205 research outputs found
Microscopic calculation of the spin-dependent neutron scattering lengths on 3He
We report on the spin.dependent neutron scattering length on 3He from a
microscopic calculation of p-3H, n-3He, and d-2H scattering employing the
Argonne v18 nucleon-nucleon potential with and without additional three-nucleon
force. The results and that of a comprehensive R-matrix analysis are compared
to a recent measurement. The overall agreement for the scattering lengths is
quite good. The imaginary parts of the scattering lengths are very sensitive to
the inclusion of three-nucleon forces, whereas the real parts are almost
insensitive.Comment: 9 pages, 1 figur
Polarons with a twist
We consider a polaron model where molecular \emph{rotations} are important.
Here, the usual hopping between neighboring sites is affected directly by the
electron-phonon interaction via a {\em twist-dependent} hopping amplitude. This
model may be of relevance for electronic transport in complex molecules and
polymers with torsional degrees of freedom, such as DNA, as well as in
molecular electronics experiments where molecular twist motion is significant.
We use a tight-binding representation and find that very different polaronic
properties are already exhibited by a two-site model -- these are due to the
nonlinearity of the restoring force of the twist excitations, and of the
electron-phonon interaction in the model. In the adiabatic regime, where
electrons move in a {\em low}-frequency field of twisting-phonons, the
effective splitting of the energy levels increases with coupling strength. The
bandwidth in a long chain shows a power-law suppression with coupling, unlike
the typical exponential dependence due to linear phonons.Comment: revtex4 source and one eps figur
Magnetic Field Generation in Stars
Enormous progress has been made on observing stellar magnetism in stars from
the main sequence through to compact objects. Recent data have thrown into
sharper relief the vexed question of the origin of stellar magnetic fields,
which remains one of the main unanswered questions in astrophysics. In this
chapter we review recent work in this area of research. In particular, we look
at the fossil field hypothesis which links magnetism in compact stars to
magnetism in main sequence and pre-main sequence stars and we consider why its
feasibility has now been questioned particularly in the context of highly
magnetic white dwarfs. We also review the fossil versus dynamo debate in the
context of neutron stars and the roles played by key physical processes such as
buoyancy, helicity, and superfluid turbulence,in the generation and stability
of neutron star fields.
Independent information on the internal magnetic field of neutron stars will
come from future gravitational wave detections. Thus we maybe at the dawn of a
new era of exciting discoveries in compact star magnetism driven by the opening
of a new, non-electromagnetic observational window.
We also review recent advances in the theory and computation of
magnetohydrodynamic turbulence as it applies to stellar magnetism and dynamo
theory. These advances offer insight into the action of stellar dynamos as well
as processes whichcontrol the diffusive magnetic flux transport in stars.Comment: 41 pages, 7 figures. Invited review chapter on on magnetic field
generation in stars to appear in Space Science Reviews, Springe
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
The LOFAR Two-metre Sky Survey. III:First data release: Optical/infrared identifications and value-added catalogue
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
Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation
DNA methylation quantitative trait locus (mQTL) analyses on 32,851 participants identify genetic variants associated with DNA methylation at 420,509 sites in blood, resulting in a database of >270,000 independent mQTLs.Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.Molecular Epidemiolog
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
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