Linear and nonlinear susceptibilities of a decoherent two-level system

The linear and nonlinear dynamical susceptibilities of a two level system are calculated as it undergoes a transition to a decoherent state. Analogously to the Glover-Tinkham-Ferrell sum rule of superconductivity, spectral weight in the linear susceptibility is continuously transferred from a finite frequency resonance to nearly zero frequency, corresponding to a broken symmetry in the thermodynamic limit. For this reason, the behavior of the present model (the Mermin model) differs significantly from the spin-boson model. The third order nonlinear susceptibility, corresponding to two-photon absorption, has an unexpected non-monotonic behavior as a function of the environmental coupling, reaching a maximum within the decoherent phase of the model. Both linear and nonlinear susceptibilities may be expressed in a universal form.Comment: 10 pages, 9 figure

Accretion and ejection in black-hole X-ray transients

Aims: We summarize the current observational picture of the outbursts of black-hole X-ray transients (BHTs), based on the evolution traced in a hardness-luminosity diagram (HLD), and we offer a physical interpretation. Methods: The basic ingredient in our interpretation is the Poynting-Robertson Cosmic Battery (PRCB, Contopoulos & Kazanas 1998), which provides locally the poloidal magnetic field needed for the ejection of the jet. In addition, we make two assumptions, easily justifiable. The first is that the mass-accretion rate to the black hole in a BHT outburst has a generic bell-shaped form. This is guaranteed by the observational fact that all BHTs start their outburst and end it at the quiescent state. The second assumption is that at low accretion rates the accretion flow is geometrically thick, ADAF-like, while at high accretion rates it is geometrically thin. Results: Both, at the beginning and the end of an outburst, the PRCB establishes a strong poloidal magnetic field in the ADAF-like part of the accretion flow, and this explains naturally why a jet is always present in the right part of the HLD. In the left part of the HLD, the accretion flow is in the form of a thin disk, and such a disk cannot sustain a strong poloidal magnetic filed. Thus, no jet is expected in this part of the HLD. The counterclockwise traversal of the HLD is explained as follows: the poloidal magnetic field in the ADAF forces the flow to remain ADAF and the source to move upwards in the HLD rather than to turn left. Thus, the history of the system determines the counterclockwise traversal of the HLD. As a result, no BHT is expected to ever traverse the entire HLD curve in the clockwise direction. Conclusions: We offer a physical interpretation of accretion and ejection in BHTs with only one parameter, the mass transfer rate.Comment: Accepted for publication in A&

Identification of clonal hematopoiesis mutations in solid tumor patients undergoing unpaired next-generation sequencing assays

Purpose: In this era of precision-based medicine, for optimal patient care, results reported from commercial next-generation sequencing (NGS) assays should adequately reflect the burden of somatic mutations in the tumor being sequenced. Here, we sought to determine the prevalence of clonal hematopoiesis leading to possible misattribution of tumor mutation calls on unpaired Foundation Medicine NGS assays. Experimental Design: This was a retrospective cohort study of individuals undergoing NGS of solid tumors from two large cancer centers. We identified and quantified mutations in genes known to be frequently altered in clonal hematopoiesis (DNMT3A, TET2, ASXL1, TP53, ATM, CHEK2, SF3B1, CBL, JAK2) that were returned to physicians on clinical Foundation Medicine reports. For a subset of patients, we explored the frequency of true clonal hematopoiesis by comparing mutations on Foundation Medicine reports with matched blood sequencing. Results: Mutations in genes that are frequently altered in clonal hematopoiesis were identified in 65% (1,139/1,757) of patients undergoing NGS. When excluding TP53, which is often mutated in solid tumors, these events were still seen in 35% (619/1,757) of patients. Utilizing paired blood specimens, we were able to confirm that 8% (18/226) of mutations reported in these genes were true clonal hematopoiesis events. The majority of DNMT3A mutations (64%, 7/11) and minority of TP53 mutations (4%, 2/50) were clonal hematopoiesis. Conclusions: Clonal hematopoiesis mutations are commonly reported on unpaired NGS testing. It is important to recognize clonal hematopoiesis as a possible cause of misattribution of mutation origin when applying NGS findings to a patient's care

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.Comment: 161 pages, Review, Eur Phys J Special-Topics, accepte

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