Comparison of the Electronic Structures of Two Non-cuprate Layered Transition Metal Oxide Superconductors

Comparison is made of the electronic structure of the little-studied layered transition metal oxide LiNbO$_2$ with that of Na$_x$CoO$_2$, which has attracted tremendous interest since superconductivity was discovered in its hydrate. Although the active transition metal $d$ states are quite different due to different crystal fields and band filling, both systems show a strong change of electronic structure with changes in the distance between the transition metal ion layer and the oxygen layers. The niobate is unusual in having a large second-neighbor hopping amplitude, and a nearest neighbor hopping amplitude that is sensitive to the Nb-O separation. Li$_x$NbO$_2$ also presents the attractive simplicity of a single band triangular lattice system with variable carrier concentration that is superconducting.Comment: 5 pages, 3 embedded figures (Proceedings in third Hiroshima international workshop

Assessing reproducibility for radiographic measurement of leg length inequality after total hip replacement

Leg length inequality (LLI) as a result of total hip replacement can cause considerable morbidity. Although LLI was described when the technique was popularised in the 1960s, it remains a significant challenge to arthroplasty surgeons. This study reviews the established practice for the measurement of LLI on plain antero-posterior radiograph, and compares these techniques to two methods used locally. The radiographs of 35 patients were measured using four techniques. All four methods yielded an interclass correlation co-efficient of ≥0.90 for inter reader reliability. This study shows that the four methods are comparable for reliability, while a composite method, measuring from the centre of femoral rotation to the inferior teardrop and then to the lesser trochanter, has the added advantage of providing extra information on component position as well as an overall measure of LLI

Strongly focused light beams interacting with single atoms in free space

We construct 3-D solutions of Maxwell's equations that describe Gaussian light beams focused by a strong lens. We investigate the interaction of such beams with single atoms in free space and the interplay between angular and quantum properties of the scattered radiation. We compare the exact results with those obtained with paraxial light beams and from a standard input-output formalism. We put our results in the context of quantum information processing with single atoms.Comment: 9 pages, 9 figure

On the Behavior of the Effective QCD Coupling alpha_tau(s) at Low Scales

The hadronic decays of the tau lepton can be used to determine the effective charge alpha_tau(m^2_tau') for a hypothetical tau-lepton with mass in the range 0 < m_tau' < m_tau. This definition provides a fundamental definition of the QCD coupling at low mass scales. We study the behavior of alpha_tau at low mass scales directly from first principles and without any renormalization-scheme dependence by looking at the experimental data from the OPAL Collaboration. The results are consistent with the freezing of the physical coupling at mass scales s = m^2_tau' of order 1 GeV^2 with a magnitude alpha_tau ~ 0.9 +/- 0.1.Comment: 15 pages, 4 figures, submitted to Physical Review D, added references, some text added, no results nor figures change

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Search for jet extinction in the inclusive jet-pT spectrum from proton-proton collisions at s=8 TeV

Published by the American Physical Society under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published articles title, journal citation, and DOI.The first search at the LHC for the extinction of QCD jet production is presented, using data collected with the CMS detector corresponding to an integrated luminosity of 10.7  fb−1 of proton-proton collisions at a center-of-mass energy of 8 TeV. The extinction model studied in this analysis is motivated by the search for signatures of strong gravity at the TeV scale (terascale gravity) and assumes the existence of string couplings in the strong-coupling limit. In this limit, the string model predicts the suppression of all high-transverse-momentum standard model processes, including jet production, beyond a certain energy scale. To test this prediction, the measured transverse-momentum spectrum is compared to the theoretical prediction of the standard model. No significant deficit of events is found at high transverse momentum. A 95% confidence level lower limit of 3.3 TeV is set on the extinction mass scale

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis

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

Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational approaches, we define genomic and proteomic features associated with MYC and the PMN across the 33 cancers of The Cancer Genome Atlas. Pan-cancer, 28% of all samples had at least one of the MYC paralogs amplified. In contrast, the MYC antagonists MGA and MNT were the most frequently mutated or deleted members, proposing a role as tumor suppressors. MYC alterations were mutually exclusive with PIK3CA, PTEN, APC, or BRAF alterations, suggesting that MYC is a distinct oncogenic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such as immune response and growth factor signaling; chromatin, translation, and DNA replication/repair were conserved pan-cancer. This analysis reveals insights into MYC biology and is a reference for biomarkers and therapeutics for cancers with alterations of MYC or the PMN. We present a computational study determining the frequency and extent of alterations of the MYC network across the 33 human cancers of TCGA. These data, together with MYC, positively correlated pathways as well as mutually exclusive cancer genes, will be a resource for understanding MYC-driven cancers and designing of therapeutics