Probability Modeling of the Number of Positive Cores in a Prostate Cancer Biopsy Session, with Applications

Abstract Among men, prostate cancer (CaP) is the most common newly diagnosed cancer and the second leading cause of death from cancer. A major issue of very large scale is avoiding both over-and under-treatment of CaP cases. The central challenge is deciding clinical significance or insignificance when the CaP biopsy results are positive but only marginally so. A related concern is deciding how to increase the number of biopsy cores for larger prostates. As a foundation for improved choice of number of cores and improved interpretation of biopsy results, we develop a probability model for the number of positive cores found in a biopsy, given the total number of cores, the volumes of the tumor nodules, and -very importantly -the prostate volume. Also, three applications are carried out: guidelines for the number of cores as a function of prostate volume, decision rules for insignificant versus significant CaP using number of positive cores, and, using prior distributions on total tumor size, Bayesian posterior probabilities for insignificant CaP and posterior median CaP. The model-based results have generality of application, take prostate volume into account, and provide attractive tradeoffs of specificity versus sensitivity

Confirmatory Factor Analysis Using PROC CALIS: A Practical Guide for Survey Researchers

ABSTRACT Survey research can provide a straightforward and effective means of collecting input on a range of topics. Survey researchers often like to group similar survey items into construct domains in order to make generalizations about a particular area of interest. Confirmatory Factor Analysis is used to test whether this pre-existing theoretical model underlies a particular set of responses to survey questions. Based on Structural Equation Modeling (SEM), Confirmatory Factor Analysis provides the survey researcher with a means to evaluate how well the actual survey response data fits within the a priori model specified by subject matter experts. PROC CALIS now provides survey researchers the ability to perform Confirmatory Factor Analysis using SAS ® . This paper provides a survey researcher with the steps needed to complete Confirmatory Factor Analysis using SAS. We discuss and demonstrate the options available to survey researchers in the handling of missing and "not applicable" survey responses using an ARRAY statement within a DATA step and imputation of item non-response. A simple demonstration of PROC CALIS is then provided with interpretation of key portions of the SAS output. Using recommendations provided by SAS from the PROC CALIS output, the analysis is then modified to provide a better fit of survey items into survey domains

Saildrone: adaptively sampling the marine environment

Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 101(6), (2020): E744-E762, doi:10.1175/BAMS-D-19-0015.1.From 11 April to 11 June 2018 a new type of ocean observing platform, the Saildrone surface vehicle, collected data on a round-trip, 60-day cruise from San Francisco Bay, down the U.S. and Mexican coast to Guadalupe Island. The cruise track was selected to optimize the science team’s validation and science objectives. The validation objectives include establishing the accuracy of these new measurements. The scientific objectives include validation of satellite-derived fluxes, sea surface temperatures, and wind vectors and studies of upwelling dynamics, river plumes, air–sea interactions including frontal regions, and diurnal warming regions. On this deployment, the Saildrone carried 16 atmospheric and oceanographic sensors. Future planned cruises (with open data policies) are focused on improving our understanding of air–sea fluxes in the Arctic Ocean and around North Brazil Current rings.The Saildrone data collection mission was sponsored by the Saildrone Award, an annual data collection mission awarded by Saildrone Inc., and the Schmidt Family Foundation. The research was funded by the NASA Physical Oceanography Program Grant 80NSSC18K0837 and 80NSSC18K1441. The work by T. M. Chin, J. Vazquez-Cuerzo, and V. Tsontos was carried out at the Jet Propulsion Laboratory (JPL), California Institute of Technology, under a contract with the National Aeronautics and Space Administration (NASA). Piero L.F. Mazzini was supported by California Sea Grant Award NA18OAR4170073. We thank CeNCOOS for providing the HF radar data in the Gulf of the Farallones. Jose Gomez-Valdes was supported by CONACYT Grant 257125, and by CICESE. Work by Joel Scott and Ivona Cetinic was supported through NASA PACE. The work by Lisan Yu was supported by NOAA Ocean Observing and Monitoring Division under Grant NA14OAR4320158

