Dynamics of living cells in a cytomorphological state space.

Cells are nonequilibrium systems that exchange matter and energy with the environment to sustain their metabolic needs. The nonequilibrium nature of this system presents considerable challenges to developing a general theory describing its behavior; however, when studied at appropriate spatiotemporal scales, the behavior of ensembles of nonequilibrium systems can resemble that of a system at equilibrium. Here we apply this principle to a population of cells within a cytomorphological state space and demonstrate that cellular transition dynamics within this space can be described using equilibrium formalisms. We use this framework to map the effective energy landscape underlying the cytomorphological state space of a population of mouse embryonic fibroblasts (MEFs) and identify topographical nonuniformity in this space, indicating nonuniform occupation of cytomorphological states within an isogenic population. The introduction of exogenous apoptotic agents fundamentally altered this energy landscape, inducing formation of additional energy minima that correlated directly with changes in sensitivity to apoptosis induction. An equilibrium framework allows us to describe the behavior of an ensemble of single cells, suggesting that although cells are complex nonequilibrium systems, the application of formalisms derived from equilibrium thermodynamics can provide insight into the basis of nongenetic heterogeneities within cell populations, as well as the relationship between cytomorphological and functional heterogeneity

Investigating lupus retention in care to inform interventions for disparities reduction: an observational cohort study.

BACKGROUND:Systemic lupus erythematous (SLE) disproportionately impacts patients of color and socioeconomically disadvantaged patients. Similar disparities in HIV were reduced through a World Health Organization-endorsed Care Continuum strategy targeting "retention in care," defined as having at least two annual visits or viral load lab tests. Using similar definitions, this study aimed to examine predictors of lupus retention in care, to develop an SLE Care Continuum and inform interventions to reduce disparities. We hypothesized that Black patients and those residing in disadvantaged neighborhoods would have lower retention in care. METHODS:Abstractors manually validated 545 potential adult cases with SLE codes in 2013-2014 using 1997 American College of Rheumatology (ACR) or 2012 Systemic Lupus Erythematosus International Collaborating Clinics (SLICC) criteria. We identified 397 SLE patients who met ACR or SLICC criteria for definite lupus, had at least one baseline rheumatology visit, and were alive through 2015. Retention in care was defined as having two ambulatory rheumatology visits or SLE labs (e.g., complement tests) during the outcome year 2015, analogous to HIV retention definitions. Explanatory variables included age, sex, race, ethnicity, smoking status, neighborhood area deprivation index (ADI), number of SLE criteria, and nephritis. We used multivariable logistic regression to test our hypothesis and model predictors of SLE retention in care. RESULTS:Among 397 SLE patients, 91% were female, 56% White, 39% Black, and 5% Hispanic. Notably, 51% of Black versus 5% of White SLE patients resided in the most disadvantaged ADI neighborhood quartile. Overall, 60% met visit-defined retention and 27% met complement lab-defined retention in 2015. Retention was 59% lower for patients in the most disadvantaged neighborhood quartile (adjusted OR 0.41, CI 0.18, 0.93). No statistical difference was seen based on age, sex, race, or ethnicity. More SLE criteria and non-smoking predicted greater retention. CONCLUSIONS:Disadvantaged neighborhood residence was the strongest factor predicting poor SLE retention in care. Future interventions could geo-target disadvantaged neighborhoods and design retention programs with vulnerable populations to improve retention in care and reduce SLE outcome disparities

Improving WIC Retention in Vermont: Beneficiary attitudes toward co-location in medical homes

Introduction: The Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) is a national program aimed at improving the nutrition and health of pregnant women and children. Those eligible for Vermont WIC include anyone pregnant or with children under 5 that has an income below 185% of federal poverty level or is enrolled in Vermont Medicaid. WIC has been shown to improve birth outcomes1, breast feeding rates2, infant growth and development, and consumption of important nutrients. Those enrolled in WIC report high levels of satisfaction Despite the benefits of WIC, retention rates of eligible families remain low. Studies have shown that mandatory bi-annual recertification appointments pose logistical problems. Rescheduling missed appointments and long waiting times at the WIC offices were also barriers. Other states have found that integration of WIC recertification appointments with the family’s primary care medical visits may improve retention. A limited scale co-localization of WIC and the medical home in Vermont showed some promise.https://scholarworks.uvm.edu/comphp_gallery/1213/thumbnail.jp

