A Universal Framework for Generalized Run Time Assurance with JAX Automatic Differentiation

With the rise of increasingly complex autonomous systems powered by black box AI models, there is a growing need for Run Time Assurance (RTA) systems that provide online safety filtering to untrusted primary controller output. Currently, research in RTA tends to be ad hoc and inflexible, diminishing collaboration and the pace of innovation. The Safe Autonomy Run Time Assurance Framework presented in this paper provides a standardized interface for RTA modules and a set of universal implementations of constraint-based RTA capable of providing safety assurance given arbitrary dynamical systems and constraints. Built around JAX, this framework leverages automatic differentiation to populate advanced optimization based RTA methods minimizing user effort and error. To validate the feasibility of this framework, a simulation of a multi-agent spacecraft inspection problem is shown with safety constraints on position and velocity

Systems Theoretic Process Analysis of a Run Time Assured Neural Network Control System

This research considers the problem of identifying safety constraints and developing Run Time Assurance (RTA) for Deep Reinforcement Learning (RL) Tactical Autopilots that use neural network control systems (NNCS). This research studies a specific use case of an NNCS performing autonomous formation flight while an RTA system provides collision avoidance and geofence assurances. First, Systems Theoretic Accident Models and Processes (STAMP) is applied to identify accidents, hazards, and safety constraints as well as define a functional control system block diagram of the ground station, manned flight lead, and surrogate unmanned wingman. Then, Systems Theoretic Process Analysis (STPA) is applied to the interactions of the the ground station, manned flight lead, surrogate unmanned wingman, and internal elements of the wingman aircraft to identify unsafe control actions, scenarios leading to each, and safety requirements to mitigate risks. This research is the first application of STAMP and STPA to an NNCS bounded by RTA

A 200-year perspective on alternative stable state theory and lake management from a biomanipulated shallow lake

Abstract. Multiple stressors to a shallow lake ecosystem have the ability to control the relative stability of alternative states (clear, macrophyte-dominated or turbid, algaldominated). As a consequence, the use of remedial biomanipulations to induce trophic cascades and shift a turbid lake to a clear state is often only a temporary solution. Here we show the instability of short-term manipulations in the shallow Lake Christina (Minnesota, USA) is governed by the long-term state following a regime shift in the lake. During the modern, managed period of the lake, three top-down manipulations (fish kills) were undertaken inducing temporary (5-10 years) unstable clear-water states. Paleoecological remains of diatoms, along with proxies of primary production (total chlorophyll a and total organic carbon accumulation rate) and trophic state (total P) from sediment records clearly show a single regime shift in the lake during the early 1950s; following this shift, the functioning of the lake ecosystem is dominated by a persistent turbid state. We find that multiple stressors contributed to the regime shift. First, the lake began to eutrophy (from agricultural land use and/or increased waterfowl populations), leading to a dramatic increase in primary production. Soon after, the construction of a dam in 1936 effectively doubled the depth of the lake, compounded by increases in regional humidity; this resulted in an increase in planktivorous and benthivorous fish reducing phytoplankton grazers. These factors further conspired to increase the stability of a turbid regime during the modern managed period, such that switches to a clear-water state were inherently unstable and the lake consistently returned to a turbid state. We conclude that while top-down manipulations have had measurable impacts on the lake state, they have not been effective in providing a return to an ecosystem similar to the stable historical period. Our work offers an example of a well-studied ecosystem forced by multiple stressors into a new long-term managed period, where manipulated clearwater states are temporary, managed features

SALL4 Expression in Gonocytes and Spermatogonial Clones of Postnatal Mouse Testes

The spermatogenic lineage is established after birth when gonocytes migrate to the basement membrane of seminiferous tubules and give rise to spermatogonial stem cells (SSC). In adults, SSCs reside within the population of undifferentiated spermatogonia (Aundiff) that expands clonally from single cells (Asingle) to form pairs (Apaired) and chains of 4, 8 and 16 Aaligned spermatogonia. Although stem cell activity is thought to reside in the population of Asingle spermatogonia, new research suggests that clone size alone does not define the stem cell pool. The mechanisms that regulate self-renewal and differentiation fate decisions are poorly understood due to limited availability of experimental tools that distinguish the products of those fate decisions. The pluripotency factor SALL4 (sal-like protein 4) is implicated in stem cell maintenance and patterning in many organs during embryonic development, but expression becomes restricted to the gonads after birth. We analyzed the expression of SALL4 in the mouse testis during the first weeks after birth and in adult seminiferous tubules. In newborn mice, the isoform SALL4B is expressed in quiescent gonocytes at postnatal day 0 (PND0) and SALL4A is upregulated at PND7 when gonocytes have colonized the basement membrane and given rise to spermatogonia. During steady-state spermatogenesis in adult testes, SALL4 expression overlapped substantially with PLZF and LIN28 in Asingle, Apaired and Aaligned spermatogonia and therefore appears to be a marker of undifferentiated spermatogonia in mice. In contrast, co-expression of SALL4 with GFRα1 and cKIT identified distinct subpopulations of Aundiff in all clone sizes that might provide clues about SSC regulation. Collectively, these results indicate that 1) SALL4 isoforms are differentially expressed at the initiation of spermatogenesis, 2) SALL4 is expressed in undifferentiated spermatogonia in adult testes and 3) SALL4 co-staining with GFRα1 and cKIT reveals distinct subpopulations of Aundiff spermatogonia that merit further investigation. © 2013 Gassei, Orwig

Clinical trial of laronidase in Hurler syndrome after hematopoietic cell transplantation.

