The Los Alamos Trapped Ion Quantum Computer Experiment

The development and theory of an experiment to investigate quantum computation with trapped calcium ions is described. The ion trap, laser and ion requirements are determined, and the parameters required for quantum logic operations as well as simple quantum factoring are described.Comment: 41 pages, 16 figures, submitted to Fortschritte der Physi

Roughness of a subglacial conduit under Hansbreen, Svalbard

K.M., J.G., X.L. and Y.C. were supported by the National Science Foundation (NSF) under Grant No. #1503928. Thefieldwork team (K.M., J.G., M.C.) were supported by the Norwegian Arctic Research Council and Svalbard Science Forum, RiS #6106. K.M. was also supported by the National Aeronautics and Space Administration (NASA)Headquarters under the NASA Earth and Space Science Fellowship Program – Grant NNX10AN83H, the University of California, Santa Cruz, and the Woods Hole Oceanographic Institution Ocean and Climate Change Institute post-graduate fellowship. Portions of this work were conducted while J.G. was supported by the NSF EAR Postdoctoral Fellowship (#0946767). S.T. was funded by NASA grant NNX11AH61G.Hydraulic roughness exerts an important but poorly understood control on water pressure in subglacial conduits. Where relative roughness values are 5%. Here we report the first quantitative assessment of roughness heights and hydraulic diameters in a subglacial conduit. We measured roughness heights in a 125 m long section of a subglacial conduit using structure-from-motion to produce a digital surface model, and hand-measurements of the b-axis of rocks. We found roughness heights from 0.07 to 0.22 m and cross-sectional areas of 1-2 m2, resulting in relative roughness of 3-12% and >5% for most locations. A simple geometric model of varying conduit diameter shows that when the conduit is small relative roughness is >30% and has large variability. Our results suggest that parameterizations of conduit hydraulic roughness in subglacial hydrological models will remain challenging until hydraulic diameters exceed roughness heights by a factor of 20, or the conduit radius is >1 m for the roughness elements observed here.Publisher PDFPeer reviewe

Role of negative ion resonances in electron scattering from atoms and molecules

Transient negative ions (resonances) formed during the collision of an electron with an atom or molecule have been extensively studied for over thirty years. The continued interest in these states, both experimentally and theoretically, stems from the profound effects that they can have on electron scattering cross sections and the role that electron-electron correlations play in their formation and quasi-stability. A selective discussion of examples of such resonances, involving one, two and three excited electrons is given for a wide range of atomic and molecular systems. © CSIRO 1999

Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas

The Epstein-Barr virus (EBV)-positive subtype of gastric adenocarcinoma is conventionally identified by in situ hybridization (ISH) for viral nucleic acids, but next-generation sequencing represents a potential alternative. We therefore determined normalized EBV read counts by whole genome, whole exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases. In pairwise comparisons, individual samples were either concordantly high or concordantly low by all genomic methods for which data were available. Empiric cut-offs of sequencing counts identified 26 (9%) tumors as EBV-positive. EBV-positivity or negativity by molecular testing was confirmed by EBER-ISH in all but one tumor evaluated by both approaches (kappa=0.91). EBV-positive gastric tumors may be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research

Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next-generation Sequencing

Human papillomaviruses (HPV) are oncogenic DNA viruses implicated in squamous cell carcinomas of several anatomic sites, as well as endocervical adenocarcinomas. Identification of HPV is an actionable finding in some carcinomas, potentially influencing tumor classification, prognosis, and management. We incorporated capture probes for oncogenic HPV strains 16 and 18 into a broader next-generation sequencing (NGS) panel designed to identify actionable mutations in solid malignancies. A total of 21 head and neck, genitourinary and gynecological squamous cell carcinomas and endocervical adenocarcinomas were sequenced as part of the UNCSeq project. Using p16 immunohistochemical results as the gold standard, we set a cutoff for proportion of aligned HPV reads that maximized performance of our NGS assay (92% sensitive, 100% specific for HPV). These results suggest that sequencing of oncogenic pathogens can be incorporated into targeted NGS panels, extending the clinical utility of genomic assays

Observation of power-law scaling for phase transitions in linear trapped ion crystals

We report an experimental confirmation of the power-law relationship between the critical anisotropy parameter and ion number for the linear-to-zigzag phase transition in an ionic crystal. Our experiment uses laser cooled calcium ions confined in a linear radio-frequency trap. Measurements for up to 10 ions are in good agreement with theoretical and numeric predictions. Implications on an upper limit to the size of data registers in ion trap quantum computers are discussed.Comment: Physical Review Letters in press, 4 pages, 4 figure

Managing toxicities associated with immune checkpoint inhibitors: consensus recommendations from the Society for Immunotherapy of Cancer (SITC) Toxicity Management Working Group.

Cancer immunotherapy has transformed the treatment of cancer. However, increasing use of immune-based therapies, including the widely used class of agents known as immune checkpoint inhibitors, has exposed a discrete group of immune-related adverse events (irAEs). Many of these are driven by the same immunologic mechanisms responsible for the drugs\u27 therapeutic effects, namely blockade of inhibitory mechanisms that suppress the immune system and protect body tissues from an unconstrained acute or chronic immune response. Skin, gut, endocrine, lung and musculoskeletal irAEs are relatively common, whereas cardiovascular, hematologic, renal, neurologic and ophthalmologic irAEs occur much less frequently. The majority of irAEs are mild to moderate in severity; however, serious and occasionally life-threatening irAEs are reported in the literature, and treatment-related deaths occur in up to 2% of patients, varying by ICI. Immunotherapy-related irAEs typically have a delayed onset and prolonged duration compared to adverse events from chemotherapy, and effective management depends on early recognition and prompt intervention with immune suppression and/or immunomodulatory strategies. There is an urgent need for multidisciplinary guidance reflecting broad-based perspectives on how to recognize, report and manage organ-specific toxicities until evidence-based data are available to inform clinical decision-making. The Society for Immunotherapy of Cancer (SITC) established a multidisciplinary Toxicity Management Working Group, which met for a full-day workshop to develop recommendations to standardize management of irAEs. Here we present their consensus recommendations on managing toxicities associated with immune checkpoint inhibitor therapy