Where it All Began

In celebration of the 20th issue of The Park Place Economist, this year\u27s Alumni Editors are thrilled to feature three outstanding alumni who made significant contributions to the successful publication of the very first issue

Simulating the weak death of the neutron in a femtoscale universe with near-Exascale computing

The fundamental particle theory called Quantum Chromodynamics (QCD) dictates everything about protons and neutrons, from their intrinsic properties to interactions that bind them into atomic nuclei. Quantities that cannot be fully resolved through experiment, such as the neutron lifetime (whose precise value is important for the existence of light-atomic elements that make the sun shine and life possible), may be understood through numerical solutions to QCD. We directly solve QCD using Lattice Gauge Theory and calculate nuclear observables such as neutron lifetime. We have developed an improved algorithm that exponentially decreases the time-to solution and applied it on the new CORAL supercomputers, Sierra and Summit. We use run-time autotuning to distribute GPU resources, achieving 20% performance at low node count. We also developed optimal application mapping through a job manager, which allows CPU and GPU jobs to be interleaved, yielding 15% of peak performance when deployed across large fractions of CORAL.Comment: 2018 Gordon Bell Finalist: 9 pages, 9 figures; v2: fixed 2 typos and appended acknowledgement

Calm Multi-Baryon Operators

Outstanding problems in nuclear physics require input and guidance from lattice QCD calculations of few baryons systems. However, these calculations suffer from an exponentially bad signal-to-noise problem which has prevented a controlled extrapolation to the physical point. The variational method has been applied very successfully to two-meson systems, allowing for the extraction of the two-meson states very early in Euclidean time through the use of improved single hadron operators. The sheer numerical cost of using the same techniques in two-baryon systems has been prohibitive. We present an alternate strategy which offers some of the same advantages as the variational method while being significantly less numerically expensive. We first use the Matrix Prony method to form an optimal linear combination of single baryon interpolating fields generated from the same source and different sink interpolators. Very early in Euclidean time this linear combination is numerically free of excited state contamination, so we coin it a calm baryon. This calm baryon operator is then used in the construction of the two-baryon correlation functions. To test this method, we perform calculations on the WM/JLab iso-clover gauge configurations at the SU(3) flavor symmetric point with m{\pi} $\sim$ 800 MeV --- the same configurations we have previously used for the calculation of two-nucleon correlation functions. We observe the calm baryon removes the excited state contamination from the two-nucleon correlation function to as early a time as the single-nucleon is improved, provided non-local (displaced nucleon) sources are used. For the local two-nucleon correlation function (where both nucleons are created from the same space-time location) there is still improvement, but there is significant excited state contamination in the region the single calm baryon displays no excited state contamination.Comment: 8 pages, 3 figures, proceedings for LATTICE 201

An accurate calculation of the nucleon axial charge with lattice QCD

We report on a lattice QCD calculation of the nucleon axial charge, $g_A$, using M\"{o}bius Domain-Wall fermions solved on the dynamical $N_f=2+1+1$ HISQ ensembles after they are smeared using the gradient-flow algorithm. The calculation is performed with three pion masses, $m_\pi\sim\{310,220,130\}$ MeV. Three lattice spacings ($a\sim\{0.15,0.12,0.09\}$ fm) are used with the heaviest pion mass, while the coarsest two spacings are used on the middle pion mass and only the coarsest spacing is used with the near physical pion mass. On the $m_\pi\sim220$ MeV, $a\sim0.12$ fm point, a dedicated volume study is performed with $m_\pi L \sim \{3.22,4.29,5.36\}$. Using a new strategy motivated by the Feynman-Hellmann Theorem, we achieve a precise determination of $g_A$ with relatively low statistics, and demonstrable control over the excited state, continuum, infinite volume and chiral extrapolation systematic uncertainties, the latter of which remains the dominant uncertainty. Our final determination at 2.6\% total uncertainty is $g_A = 1.278(21)(26)$, with the first uncertainty including statistical and systematic uncertainties from fitting and the second including model selection systematics related to the chiral and continuum extrapolation. The largest reduction of the second uncertainty will come from a greater number of pion mass points as well as more precise lattice QCD results near the physical pion mass.Comment: 17 pages + 11 pages of references and appendices. 15 figures. Interested readers can download the Python analysis scripts and an hdf5 data file at https://github.com/callat-qcd/project_gA_v