BackgroundMucopolysaccharidosis I (MPS IH) is a lysosomal storage disease treated with hematopoietic cell transplantation (HCT) because it stabilizes cognitive deterioration, but is insufficient to alleviate all somatic manifestations. Intravenous laronidase improves somatic burden in attenuated MPS I. It is unknown whether laronidase can improve somatic disease following HCT in MPS IH. The objective of this study was to evaluate the effects of laronidase on somatic outcomes of patients with MPS IH previously treated with HCT.MethodsThis 2-year open-label pilot study of laronidase included ten patients (age 5-13 years) who were at least 2 years post-HCT and donor engrafted. Outcomes were assessed semi-annually and compared to historic controls.ResultsThe two youngest participants had a statistically significant improvement in growth compared to controls. Development of persistent high-titer anti-drug antibodies (ADA) was associated with poorer 6-min walk test (6MWT) performance; when patients with high ADA titers were excluded, there was a significant improvement in the 6MWT in the remaining seven patients.ConclusionsLaronidase seemed to improve growth in participants <8 years old, and 6MWT performance in participants without ADA. Given the small number of patients treated in this pilot study, additional study is needed before definitive conclusions can be made

CPUF - a chemical-structure-based polyurethane foam decomposition and foam response model.

A Chemical-structure-based PolyUrethane Foam (CPUF) decomposition model has been developed to predict the fire-induced response of rigid, closed-cell polyurethane foam-filled systems. The model, developed for the B-61 and W-80 fireset foam, is based on a cascade of bondbreaking reactions that produce CO2. Percolation theory is used to dynamically quantify polymer fragment populations of the thermally degrading foam. The partition between condensed-phase polymer fragments and gas-phase polymer fragments (i.e. vapor-liquid split) was determined using a vapor-liquid equilibrium model. The CPUF decomposition model was implemented into the finite element (FE) heat conduction codes COYOTE and CALORE, which support chemical kinetics and enclosure radiation. Elements were removed from the computational domain when the calculated solid mass fractions within the individual finite element decrease below a set criterion. Element removal, referred to as ?element death,? creates a radiation enclosure (assumed to be non-participating) as well as a decomposition front, which separates the condensed-phase encapsulant from the gas-filled enclosure. All of the chemistry parameters as well as thermophysical properties for the CPUF model were obtained from small-scale laboratory experiments. The CPUF model was evaluated by comparing predictions to measurements. The validation experiments included several thermogravimetric experiments at pressures ranging from ambient pressure to 30 bars. Larger, component-scale experiments were also used to validate the foam response model. The effects of heat flux, bulk density, orientation, embedded components, confinement and pressure were measured and compared to model predictions. Uncertainties in the model results were evaluated using a mean value approach. The measured mass loss in the TGA experiments and the measured location of the decomposition front were within the 95% prediction limit determined using the CPUF model for all of the experiments where the decomposition gases were vented sufficiently. The CPUF model results were not as good for the partially confined radiant heat experiments where the vent area was regulated to maintain pressure. Liquefaction and flow effects, which are not considered in the CPUF model, become important when the decomposition gases are confined

Azimuthal Angle Correlations for Rapidity Separated Hadron Pairs in d+Au Collisions at sqrt(s_NN) = 200 GeV

We report on two-particle azimuthal angle correlations between charged hadrons at forward/backward (deuteron/gold going direction) rapidity and charged hadrons at mid-rapidity in deuteron-gold (d+Au) and proton-proton (p+p) collisions at sqrt(s_NN) = 200 GeV. Jet structures are observed in the correlations which we quantify in terms of the conditional yield and angular width of away side partners. The kinematic region studied here samples partons in the gold nucleus carrying nucleon momentum fraction x~0.1 to x~0.01. Within this range, we find no x dependence of the jet structure in d+Au collisions.Comment: 330 authors, 6 pages text, 4 figures, no tables. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Dilepton mass spectra in p+p collisions at sqrt(s)= 200 GeV and the contribution from open charm

The PHENIX experiement has measured the electron-positron pair mass spectrum from 0 to 8 GeV/c^2 in p+p collisions at sqrt(s)=200 GeV. The contributions from light meson decays to e^+e^- pairs have been determined based on measurements of hadron production cross sections by PHENIX. They account for nearly all e^+e^- pairs in the mass region below 1 GeV/c^2. The e^+e^- pair yield remaining after subtracting these contributions is dominated by semileptonic decays of charmed hadrons correlated through flavor conservation. Using the spectral shape predicted by PYTHIA, we estimate the charm production cross section to be 544 +/- 39(stat) +/- 142(syst) +/- 200(model) \mu b, which is consistent with QCD calculations and measurements of single leptons by PHENIX.Comment: 375 authors from 57 institutions, 18 pages, 4 figures, 2 tables. Submitted to Physics Letters B. v2 fixes technical errors in matching authors to institutions. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Inclusive cross section and double helicity asymmetry for \pi^0 production in p+p collisions at sqrt(s)=200 GeV: Implications for the polarized gluon distribution in the proton

The PHENIX experiment presents results from the RHIC 2005 run with polarized proton collisions at sqrt(s)=200 GeV, for inclusive \pi^0 production at mid-rapidity. Unpolarized cross section results are given for transverse momenta p_T=0.5 to 20 GeV/c, extending the range of published data to both lower and higher p_T. The cross section is described well for p_T < 1 GeV/c by an exponential in p_T, and, for p_T > 2 GeV/c, by perturbative QCD. Double helicity asymmetries A_LL are presented based on a factor of five improvement in uncertainties as compared to previously published results, due to both an improved beam polarization of 50%, and to higher integrated luminosity. These measurements are sensitive to the gluon polarization in the proton, and exclude maximal values for the gluon polarization.Comment: 375 authors, 7 pages, 3 figures. Submitted to Phys. Rev. D, Rapid Communications. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm