Rate-equation approach to atomic-laser light statistics

We consider three- and four-level atomic lasers that are either incoherently (unidirectionally) or coherently (bidirectionally) pumped, the single-mode cavity being resonant with the laser transition. The intra-cavity Fano factor and the photo-current spectral density are evaluated on the basis of rate equations. According to that approach, fluctuations are caused by jumps in active and detecting atoms. The algebra is considerably simpler than the one required by Quantum-Optics treatments. Whenever a comparison can be made, the expressions obtained coincide. The conditions under which the output light exhibits sub-Poissonian statistics are considered in detail. Analytical results, based on linearization, are verified by comparison with Monte Carlo simulations. An essentially exhaustive investigation of sub-Poissonian light generation by three- and four-level atoms lasers has been performed. Only special forms were reported earlier.Comment: 9 pages, 7 figures, RevTeX

Field- and pressure-induced magnetic quantum phase transitions in TlCuCl_3

Thallium copper chloride is a quantum spin liquid of S = 1/2 Cu^2+ dimers. Interdimer superexchange interactions give a three-dimensional magnon dispersion and a spin gap significantly smaller than the dimer coupling. This gap is closed by an applied hydrostatic pressure of approximately 2kbar or by a magnetic field of 5.6T, offering a unique opportunity to explore the both types of quantum phase transition and their associated critical phenomena. We use a bond-operator formulation to obtain a continuous description of all disordered and ordered phases, and thus of the transitions separating these. Both pressure- and field-induced transitions may be considered as the Bose-Einstein condensation of triplet magnon excitations, and the respective phases of staggered magnetic order as linear combinations of dimer singlet and triplet modes. We focus on the evolution with applied pressure and field of the magnetic excitations in each phase, and in particular on the gapless (Goldstone) modes in the ordered regimes which correspond to phase fluctuations of the ordered moment. The bond-operator description yields a good account of the magnetization curves and of magnon dispersion relations observed by inelastic neutron scattering under applied fields, and a variety of experimental predictions for pressure-dependent measurements.Comment: 20 pages, 17 figure

Specific heat of an S=1/2 Heisenberg ladder compound Cu2_2(C5_5H12_{12}N2_2)2_2Cl4_4 under magnetic fields

Specific heat measurements down to 0.5 K have been performed on a single crystal sample of a spin-ladder like compound Cu$_{2}$(C$_{5}$H$_{12}$N$_{2}$)$_{2}$Cl$_{4}$ under magnetic fields up to 12 T. The temperature dependence of the observed data in a magnetic field below 6 T is well reproduced by numerical results calculated for the S=1/2 two-leg ladder with $J_{\rm{rung}}$/$J_{\rm{leg}}$=5. In the gapless region above 7 T ($H_{\rm{c1}}$), the agreement between experiment and calculation is good above about 2 K and a sharp and a round peak were observed below 2 K in a magnetic field around 10 T, but the numerical data show only a round peak, the magnitude of which is smaller than that of the observed one. The origin of the sharp peak and the difference between the experimental and numerical round peak are discussed.Comment: 14 pages, 11 figures, Submitted to PR

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

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

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Axonal swellings are related to type 2 diabetes, but not to distal diabetic sensorimotor polyneuropathy

Aims/hypothesis Distal diabetic sensorimotor polyneuropathy (DSP) is a common complication of diabetes with many patients showing a reduction of intraepidermal nerve fibre density (IENFD) from skin biopsy, a validated and sensitive diagnostic tool for the assessment of DSP. Axonal swelling ratio is a morphological quantification altered in DSP. It is, however, unclear if axonal swellings are related to diabetes or DSP. The aim of this study was to investigate how axonal swellings in cutaneous nerve fibres are related to type 2 diabetes mellitus, DSP and neuropathic pain in a well-defined cohort of patients diagnosed with type 2 diabetes. Methods A total of 249 participants, from the Pain in Neuropathy Study (UK) and the International Diabetic Neuropathy Consortium (Denmark), underwent a structured neurological examination, nerve conduction studies, quantitative sensory testing and skin biopsy. The study included four groups: healthy control study participants without diabetes (n = 45); participants with type 2 diabetes without DSP (DSP−; n = 31); and participants with evidence of DSP (DSP+; n = 173); the last were further separated into painless DSP+ (n = 74) and painful DSP+ (n = 99). Axonal swellings were defined as enlargements on epidermal-penetrating fibres exceeding 1.5 μm in diameter. Axonal swelling ratio is calculated by dividing the number of axonal swellings by the number of intraepidermal nerve fibres. Results Median (IQR) IENFD (fibres/mm) was: 6.7 (5.2–9.2) for healthy control participants; 6.2 (4.4–7.3) for DSP−; 1.3 (0.5–2.2) for painless DSP+; and 0.84 (0.4–1.6) for painful DSP+. Swelling ratios were calculated for all participants and those with IENFD > 1.0 fibre/mm. When only those participants with IENFD > 1.0 fibre/mm were included, the axonal swelling ratio was higher in participants with type 2 diabetes when compared with healthy control participants (p < 0.001); however, there was no difference between DSP− and painless DSP+ participants, or between painless DSP+ and painful DSP+ participants. The axonal swelling ratio correlated weakly with HbA1c (r = 0.16, p = 0.04), but did not correlate with the Toronto Clinical Scoring System (surrogate measure of DSP severity), BMI or type 2 diabetes duration. Conclusions/interpretation In individuals with type 2 diabetes where IENFD is >1.0 fibre/mm, axonal swelling ratio is related to type 2 diabetes but is not related to DSP or painful DSP. Axonal swellings may be an early marker of sensory nerve injury in type 2 diabetes