BAT - The Bayesian Analysis Toolkit

We describe the development of a new toolkit for data analysis. The analysis package is based on Bayes' Theorem, and is realized with the use of Markov Chain Monte Carlo. This gives access to the full posterior probability distribution. Parameter estimation, limit setting and uncertainty propagation are implemented in a straightforward manner. A goodness-of-fit criterion is presented which is intuitive and of great practical use.Comment: 31 pages, 10 figure

PWD-3DNet: A Deep Learning-Based Fully-Automated Segmentation of Multiple Structures on Temporal Bone CT Scans

The temporal bone is a part of the lateral skull surface that contains organs responsible for hearing and balance. Mastering surgery of the temporal bone is challenging because of this complex and microscopic three-dimensional anatomy. Segmentation of intra-temporal anatomy based on computed tomography (CT) images is necessary for applications such as surgical training and rehearsal, amongst others. However, temporal bone segmentation is challenging due to the similar intensities and complicated anatomical relationships among critical structures, undetectable small structures on standard clinical CT, and the amount of time required for manual segmentation. This paper describes a single multi-class deep learning-based pipeline as the first fully automated algorithm for segmenting multiple temporal bone structures from CT volumes, including the sigmoid sinus, facial nerve, inner ear, malleus, incus, stapes, internal carotid artery and internal auditory canal. The proposed fully convolutional network, PWD-3DNet, is a patch-wise densely connected (PWD) three-dimensional (3D) network. The accuracy and speed of the proposed algorithm was shown to surpass current manual and semi-automated segmentation techniques. The experimental results yielded significantly high Dice similarity scores and low Hausdorff distances for all temporal bone structures with an average of 86% and 0.755 millimeter (mm), respectively. We illustrated that overlapping in the inference sub-volumes improves the segmentation performance. Moreover, we proposed augmentation layers by using samples with various transformations and image artefacts to increase the robustness of PWD-3DNet against image acquisition protocols, such as smoothing caused by soft tissue scanner settings and larger voxel sizes used for radiation reduction. The proposed algorithm was tested on low-resolution CTs acquired by another center with different scanner parameters than the ones used to create the algorithm and shows potential for application beyond the particular training data used in the study

Pregnancy in teenagers diagnosed with type 1 diabetes mellitus in childhood: a national population-based e-cohort study

The aim of this study was to describe the characteristics and outcomes of pregnancies in a national cohort of teenage (<20 years) and young adult women (≥20 years) with and without childhood-onset (<15 years) type 1 diabetes. We hypothesised that, owing to poor glycaemic control during the teenage years, pregnancy outcomes would be poorer in teenage mothers with type 1 diabetes than young adult mothers with type 1 diabetes and mothers without diabetes

Understanding breast-cancer patients’ perceptions: Health information-seeking behaviour and passive information receipt

It is critical to understand patients’ information use from the patient perspective, especially when patients are from different cultures and levels of health literacy. A cross-sectional survey supplemented with interviews of breast cancer survivors including both Latina and non- Latina women was undertaken. Subjects were classified as active information seekers, passive information receivers, and/or users of information. Subjects were further classified by stage of information use, progressing from unawareness or awareness of available information to use or non-use of information to make health decisions. Information sources used and use patterns were examined. Most were active information seekers; many were also passive receivers. Healthcare providers remain the primary information source. Interpersonal communication was far more often cited than either the internet or traditional print and broadcast media. Important cross-cultural differences were found. This study provides insight into how patients use actively sought and passively received information. Despite dramatic growth of the internet and other new media, healthcare providers currently remain keys to health information. Findings may help develop more successful communication strategies when viewed in light of the National Cancer Institute’s ‘Making Health Communication Programs Work’ and the four stages it proposes. It is hoped that future work will focus on evidence-based methods to improve health communication, especially for vulnerable populations. A major lesson learned is the importance of understanding where patients decided to seek information outside the traditional provideroriented approach taken in many health education programmes

Novel detection methods for radiation-induced electron-hole pairs.

Most common ionizing radiation detectors typically rely on one of two general methods: collection of charge generated by the radiation, or collection of light produced by recombination of excited species. Substantial efforts have been made to improve the performance of materials used in these types of detectors, e.g. to raise the operating temperature, to improve the energy resolution, timing or tracking ability. However, regardless of the material used, all these detectors are limited in performance by statistical variation in the collection efficiency, for charge or photons. We examine three alternative schemes for detecting ionizing radiation that do not rely on traditional direct collection of the carriers or photons produced by the radiation. The first method detects refractive index changes in a resonator structure. The second looks at alternative means to sense the chemical changes caused by radiation on a scintillator-type material. The final method examines the possibilities of sensing the perturbation caused by radiation on the transmission of a RF transmission line structure. Aspects of the feasibility of each approach are examined and recommendations made for further work

Single electron Sensitive Readout (SiSeRO) X-ray detectors: Technological progress and characterization

Single electron Sensitive Read Out (SiSeRO) is a novel on-chip charge detector output stage for charge-coupled device (CCD) image sensors. Developed at MIT Lincoln Laboratory, this technology uses a p-MOSFET transistor with a depleted internal gate beneath the transistor channel. The transistor source-drain current is modulated by the transfer of charge into the internal gate. At Stanford, we have developed a readout module based on the drain current of the on-chip transistor to characterize the device. Characterization was performed for a number of prototype sensors with different device architectures, e.g. location of the internal gate, MOSFET polysilicon gate structure, and location of the trough in the internal gate with respect to the source and drain of the MOSFET (the trough is introduced to confine the charge in the internal gate). Using a buried-channel SiSeRO, we have achieved a charge/current conversion gain of >700 pA per electron, an equivalent noise charge (ENC) of around 6 electrons root mean square (RMS), and a full width half maximum (FWHM) of approximately 140 eV at 5.9 keV at a readout speed of 625 Kpixel/s. In this paper, we discuss the SiSeRO working principle, the readout module developed at Stanford, and the characterization test results of the SiSeRO prototypes. We also discuss the potential to implement Repetitive Non-Destructive Readout (RNDR) with these devices and the preliminary results which can in principle yield sub-electron ENC performance. Additional measurements and detailed device simulations will be essential to mature the SiSeRO technology. However, this new device class presents an exciting technology for next generation astronomical X-ray telescopes requiring fast, low-noise, radiation hard megapixel imagers with moderate spectroscopic resolution.Comment: To appear in SPIE Proceedings of Astronomical Telescopes + Instrumentation, 202

Wet scavenging of soluble gases in DC3 deep convective storms using WRF-Chem simulations and aircraft observations

We examine wet scavenging of soluble trace gases in storms observed during the Deep Convective Clouds and Chemistry (DC3) field campaign. We conduct high-resolution simulations with the Weather Research and Forecasting model with Chemistry (WRF-Chem) of a severe storm in Oklahoma. The model represents well the storm location, size, and structure as compared with Next Generation Weather Radar reflectivity, and simulated CO transport is consistent with aircraft observations. Scavenging efficiencies (SEs) between inflow and outflow of soluble species are calculated from aircraft measurements and model simulations. Using a simple wet scavenging scheme, we simulate the SE of each soluble species within the error bars of the observations. The simulated SEs of all species except nitric acid (HNO_3) are highly sensitive to the values specified for the fractions retained in ice when cloud water freezes. To reproduce the observations, we must assume zero ice retention for formaldehyde (CH_2O) and hydrogen peroxide (H_2O_2) and complete retention for methyl hydrogen peroxide (CH_3OOH) and sulfur dioxide (SO_2), likely to compensate for the lack of aqueous chemistry in the model. We then compare scavenging efficiencies among storms that formed in Alabama and northeast Colorado and the Oklahoma storm. Significant differences in SEs are seen among storms and species. More scavenging of HNO_3 and less removal of CH_3OOH are seen in storms with higher maximum flash rates, an indication of more graupel mass. Graupel is associated with mixed-phase scavenging and lightning production of nitrogen oxides (NO_x), processes that may explain the observed differences in HNO_3 and CH_3OOH scavenging

Variability in Blood Pressure Assessment in Patients Supported with the HeartMate 3TM

Targeted blood pressure (BP) control is a goal of left ventricular assist device medical management, but the interpretation of values obtained from noninvasive instruments is challenging. In the MOMENTUM 3 Continued Access Protocol, paired BP values in HeartMate 3 (HM3) patients were compared from arterial (A)-line and Doppler opening pressure (DOP) (319 readings in 261 patients) and A-line and automated cuff (281 readings in 247 patients). Pearson (R) correlations between A-line mean arterial (MAP) and systolic blood pressures (SBP) were compared with DOP and cuff measures according to the presence (\u3e1 pulse in 5 seconds) or absence of a palpable radial pulse. There were only moderate correlations between A-line and noninvasive measurements of SBP (DOP R = 0.58; cuff R = 0.47) and MAP (DOP R = 0.48; cuff R = 0.37). DOP accuracy for MAP estimation, defined as the % of readings within ± 10 mmHg of A-line MAP, decreased from 80% to 33% for DOP ≤ 90 vs. \u3e90 mmHg, and precision also diminished (mean absolute difference [MAD] increased from 6.3 ± 5.6 to 16.1 ± 11.4 mmHg). Across pulse pressures, cuff MAPs were within ±10 mmHg of A-line 62.9%-68.8% of measures and MADs were negligible. The presence of a palpable pulse reduced the accuracy and precision of the DOP-MAP estimation but did not impact cuff-MAP accuracy or precision. In summary, DOP may overestimate MAP in some patients on HM3 support. Simultaneous use of DOP and automated cuff and radial pulse may be needed to guide antihypertensive medication titration in outpatients on HM3 support

The Impossibility of a Perfectly Competitive Labor Market

Using the institutional theory of transaction cost, I demonstrate that the assumptions of the competitive labor market model are internally contradictory and lead to the conclusion that on purely theoretical grounds a perfectly competitive labor market is a logical impossibility. By extension, the familiar diagram of wage determination by supply and demand is also a logical impossibility and the neoclassical labor demand curve is not a well-defined construct. The reason is that the perfectly competitive market model presumes zero transaction cost and with zero transaction cost all labor is hired as independent contractors, implying multi-person firms, the employment relationship, and labor market disappear. With positive transaction cost, on the other hand, employment contracts are incomplete and the labor supply curve to the firm is upward sloping, again causing the labor demand curve to be ill-defined. As a result, theory suggests that wage rates are always and everywhere an amalgam of an administered and bargained price. Working Paper 06-0

Atmospheric Acetaldehyde: Importance of Air-Sea Exchange and a Missing Source in the Remote Troposphere.

We report airborne measurements of acetaldehyde (CH3CHO) during the first and second deployments of the National Aeronautics and Space Administration (NASA) Atmospheric Tomography Mission (ATom). The budget of CH3CHO is examined using the Community Atmospheric Model with chemistry (CAM-chem), with a newly-developed online air-sea exchange module. The upper limit of the global ocean net emission of CH3CHO is estimated to be 34 Tg a-1 (42 Tg a-1 if considering bubble-mediated transfer), and the ocean impacts on tropospheric CH3CHO are mostly confined to the marine boundary layer. Our analysis suggests that there is an unaccounted CH3CHO source in the remote troposphere and that organic aerosols can only provide a fraction of this missing source. We propose that peroxyacetic acid (PAA) is an ideal indicator of the rapid CH3CHO production in the remote troposphere. The higher-than-expected CH3CHO measurements represent a missing sink of hydroxyl radicals (and halogen radical) in current chemistry-climate models