Scaling Nonparametric Bayesian Inference via Subsample-Annealing

We describe an adaptation of the simulated annealing algorithm to nonparametric clustering and related probabilistic models. This new algorithm learns nonparametric latent structure over a growing and constantly churning subsample of training data, where the portion of data subsampled can be interpreted as the inverse temperature beta(t) in an annealing schedule. Gibbs sampling at high temperature (i.e., with a very small subsample) can more quickly explore sketches of the final latent state by (a) making longer jumps around latent space (as in block Gibbs) and (b) lowering energy barriers (as in simulated annealing). We prove subsample annealing speeds up mixing time N^2 -> N in a simple clustering model and exp(N) -> N in another class of models, where N is data size. Empirically subsample-annealing outperforms naive Gibbs sampling in accuracy-per-wallclock time, and can scale to larger datasets and deeper hierarchical models. We demonstrate improved inference on million-row subsamples of US Census data and network log data and a 307-row hospital rating dataset, using a Pitman-Yor generalization of the Cross Categorization model.Comment: To appear in AISTATS 201

Image-Based Quantification of Benzoporphyrin Derivative Uptake, Localization, and Photobleaching in 3D Tumor Models, for Optimization of PDT Parameters

Photodynamic therapy (PDT) is a light-based treatment modality in which wavelength specific activation of a photosensitizer (PS) generates cytotoxic response in the irradiated region. PDT response is critically dependent on several parameters including light dose, PS dose, uptake time, fluence rate, and the mode of light delivery. While the systematic optimization of these treatment parameters can be complex, it also provides multiple avenues for en- hancement of PDT efficacy under diverse treatment conditions, provided that a rational framework is established to quantify the impact of parameter selection upon treatment re- sponse. Here we present a theranostic technique, combining the inherent ability of the PS to serve simultaneously as a therapeutic and imaging agent, with the use of image-based treatment assessment in three dimensional (3D) in vitro tumor models, to comprise a platform to evaluate the impact of PDT parameters on treatment outcomes. We use this approach to visualize and quantify the uptake, localization, and photobleaching of the PS benzoporphyrin derivative monoacid ring-A (BPD) in a range of treatment conditions with varying uptake times as well as continuous and fractionated light delivery regimens in 3D cultures of AsPC-1 and PANC-1 cells. Informed by photobleaching patterns and correlation with cytotoxic re- sponse, asymmetric fractionated light delivery at 4 hours BPD uptake was found to be the most effective regimen assessed. Quantification of the spatial profile of cell killing within multicellular nodules revealed that these conditions also achieve the highest depth of cyto- toxicity along the radial axis of 3D nodules. The framework introduced here provides a means for systematic assessment of PDT treatment parameters in biologically relevant 3D tumor models with potential for broader application to other systems

An imaging-based platform for high-content, quantitative evaluation of therapeutic response in 3D tumour models

While it is increasingly recognized that three-dimensional (3D) cell culture models recapitulate drug responses of human cancers with more fidelity than monolayer cultures, a lack of quantitative analysis methods limit their implementation for reliable and routine assessment of emerging therapies. Here, we introduce an approach based on computational analysis of fluorescence image data to provide high-content readouts of dose-dependent cytotoxicity, growth inhibition, treatment-induced architectural changes and size-dependent response in 3D tumour models. We demonstrate this approach in adherent 3D ovarian and pancreatic multiwell extracellular matrix tumour overlays subjected to a panel of clinically relevant cytotoxic modalities and appropriately designed controls for reliable quantification of fluorescence signal. This streamlined methodology reads out the high density of information embedded in 3D culture systems, while maintaining a level of speed and efficiency traditionally achieved with global colorimetric reporters in order to facilitate broader implementation of 3D tumour models in therapeutic screening

Coordination and control – limits in standard representations of multi-reservoir operations in hydrological modeling