Reevaluating the roles of eddies in multiple barotropic wind-driven gyres

Author Posting. © American Meteorological Society, 2005. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 35 (2005): 1263–1278, doi:10.1175/JPO2743.1.Multiple-gyre ocean models have a weaker mean subtropical circulation than single-gyre calculations with the same viscosity and subtropical forcing. Traditionally, this reduction in circulation is attributed to an intergyre eddy vorticity flux that cancels some of the wind input, part of which does not require a Lagrangian mass exchange (theory of dissipative meandering). Herein the intergyre eddy vorticity flux is shown to be a controlling factor in barotropic models at high Reynolds number only with exactly antisymmetric gyres and slip boundary conditions. Almost no intergyre flux occurs when no-slip boundary conditions are used, yet the subtropical gyre is still significantly weaker in multiple-gyre calculations. Sinuous modes of instability present only in multiple gyres are shown here to vastly increase the eddy vorticity transport efficiency. This increase in efficiency reduces the mean circulation necessary for equilibrium. With slip boundary conditions, the intergyre eddy transport is possibly much larger. However, with wind forcing relevant for the ocean—two unequal gyres—a mean flow flux of vorticity rather than an eddy flux between the regions of opposing wind forcing is increasingly important with increasing Reynolds number. A physical rationalization of the differing results is provided by diagnosis of the equilibrium vorticity budget and eddy transport efficiency. Calculations varying 1) boundary conditions, 2) sources and sinks of vorticity, 3) eddy transport efficiency, and 4) the degree of symmetry of the gyres are discussed.The author was supported by an ONR-supported NDSEG fellowship, an MIT Presidential Fellowship, NSF OCE 9910654, a Princeton University/GFDL fellowship, and a NOAA Climate and Global Change postdoctoral fellowship managed by UCAR

Studies of Impurity Assimilation During Massive Argon Gas Injection in DIII-D

Fast shutdown of discharges using massive gas injection (MGI) is a promising technique for reducing tokamak wall damage during disruptions [1]. An outstanding concern, however, is the generation of runaway electrons (RE) during the shutdown. Although RE formation observed during MGI in present-day experiments is quite small (typically <1% of the main plasma current I{sub p} in DIII-D), it is thought that even this small RE current could be amplified to significant levels in reactor-scale tokamaks such as ITER [2]. It is expected that complete collisional suppression of any potential RE amplification during the CQ can be achieved for suppression parameters {gamma}{sub crit} {triple_bond} E{sub crit}/E{sub {psi}} > 1, where E{sub crit} = [2{pi}e{sup 3}ln{Lambda}(2n{sub e} + n{sub B})]/mc{sup 2} is the critical electric field [2] and E{sub {psi}} {approx} -[({mu}{sub 0}l{sub i})/4{pi}][-({partial_derivative}I{sub p}/{partial_derivative}t)+ {alpha}{sub L}(I{sub W}/{tau}{sub W})] is the toroidal electric field resulting from the decay of the plasma current I{sub p}. n{sub e} is the free electron density, n{sub B} is the bound electron density, {alpha}{sub L} {approx} 2[ln(8R/r{sub w})-2]/l{sub i} is the ratio of external (outside conducting wall) to internal (inside conducting wall) self-inductance, I{sub w} is the wall current, and {tau}{sub w} is the wall time. The densities required to achieve {gamma}{sub crit} > 1 are typically quite large, e.g. n{sub tot} {triple_bond} n{sub e} + n{sub B}/2 {approx} 10{sup 16} cm{sup -3} for DIII-D. To have a possibility of achieving the required density in the DIII-D plasma (with volume V{sub p} {approx} 20 m{sup 3}), an MGI system using argon must be able to deliver of order 10{sup 22} argon atoms to the plasma within the shutdown timescale of about 10 ms

Absolute visual sensitivity of the goldfish

Absolute visual threshold was measured in dark-adapted goldfish, using classical conditioning of heart and respiration rates. For threshold detection of a 132[deg] diameter stimulus near the peak of the rod pigment's sensitivity, only 1 quantum was incident for every 2000-4000 rods, and 400-830 photoisomerizations were needed for vision. Spectral sensitivity was also determined at absolute threshold, sing respiration rate conditioning. The shape of the function matches the electrophysiologically determined spectral sensitivity of goldfish retinal ganglion cells, but both curves are relatively more sensitive in the long wavelengths than would be predicted on the basis of the rod pigment alone. A dim 703 nm background depressed sensitivity to a 636 nm test light more than to a 532 nm test, proving that another class of photoreceptors is active at absolute threshold. If the other receptors were the red cones, as seems most likely, then only 1 quantum was incident per 220 red cones at their absolute threshold, and photoisomerizations occurred in each of 164 red cones at threshold.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22776/1/0000331.pd

