SBMLToolbox: an SBML toolbox for MATLAB users

We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML

RadVel: The Radial Velocity Modeling Toolkit

RadVel is an open source Python package for modeling Keplerian orbits in radial velocity (RV) time series. RadVel provides a convenient framework to fit RVs using maximum a posteriori optimization and to compute robust confidence intervals by sampling the posterior probability density via Markov Chain Monte Carlo (MCMC). RadVel allows users to float or fix parameters, impose priors, and perform Bayesian model comparison. We have implemented realtime MCMC convergence tests to ensure adequate sampling of the posterior. RadVel can output a number of publication-quality plots and tables. Users may interface with RadVel through a convenient command-line interface or directly from Python. The code is object-oriented and thus naturally extensible. We encourage contributions from the community. Documentation is available at http://radvel.readthedocs.io.Comment: prepared for resubmission to PAS

A trained perceptual bias that lasts for weeks

AbstractClassical (Pavlovian) conditioning procedures can be used to bias the appearance of physical stimuli. Under natural conditions this form of perceptual learning could cause perception to become more accurate by changing prior belief to be in accord with what is statistically likely. However, for learning to be of functional significance, it must last until similar stimuli are encountered again. Here, we used the apparent rotation direction of a revolving wire frame (Necker) cube to test whether a learned perceptual bias is long lasting. Apparent rotation direction was trained to have a different bias at two different retinal locations by interleaving the presentation of ambiguous cubes with presentation of cubes that were disambiguated by disparity and occlusion cues. Four groups of eight subjects were subsequently tested either 1, 7, 14, or 28days after initial training, respectively, using a counter-conditioning procedure. All four groups showed incomplete re-learning of the reversed contingency relationship during their second session. One group repeated the counter-conditioning and showed an increase in the reverse bias, showing that the first counter-conditioning session also had a long-lasting effect. The fact that the original learning was still evident four weeks after the initial training is consistent with the operation of a mechanism that ordinarily would improve the accuracy and efficiency of perception

Disease risks from foods, England and Wales, 1996-2000.

Data from population-based studies and national surveillance systems were collated and analyzed to estimate the impact of disease and risks associated with eating different foods in England and Wales. From 1996 to 2000, an estimated 1,724,315 cases of indigenous foodborne disease per year resulted in 21,997 hospitalizations and 687 deaths. The greatest impact on the healthcare sector arose from foodborne Campylobacter infection (160,788 primary care visits and 15,918 hospitalizations), while salmonellosis caused the most deaths (209). The most important cause of indigenous foodborne disease was contaminated chicken (398,420 cases, risk [cases/million servings] = 111; case-fatality rate [deaths/100,000 cases] = 35, deaths = 141). Red meat (beef, lamb, and pork) contributed heavily to deaths, despite lower levels of risk (287,485 cases, risk = 24, case-fatality rate = 57, deaths = 164). Reducing the impact of indigenous foodborne disease is mainly dependent on controlling the contamination of chicken

Long term cognitive outcomes of early term (37-38 weeks) and late preterm (34-36 weeks) births: a systematic review

Background: There is a paucity of evidence regarding long-term outcomes of late preterm (34-36 weeks) and early term (37-38 weeks) delivery.  The objective of this systematic review was to assess long-term cognitive outcomes of children born at these gestations. Methods: Four electronic databases (Medline, Embase, clinicaltrials.gov and PsycINFO) were searched.  Last search was 5 th August 2016.  Studies were included if they reported gestational age, IQ measure and the ages assessed.  The protocol was registered with the International prospective register of systematic reviews (PROSPERO Record CRD42015015472).  Two independent reviewers assessed the studies.  Data were abstracted and critical appraisal performed of eligible papers. Results: Of 11,905 potential articles, seven studies reporting on 41,344 children were included.  For early term births, four studies (n = 35,711) consistently showed an increase in cognitive scores for infants born at full term (39-41 weeks) compared to those born at early term (37-38 weeks) with increases for each week of term (difference between 37 and 40 weeks of around 3 IQ points), despite differences in age of testing and method of IQ/cognitive testing.  Four studies (n = 5644) reporting childhood cognitive outcomes of late preterm births (34 - 36 weeks) also differed in study design (cohort and case control); age of testing; and method of IQ testing, and found no differences in outcomes between late preterm and term births, although risk of bias was high in included studies. Conclusion:  Children born at 39-41 weeks have higher cognitive outcome scores compared to those born at early term (37-38 weeks).  This should be considered when discussing timing of delivery.  For children born late preterm, the data is scarce and when compared to full term (37-42 weeks) did not show any difference in IQ scores

Experimental observations of dynamic critical phenomena in a lipid membrane

Near a critical point, the time scale of thermally-induced fluctuations diverges in a manner determined by the dynamic universality class. Experiments have verified predicted 3D dynamic critical exponents in many systems, but similar experiments in 2D have been lacking for the case of conserved order parameter. Here we analyze time-dependent correlation functions of a quasi-2D lipid bilayer in water to show that its critical dynamics agree with a recently predicted universality class. In particular, the effective dynamic exponent $z_{\text{eff}}$ crosses over from $\sim 2$ to $\sim 3$ as the correlation length of fluctuations exceeds a hydrodynamic length set by the membrane and bulk viscosities.Comment: 5 pages, 3 figures and 2 additional pages of supplemen