Major multi-reservoir cascades represent a primary mechanism for dealing with hydrologic variability and extremes within institutionally complex river basins worldwide. These coordinated management processes fundamentally reshape water balance dynamics. Yet, multi-reservoir coordination processes have been largely ignored in the increasingly sophisticated representations of reservoir operations within large-scale hydrological models. The aim of this paper is twofold, namely (i) to provide evidence that the common modeling practice of parameterizing each reservoir in a cascade independently from the others is a significant approximation and (ii) to demonstrate potential unintended consequences of this independence approximation when simulating the dynamics of hydrological extremes in complex reservoir cascades. We explore these questions using the Water Balance Model, which features detailed representations of the human infrastructure coupled to the natural processes that shape water balance dynamics. It is applied to the Upper Snake River basin in the western US and its heavily regulated multi-reservoir cascade. We employ a time-varying sensitivity analysis that utilizes the method of Morris factor screening to explicitly track how the dominant release rule parameters evolve both along the cascade and in time according to seasonal high- and low-flow events. This enables us to address aim (i) by demonstrating how the progressive and cumulative dominance of upstream releases significantly dampens the ability of downstream reservoir rules\u27 parameters to influence flow conditions. We address aim (ii) by comparing simulation results with observed reservoir operations during critical low-flow and high-flow events in the basin. Our time-varying parameter sensitivity analysis with the method of Morris clarifies how independent single-reservoir parameterizations and their tacit assumption of independence leads to reservoir release behaviors that generate artificial water shortages and flooding, whereas the observed coordinated cascade operations avoided these outcomes for the same events. To further explore the role of (non-)coordination in the large deviations from the observed operations, we use an offline multi-reservoir water balance model in which adding basic coordination mechanisms drawn from the observed emergency operations is sufficient to correct the deficiencies of the independently parameterized reservoir rules from the hydrological model. These results demonstrate the importance of understanding the state–space context in which reservoir releases occur and where operational coordination plays a crucial role in avoiding or mitigating water-related extremes. Understanding how major infrastructure is coordinated and controlled in major river basins is essential for properly assessing future flood and drought hazards in a changing world

Dimension Reduction Near Periodic Orbits of Hybrid Systems

When the Poincar\'{e} map associated with a periodic orbit of a hybrid dynamical system has constant-rank iterates, we demonstrate the existence of a constant-dimensional invariant subsystem near the orbit which attracts all nearby trajectories in finite time. This result shows that the long-term behavior of a hybrid model with a large number of degrees-of-freedom may be governed by a low-dimensional smooth dynamical system. The appearance of such simplified models enables the translation of analytical tools from smooth systems-such as Floquet theory-to the hybrid setting and provides a bridge between the efforts of biologists and engineers studying legged locomotion.Comment: Full version of conference paper appearing in IEEE CDC/ECC 201

An ultra-stable single-chain insulin analog resists thermal inactivation and exhibits biological signaling duration equivalent to the native protein

Thermal degradation of insulin complicates its delivery and use. Previous efforts to engineer ultra-stable analogs were confounded by prolonged cellular signaling in vivo, of unclear safety and complicating mealtime therapy. We therefore sought an ultra-stable analog whose potency and duration of action on intravenous bolus injection in diabetic rats are indistinguishable from wild-type (WT) insulin. Here, we describe the structure, function, and stability of such an analog, a 57-residue single-chain insulin (SCI) with multiple acidic substitutions. Cell-based studies revealed native-like signaling properties with negligible mitogenic activity. Its crystal structure, determined as a novel zinc-free hexamer at 2.8 Å, revealed a native insulin fold with incomplete or absent electron density in the C domain; complementary NMR studies are described in the accompanying article. The stability of the analog (ΔGU 5.0(±0.1) kcal/mol at 25 °C) was greater than that of WT insulin (3.3(±0.1) kcal/mol). On gentle agitation, the SCI retained full activity for >140 days at 45 °C and >48 h at 75 °C. These findings indicate that marked resistance to thermal inactivation in vitro is compatible with native duration of activity in vivo Further, whereas WT insulin forms large and heterogeneous aggregates above the standard 0.6 mm pharmaceutical strength, perturbing the pharmacokinetic properties of concentrated formulations, dynamic light scattering, and size-exclusion chromatography revealed only limited SCI self-assembly and aggregation in the concentration range 1-7 mm Such a combination of favorable biophysical and biological properties suggests that SCIs could provide a global therapeutic platform without a cold chain

TESS Discovery of an ultra-short-period planet around the nearby M dwarf LHS 3844

Data from the newly-commissioned \textit{Transiting Exoplanet Survey Satellite} (TESS) has revealed a "hot Earth" around LHS 3844, an M dwarf located 15 pc away. The planet has a radius of $1.32\pm 0.02$ $R_\oplus$ and orbits the star every 11 hours. Although the existence of an atmosphere around such a strongly irradiated planet is questionable, the star is bright enough ($I=11.9$, $K=9.1$) for this possibility to be investigated with transit and occultation spectroscopy. The star's brightness and the planet's short period will also facilitate the measurement of the planet's mass through Doppler spectroscopy.Comment: 10 pages, 4 figures. Submitted to ApJ Letters. This letter makes use of the TESS Alert data, which is currently in a beta test phase, using data from the pipelines at the TESS Science Office and at the TESS Science Processing Operations Cente