Modelling of the effect of ELMs on fuel retention at the bulk W divertor of JET

Effect of ELMs on fuel retention at the bulk W target of JET ITER-Like Wall was studied with multi-scale calculations. Plasma input parameters were taken from ELMy H-mode plasma experiment. The energetic intra-ELM fuel particles get implanted and create near-surface defects up to depths of few tens of nm, which act as the main fuel trapping sites during ELMs. Clustering of implantation-induced vacancies were found to take place. The incoming flux of inter-ELM plasma particles increases the different filling levels of trapped fuel in defects. The temperature increase of the W target during the pulse increases the fuel detrapping rate. The inter-ELM fuel particle flux refills the partially emptied trapping sites and fills new sites. This leads to a competing effect on the retention and release rates of the implanted particles. At high temperatures the main retention appeared in larger vacancy clusters due to increased clustering rate

Shattered pellet injection experiments at JET in support of the ITER disruption mitigation system design

A series of experiments have been executed at JET to assess the efficacy of the newly installed shattered pellet injection (SPI) system in mitigating the effects of disruptions. Issues, important for the ITER disruption mitigation system, such as thermal load mitigation, avoidance of runaway electron (RE) formation, radiation asymmetries during thermal quench mitigation, electromagnetic load control and RE energy dissipation have been addressed over a large parameter range. The efficiency of the mitigation has been examined for the various SPI injection strategies. The paper summarises the results from these JET SPI experiments and discusses their implications for the ITER disruption mitigation scheme

The role of ETG modes in JET-ILW pedestals with varying levels of power and fuelling

We present the results of GENE gyrokinetic calculations based on a series of JET-ITER-like-wall (ILW) type I ELMy H-mode discharges operating with similar experimental inputs but at different levels of power and gas fuelling. We show that turbulence due to electron-temperature-gradient (ETGs) modes produces a significant amount of heat flux in four JET-ILW discharges, and, when combined with neoclassical simulations, is able to reproduce the experimental heat flux for the two low gas pulses. The simulations plausibly reproduce the high-gas heat fluxes as well, although power balance analysis is complicated by short ELM cycles. By independently varying the normalised temperature gradients (omega(T)(e)) and normalised density gradients (omega(ne )) around their experimental values, we demonstrate that it is the ratio of these two quantities eta(e) = omega(Te)/omega(ne) that determines the location of the peak in the ETG growth rate and heat flux spectra. The heat flux increases rapidly as eta(e) increases above the experimental point, suggesting that ETGs limit the temperature gradient in these pulses. When quantities are normalised using the minor radius, only increases in omega(Te) produce appreciable increases in the ETG growth rates, as well as the largest increases in turbulent heat flux which follow scalings similar to that of critical balance theory. However, when the heat flux is normalised to the electron gyro-Bohm heat flux using the temperature gradient scale length L-Te, it follows a linear trend in correspondence with previous work by different authors

Spectroscopic camera analysis of the roles of molecularly assisted reaction chains during detachment in JET L-mode plasmas

The roles of the molecularly assisted ionization (MAI), recombination (MAR) and dissociation (MAD) reaction chains with respect to the purely atomic ionization and recombination processes were studied experimentally during detachment in low-confinement mode (L-mode) plasmas in JET with the help of experimentally inferred divertor plasma and neutral conditions, extracted previously from filtered camera observations of deuterium Balmer emission, and the reaction coefficients provided by the ADAS, AMJUEL and H2VIBR atomic and molecular databases. The direct contribution of MAI and MAR in the outer divertor particle balance was found to be inferior to the electron-atom ionization (EAI) and electron-ion recombination (EIR). Near the outer strike point, a strong atom source due to the D+2-driven MAD was, however, observed to correlate with the onset of detachment at outer strike point temperatures of Te,osp = 0.9-2.0 eV via increased plasma-neutral interactions before the increasing dominance of EIR at Te,osp < 0.9 eV, followed by increasing degree of detachment. The analysis was supported by predictions from EDGE2D-EIRENE simulations which were in qualitative agreement with the experimental observations