Bounded Refinement Types

We present a notion of bounded quantification for refinement types and show how it expands the expressiveness of refinement typing by using it to develop typed combinators for: (1) relational algebra and safe database access, (2) Floyd-Hoare logic within a state transformer monad equipped with combinators for branching and looping, and (3) using the above to implement a refined IO monad that tracks capabilities and resource usage. This leap in expressiveness comes via a translation to "ghost" functions, which lets us retain the automated and decidable SMT based checking and inference that makes refinement typing effective in practice.Comment: 14 pages, International Conference on Functional Programming, ICFP 201

Blackbody radiation shift in 87Rb frequency standard

The operation of atomic clocks is generally carried out at room temperature, whereas the definition of the second refers to the clock transition in an atom at absolute zero. This implies that the clock transition frequency should be corrected in practice for the effect of finite temperature of which the leading contributor is the blackbody radiation (BBR) shift. Experimental measurements of the BBR shifts are difficult. In this work, we have calculated the blackbody radiation shift of the ground-state hyperfine microwave transition in 87Rb using the relativistic all-order method and carried out detailed evaluation of the accuracy of our final value. Particular care is taken to accurately account for the contributions from highly-excited states. Our predicted value for the Stark coefficient, k_S=-1.240(4)\times 10^{-10}\text{Hz/(V/m)}^{2} is three times more accurate than the previous calculation [1].Comment: 7 page

Information Use by PhD Students in Agriculture and Biology: A Dissertation Citation Analysis

This article reports the findings of a study conducted to examine the types of information used by graduate students in the fields of biological and agricultural sciences at Iowa State University (ISU). The citations of doctoral dissertations submitted in nine agriculture and biological science subject fields (crop production and physiology; molecular, cellular, and developmental biology; entomology; genetics; microbiology; plant breeding; plant pathology; plant physiology; and soil science) at ISU from 1997–2006 were analyzed. The article discusses the types and ages of resources cited in the different subject fields studied. The most cited journals in each discipline were identified, and the journal title dispersion was examined

Foldy-Wouthuysen Transformation in Strong Magnetic Fields and Relativistic Corrections for Quantum Cyclotron Energy Levels

We carry out a direct, iterative Foldy--Wouthuysen transformation of a general Dirac Hamiltonian coupled to an electromagnetic field, including the anomalous magnetic moment. The transformation is carried out through an iterative disentangling of the particle and antiparticle Hamiltonians, in the expansion for higher orders of the momenta. The time-derivative term from the unitary transformation is found to be crucial in supplementing the transverse component of the electric field in higher orders. Final expressions are obtained for general combined electric and magnetic fields, including strong magnetic fields. The time-derivative of the electric field is shown to enter only in the seventh order of the fine-structure constant if the transformation is carried out in the standard fashion. We put special emphasis on the case of strong fields, which are important for a number of applications, such as electrons bound in Penning traps.Comment: 12 pages; RevTe

Intraoperative Organ Motion Models with an Ensemble of Conditional Generative Adversarial Networks

In this paper, we describe how a patient-specific, ultrasound-probe-induced prostate motion model can be directly generated from a single preoperative MR image. Our motion model allows for sampling from the conditional distribution of dense displacement fields, is encoded by a generative neural network conditioned on a medical image, and accepts random noise as additional input. The generative network is trained by a minimax optimisation with a second discriminative neural network, tasked to distinguish generated samples from training motion data. In this work, we propose that 1) jointly optimising a third conditioning neural network that pre-processes the input image, can effectively extract patient-specific features for conditioning; and 2) combining multiple generative models trained separately with heuristically pre-disjointed training data sets can adequately mitigate the problem of mode collapse. Trained with diagnostic T2-weighted MR images from 143 real patients and 73,216 3D dense displacement fields from finite element simulations of intraoperative prostate motion due to transrectal ultrasound probe pressure, the proposed models produced physically-plausible patient-specific motion of prostate glands. The ability to capture biomechanically simulated motion was evaluated using two errors representing generalisability and specificity of the model. The median values, calculated from a 10-fold cross-validation, were 2.8+/-0.3 mm and 1.7+/-0.1 mm, respectively. We conclude that the introduced approach demonstrates the feasibility of applying state-of-the-art machine learning algorithms to generate organ motion models from patient images, and shows significant promise for future research.Comment: Accepted to MICCAI 201

Excitation energies, hyperfine constants, E1, E2, M1 transition rates, and lifetimes of (6s2)nl states in Tl I and Pb II

Energies of np (n=6-9), ns (n=7-9), nd (n=6-8), and nf (n=5-6) states in Tl I and Pb II are obtained using relativistic many-body perturbation theory. Reduced matrix elements, oscillator strengths, transition rates, and lifetimes are determined for the 72 possible electric-dipole transitions. Electric-quadrupole and magnetic-dipole matrix elements are evaluated to obtain np(3/2) - mp(1/2) (n,m=6,7) transition rates. Hyperfine constants A are evaluated for a number of states in 205Tl. First-, second-, third-, and all-order corrections to the energies and matrix elements and first- and second-order Breit corrections to energies are calculated. In our implementation of the all-order method, single and double excitations of Dirac-Fock wave functions are included to all orders in perturbation theory. These calculations provide a theoretical benchmark for comparison with experiment and theory.Comment: twelve tables, no figure

