ia. The photo- metric record of the SN includes a dozen flux measurements in the I, J, and H bands spanning 35 days in the observed frame. The redshift derived from the SN photometry, z=1.7+/-0.1, is in excellent agreement with the redshift estimate of z=1.65+/-0.15 derived from the U_300,B_450,V_606,I_814,J_110,J_125,H_160, H_165,K_s photometry of the galaxy. Optical and near-infrared spectra of the host provide a very tentative spectroscopic redshift of 1.755. Fits to observations of the SN provide constraints for the redshift-distance relation of SNe~Ia and a powerful test of the current accelerating Universe hypothesis. The apparent SN brightness is consistent with that expected in the decelerating phase of the preferred cosmological model, Omega_M~1/3, Omega_Lambda~2/3. It is inconsistent with grey dust or simple luminosity evolution, candidate astro- physical effects which could mimic past evidence for an accelerating Universe from SNe Ia at z~0.5.We consider several sources of possible systematic error including lensing, SN misclassification, selection bias, and calibration errors. Currently, none of these effects appears likely to challenge our conclusions.Comment: Accepted to the Astrophysical Journal 38 pages, 15 figures, Pretty version available at http://icarus.stsci.edu/~stefano/ariess.tar.g

Holocene tephrochronology around Cochrane (~47° S), southern Chile

Two Holocene tephras encountered in outcrops, cores and trenches in bogs, and lake cores in the area around Cochrane, southern Chile, are identified (based on their age, tephra glass color and morphology, mineralogy, and both bulk and glass chemistry) as H1 derived from Hudson volcano, and MEN1 derived from Mentolat volcano. New AMS radiocarbon ages indicate systematic differences between those determined in lake cores (MEN1=7,689 and H1=8,440 cal yrs BP) and surface deposits (MEN1=7,471 and H1=7,891 cal yrs BP), with the lake cores being somewhat older. H1 tephra layers range from 8 to 18 cm thick, suggesting that both the area of the 10 cm isopach and the volume of this eruption were larger than previously suggested, but not greatly, and that the direction of maximum dispersion was more to the south. MEN1 tephra layers range from 1-4 cm in thickness, indicating that this was probably a reasonably large (&gt;5 km3) eruption. Some of the lake cores also contain thin layers (&lt; 2 cm) of late Holocene H2 tephra and the recent H3 (1991 AD) tephra, both derived from the Hudson volcano. No tephra evidence has been observed for any late Pleistocene tephra, nor for the existence of the supposed Arenales volcano, proposed to be located west of Cochrane.</p

Identifying Reduced-Form Relations with Panel Data

The literature that tests for U-shaped relationships using panel data, such as those between pollution and income or inequality and growth, reports widely divergent (parametric and non-parametric) empirical findings. We explain why lack of identification lies at the root of these differences. To deal with this lack of identification, we propose an identification strategy that explicitly distinguishes between what can be identified on the basis of the data and what is a consequence of subjective choices due to a lack of identification. We apply our methodology to the pollution-income relationship of both CO2- and SO2-emissions. Interestingly, our approach yields estimates of both income (scale) and time (composition and/or technology) effects for these reduced-form relationships that are insensitive to the required subjective choices and consistent with theoretical predictions

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 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

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

Communications Biophysics

Contains research objectives and summary of research on five research projects, with ten sub-topics.National Institutes of Health (Grant 1 RO1 NS10916-01)National Institutes of Health (Grant 5 RO1 NS11000-03)National Institutes of Health (Grant 1 RO1 NS11153-01)Harvard-M.I.T. Rehabilitation Engineering CenterU. S. Department of Health, Education, and Welfare (Grant 23-P-55854)National Institutes of Health (Grant 1 RO1 NS11680-01)National Institutes of Health (Grant 5 ROI NS11080-02)M.I.T. Health Sciences FundNational Aeronautics and Space Administration (Grant NSG-2032)National Institutes of Health (Grant 5 TO1 GM01555-09)Massachusetts General Hospital Purchase Order F63853Boston City Hospital Purchase Order 4338-7543