250 research outputs found
Shape Space Methods for Quantum Cosmological Triangleland
With toy modelling of conceptual aspects of quantum cosmology and the problem
of time in quantum gravity in mind, I study the classical and quantum dynamics
of the pure-shape (i.e. scale-free) triangle formed by 3 particles in 2-d. I do
so by importing techniques to the triangle model from the corresponding 4
particles in 1-d model, using the fact that both have 2-spheres for shape
spaces, though the latter has a trivial realization whilst the former has a
more involved Hopf (or Dragt) type realization. I furthermore interpret the
ensuing Dragt-type coordinates as shape quantities: a measure of
anisoscelesness, the ellipticity of the base and apex's moments of inertia, and
a quantity proportional to the area of the triangle. I promote these quantities
at the quantum level to operators whose expectation and spread are then useful
in understanding the quantum states of the system. Additionally, I tessellate
the 2-sphere by its physical interpretation as the shape space of triangles,
and then use this as a back-cloth from which to read off the interpretation of
dynamical trajectories, potentials and wavefunctions. I include applications to
timeless approaches to the problem of time and to the role of uniform states in
quantum cosmological modelling.Comment: A shorter version, as per the first stage in the refereeing process,
and containing some new reference
Physics of Solar Prominences: II - Magnetic Structure and Dynamics
Observations and models of solar prominences are reviewed. We focus on
non-eruptive prominences, and describe recent progress in four areas of
prominence research: (1) magnetic structure deduced from observations and
models, (2) the dynamics of prominence plasmas (formation and flows), (3)
Magneto-hydrodynamic (MHD) waves in prominences and (4) the formation and
large-scale patterns of the filament channels in which prominences are located.
Finally, several outstanding issues in prominence research are discussed, along
with observations and models required to resolve them.Comment: 75 pages, 31 pictures, review pape
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
Research trends in combinatorial optimization
Acknowledgments This work has been partially funded by the Spanish Ministry of Science, Innovation, and Universities through the project COGDRIVE (DPI2017-86915-C3-3-R). In this context, we would also like to thank the Karlsruhe Institute of Technology. Open access funding enabled and organized by Projekt DEAL.Peer reviewedPublisher PD
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
The criminal justice voluntary sector: concepts and an agenda for an emerging field
This is the peer reviewed version of the following article: Tomczak, P. & Buck, G. (2019). The criminal justice voluntary sector: concepts and an agenda for an emerging field. Howard Journal of Crime and Justice, 58(3), which has been published in final form at https://doi.org/10.1111/hojo.12326. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.Volunteers and voluntary organisations play significant roles pervading criminal justice. They are key actors, with unrecognised potential to shore up criminal justice and/or collaboratively reshape social justice. Unlike public and for-profit agents, criminal justice volunteers and voluntary organisations (CJVVOs) have been neglected by scholars. We call for analyses of diverse CJVVOs, in national and comparative contexts. We provide three categories to highlight distinctive organising auspices, which hold across criminal justice: statutory volunteers, quasi-statutory volunteers and voluntary organisations. The unknown implications of these different forms of non-state, non-profit justice involvement deserve far greater attention from academics, policymakers and practitioners
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
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