Quantum walks on Cayley graphs

We address the problem of the construction of quantum walks on Cayley graphs. Our main motivation is the relationship between quantum algorithms and quantum walks. In particular, we discuss the choice of the dimension of the local Hilbert space and consider various classes of graphs on which the structure of quantum walks may differ. We completely characterise quantum walks on free groups and present partial results on more general cases. Some examples are given, including a family of quantum walks on the hypercube involving a Clifford Algebra.Comment: J. Phys. A (accepted for publication

Direct Optical Coupling to an Unoccupied Dirac Surface State in the Topological Insulator Bi2_2Se3_3

We characterize the occupied and unoccupied electronic structure of the topological insulator Bi$_2$Se$_3$ by one-photon and two-photon angle-resolved photoemission spectroscopy and slab band structure calculations. We reveal a second, unoccupied Dirac surface state with similar electronic structure and physical origin to the well-known topological surface state. This state is energetically located 1.5 eV above the conduction band, which permits it to be directly excited by the output of a Ti:Sapphire laser. This discovery demonstrates the feasibility of direct ultrafast optical coupling to a topologically protected, spin-textured surface state.Comment: Accepted to Physical Review Letter

The Arabidopsis mutant feronia disrupts the female gametophytic control of pollen tube reception

Reproduction in angiosperms depends on communication processes of the male gametophyte (pollen) with the female floral organs (pistil, transmitting tissue) and the female gametophyte (embryo sac). Pollen-pistil interactions control pollen hydration, germination and growth through the stylar tissue. The female gametophyte is involved in guiding the growing pollen tube towards the micropyle and embryo sac. One of the two synergids flanking the egg cell starts to degenerate and becomes receptive for pollen tube entry. Pollen tube growth arrests and the tip of the pollen tube ruptures to release the sperm cells. Failures in the mutual interaction between the synergid and the pollen tube necessarily impair fertility. But the control of pollen tube reception is not understood. We isolated a semisterile, female gametophytic mutant from Arabidopsis thaliana, named feronia after the Etruscan goddess of fertility, which impairs this process. In the feronia mutant, embryo sac development and pollen tube guidance were unaffected in all ovules, although one half of the ovules bore mutant female gametophytes. However, when the pollen tube entered the receptive synergid of a feronia mutant female gametophyte, it continued to grow, failed to rupture and release the sperm cells, and invaded the embryo sac. Thus, the feronia mutation disrupts the interaction between the male and female gametophyte required to elicit these processes. Frequently, mutant embryo sacs received supernumerary pollen tubes. We analysed feronia with synergid-specific GUS marker lines, which demonstrated that the specification and differentiation of the synergids was normal. However, GUS expression in mutant gametophytes persisted after pollen tube entry, in contrast to wild-type embryo sacs where it rapidly decreased. Apparently, the failure in pollen tube reception results in the continued expression of synergid-specific genes, probably leading to an extended expression of a potential pollen tube attractant

Multiparametric MR imaging for detection of clinically significant prostate cancer: a validation cohort study with transperineal template prostate mapping as the reference standard.

PURPOSE: To evaluate the diagnostic performance of multiparametric (MP) magnetic resonance (MR) imaging for prostate cancer detection by using transperineal template prostate mapping (TTPM) biopsies as the reference standard and to determine the potential ability of MP MR imaging to identify clinically significant prostate cancer. MATERIALS AND METHODS: Institutional review board exemption was granted by the local research ethics committee for this retrospective study. Included were 64 men (mean age, 62 years [range, 40-76]; mean prostate-specific antigen, 8.2 ng/mL [8.2 μg/L] [range, 2.1-43 ng/mL]), 51 with biopsy-proved cancer and 13 suspected of having clinically significant cancer that was biopsy negative or without prior biopsy. MP MR imaging included T2-weighted, dynamic contrast-enhanced and diffusion-weighted imaging (1.5 T, pelvic phased-array coil). Three radiologists independently reviewed images and were blinded to results of biopsy. Two-by-two tables were derived by using sectors of analysis of four quadrants, two lobes, and one whole prostate. Primary target definition for clinically significant disease necessary to be present within a sector of analysis on TTPM for that sector to be deemed positive was set at Gleason score of 3+4 or more and/or cancer core length involvement of 4 mm or more. Sensitivity, negative predictive value, and negative likelihood ratio were calculated to determine ability of MP MR imaging to rule out cancer. Specificity, positive predictive value, positive likelihood ratio, accuracy (overall fraction correct), and area under receiver operating characteristic curves were also calculated. RESULTS: Twenty-eight percent (71 of 256) of sectors had clinically significant cancer by primary endpoint definition. For primary endpoint definition (≥ 4 mm and/or Gleason score ≥ 3+4), sensitivity, negative predictive value, and negative likelihood ratios were 58%-73%, 84%-89%, and 0.3-0.5, respectively. Specificity, positive predictive value, and positive likelihood ratios were 71%-84%, 49%-63%, and 2.-3.44, respectively. Area under the curve values were 0.73-0.84. CONCLUSION: Results of this study indicate that MP MR imaging has a high negative predictive value to rule out clinically significant prostate cancer and may potentially have clinical use in diagnostic pathways of men at risk