Adherence to prescribing restrictions for HER2-positive metastatic breast cancer in Australia: A national population-based observational study (2001-2016)

Background: Targeted cancer therapy is often complex, involving multiple agents and chemotherapeutic partners. In Australia, prescribing restrictions are put in place to reflect existing evidence of cost-effectiveness of these medicines. As therapeutic options continue to expand, these restrictions may not be perceived to align with best practice and it is not known if their use in the real-world clinic adheres to these restrictions. We examined the treatment of women receiving trastuzumab for HER2-positive metastatic breast cancer (HER2+MBC) to determine the extent to which treatment adhered to national prescribing restrictions. Patients and methods: Our population-based, retrospective cohort study used dispensing records for every Australian woman initiating publicly-subsidised trastuzumab for HER2+MBC between 2001±2013, followed through 2016. We used group-based trajectory models (GBTMs) to cluster patients, first on their patterns of trastuzumab exposure, and then on their patterns of lapatinib and chemotherapy exposure. We described the characteristics of patients within each cluster, and examined their treatments and combinations of treatments to determine restriction adherence. Results: Of 5,052 patients initiating trastuzumab, 1,795 (36%) received at least one non-adherent HER2-targeted treatment. The most common non-adherent treatments were trastuzumab combinations involving vinorelbine (24% of non-adherent treatments); capecitabine (24%); and anthracyclines (10%). Non-adherent lapatinib use was observed in 4% of patients. GBTM identified three trastuzumab exposure clusters, each containing three further subclusters. The largest proportions of non-adherent treatments were in sub-clusters with longer trastuzumab exposure and more non-taxane chemotherapy. Patients in these sub-clusters were younger than those in sub-clusters with less non-adherent treatment. Conclusions: Our study highlights that, even during the relatively simpler treatment era of our study period, a substantial amount of treatment did not adhere to prescribing restrictions. As more trials are conducted exploring pertuzumab and T-DM1 in combination with different chemotherapies and other HER2-targeted therapies, the regulation and funding of HER2-targeted treatment will become more challenging

Disambiguation of Necker cube rotation by monocular and binocular depth cues: Relative effectiveness for establishing long-term bias

AbstractThe apparent direction of rotation of perceptually bistable wire-frame (Necker) cubes can be conditioned to depend on retinal location by interleaving their presentation with cubes that are disambiguated by depth cues (Haijiang, Saunders, Stone, & Backus, 2006; Harrison & Backus, 2010a). The long-term nature of the learned bias is demonstrated by resistance to counter-conditioning on a consecutive day. In previous work, either binocular disparity and occlusion, or a combination of monocular depth cues that included occlusion, internal occlusion, haze, and depth-from-shading, were used to control the rotation direction of disambiguated cubes. Here, we test the relative effectiveness of these two sets of depth cues in establishing the retinal location bias. Both cue sets were highly effective in establishing a perceptual bias on Day 1 as measured by the perceived rotation direction of ambiguous cubes. The effect of counter-conditioning on Day 2, on perceptual outcome for ambiguous cubes, was independent of whether the cue set was the same or different as Day 1. This invariance suggests that a common neural population instantiates the bias for rotation direction, regardless of the cue set used. However, in a further experiment where only disambiguated cubes were presented on Day 1, perceptual outcome of ambiguous cubes during Day 2 counter-conditioning showed that the monocular-only cue set was in fact more effective than disparity-plus-occlusion for causing long-term learning of the bias. These results can be reconciled if the conditioning effect of Day 1 ambiguous trials in the first experiment is taken into account (Harrison & Backus, 2010b). We suggest that monocular disambiguation leads to stronger bias either because it more strongly activates a single neural population that is necessary for perceiving rotation, or because ambiguous stimuli engage cortical areas that are also engaged by monocularly disambiguated stimuli but not by disparity-disambiguated stimuli

Reconciling optical and radio observations of the binary millisecond pulsar PSR J1640+2224

Previous optical and radio observations of the binary millisecond pulsar PSR J1640+2224 have come to inconsistent conclusions about the identity of its companion, with some observations suggesting the companion is a low-mass helium-core (He-core) white dwarf (WD), while others indicate it is most likely a high-mass carbon-oxygen (CO) WD. Binary evolution models predict PSR J1640+2224 most likely formed in a low-mass X-ray binary (LMXB) based on the pulsar's short spin period and long-period, low-eccentricity orbit, in which case its companion should be a He-core WD with mass about $0.35 - 0.39 \, M_\odot$, depending on metallicity. If it is instead a CO WD, that would suggest the system has an unusual formation history. In this paper we present the first astrometric parallax measurement for this system from observations made with the Very Long Baseline Array (VLBA), from which we determine the distance to be $1520^{+170}_{-150}\,\mathrm{pc}$. We use this distance and a reanalysis of archival optical observations originally taken in 1995 with the Wide Field Planetary Camera 2 (WFPC2) on the Hubble Space Telescope (HST) in order to measure the WD's mass. We also incorporate improvements in calibration, extinction model, and WD cooling models. We find that the existing observations are not sufficient to tightly constrain the companion mass, but we conclude the WD mass is $>0.4\,M_\odot$ with $>90\%$ confidence. The limiting factor in our analysis is the low signal-to-noise ratio of the original HST observations.Comment: 6 pages, 5 figure

The Decoupling of Marriage and Parenthood? Trends in the Timing of Marital First Births, 1945–2002

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106837/1/jomf12114.pd