A Model for Type 2 Coronal Line Forest (CLiF) AGNs

We present a model for the classification of Coronal Line Forest Active Galactic Nuclei (CLiF AGNs). CLiF AGNs are of special interest due to their remarkably large number of emission lines, especially forbidden highionization lines (FHILs). Rose et al. suggest that their emission is dominated by reflection from the inner wall of the obscuring region rather than direct emission from the accretion disk. This makes CLiF AGNs laboratories to test AGN-torus models. Modeling an AGN as an accreting supermassive black hole surrounded by a cylinder of dust and gas, we show a relationship between the viewing angle and the revealed area of the inner wall. From the revealed area, we can determine the amount of FHIL emission at various angles. We calculate the strength of [Fe VII]λ6087 emission for a number of intermediate angles (30°, 40°, and 50°) and compare the results with the luminosity of the observed emission line from six known CLiF AGNs. We find that there is good agreement between our model and the observational results. The model also enables us to determine the relationship between the type 2:type 1 AGN fraction vs the ratio of torus height to radius, h/r

PROmotion of COvid-19 VA(X)ccination in the Emergency Department-PROCOVAXED: study protocol for a cluster randomized controlled trial.

Background: We conducted in-depth interviews to characterize reasons for COVID-19 vaccine hesitancy in emergency department (ED) patients and developed messaging platforms that may address their concerns. In this trial, we seek to determine whether provision of these COVID-19 vaccine messaging platforms in EDs will be associated with greater COVID-19 vaccine acceptance and uptake in unvaccinated ED patients. Methods: This is a cluster-randomized controlled trial (RCT) evaluating our COVID-19 vaccine messaging platforms in seven hospital EDs (mix of academic, community, and safety-net EDs) in four US cities. Within each study site, we randomized 30 1-week periods to the intervention and 30 1-week periods to the control. Adult patients who have not received a COVID-19 vaccine are eligible with these exclusions: (1) major trauma, intoxication, altered mental status, or critical illness; (2) incarceration; (3) psychiatric chief complaint; and (4) suspicion of acute COVID-19 illness. Participants receive an orally administered Intake survey. During intervention weeks, participants then receive three COVID-19 vaccine messaging platforms (4-min video, one-page informational flyer and a brief, scripted face-to-face message delivered by an ED physician or nurse); patients enrolled during non-intervention weeks do not receive these platforms. Approximately, an hour after intake surveys, participants receive a Vaccine Acceptance survey during which the primary outcome of acceptance of the COVID-19 vaccine in the ED is ascertained. The other primary outcome of receipt of a COVID-19 vaccine within 32 days is ascertained by electronic health record review and phone follow-up. To determine whether provision of vaccine messaging platforms is associated with a 7% increase in vaccine acceptance and uptake, we will need to enroll 1290 patients. Discussion: Highlighting the difficulties of trial implementation during the COVID-19 pandemic in acute care settings, our novel trial will lay the groundwork for delivery of public health interventions to vulnerable populations whose only health care access occurs in EDs. Conclusions: Toward addressing vaccine hesitancy in vulnerable populations who seek care in EDs, our cluster-RCT will determine whether implementation of vaccine messaging platforms is associated with greater COVID-19 vaccine acceptance and uptake in unvaccinated ED patients. Trial status: We began enrollment in December 2021 and expect to continue through 2022. Trial registration: ClinicalTrials.gov NCT05142332 . Registered 02 December 2021

Reproductive Intentions and Outcomes among Women on Antiretroviral Therapy in Rural Uganda: A Prospective Cohort Study

Background: Antiretroviral therapy (ART) may influence the biological, social and behavioral determinants of pregnancy in HIV-infected women. However, there are limited longitudinal data on the reproductive intentions and outcomes among women on ART in Africa. Methodology /Principal Findings: Using a prospective cohort design, we analyzed trends in desire for children and predictors of pregnancy among a cohort of 733 HIV-infected women in rural Uganda who initiated ART between May 2003 and May 2004 and were followed up in their homes until June 2006. Women answered in-depth social and behavioral questionnaires administered every quarter in year 1 after initiating ART, and every 6 to 12 months thereafter. Use of family planning methods was assessed at 18 and 24 months after starting ART. We tested for non-constant pregnancy incidence by using a shape parameter test from the Weibull distribution. We modeled repeated measurements of all variables related to the women’s desire for children over time using a generalized estimating equation (GEE) extension to the logistic regression model. Risk factors for pregnancy were examined using Cox proportional hazards model. 711 women eligible for the study were followed-up for a median time of 2.4 years after starting ART. During this time, less than 7 % of women reported wanting more children at any time point yet 120 (16.9%) women experienced 140 pregnancies and pregnancy incidence increased from 3.46 per 100 women-years (WY) in the first quarter to 9.5 per 100 WY at 24 months (p,0.0001). This wa