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Biologists study Diatoms, a fundamental algae, to assess the health of aquatic systems. Diatom specimens have traditionally been preserved on analog slides, where a single slide can contain thousands of these microscopic organisms. Digitization of these collections presents both metadata challenges and opportunities. This paper reports on metadata research aimed at providing access to a digital portion of the Academy of Natural Sciences' Diatom Herbarium, Drexel University. We report results of a 3-part study covering 1) a review of relevant metadata standards and a microscopy metadata framework shared by Hammer et al., 2) a baseline metadata alignment mapping current diatom metadata properties to standard metadata types, and 3) a metadata risk analysis associated with the course of standard data curation practices. This research is part of an effort involving the transfer of these digital slides to an new system, DataFed, to support global accessible. The final section of this paper includes a conclusion and discusses next steps., Comment: 13 pages, 2 figures, 1 table, to be published in MTSR 2024 conference proceedings

The key difficulty faced by 2D models for planet-disc interaction is in appropriately accounting for the impact of the disc's vertical structure on the dynamics. 3D effects are often mimicked via softening of the planet's potential; however, the planet-induced flow and torques often depend strongly on the choice of softening length. We show that for a linear adiabatic flow perturbing a vertically isothermal disc, there is a particular vertical average of the 3D equations of motion which exactly reproduces 2D fluid equations for arbitrary adiabatic index. There is a strong connection here with the Lubow-Pringle 2D mode of the disc. Correspondingly, we find a simple, general prescription for the consistent treatment of planetary potentials embedded within '2D' discs. The flow induced by a low-mass planet involves large-scale excited spiral density waves which transport angular momentum radially away from the planet, and 'horseshoe streamlines' within the co-orbital region. We derive simple linear equations governing the flow which locally capture both effects faithfully simultaneously. We present an accurate co-orbital flow solution allowing for inexpensive future study of corotation torques, and predict the vertical structure of the co-orbital flow and horseshoe region width for different values of adiabatic index, as well as the vertical dependence of the initial shock location. We find strong agreement with the flow computed in 3D numerical simulations, and with 3D one-sided Lindblad torque estimates, which are a factor of 2 to 3 times lower than values from previous 2D simulations., Comment: Accepted MNRAS, 18 pages, 6 figures

While error backpropagation (BP) has dominated the training of nearly all modern neural networks for a long time, it suffers from several biological plausibility issues such as the symmetric weight requirement and synchronous updates. Feedback Alignment (FA) was proposed as an alternative to BP to address those dilemmas and has been demonstrated to be effective on various tasks and network architectures. Despite its simplicity and effectiveness, a satisfying explanation of how FA works across different architectures is still lacking. Here we propose a novel, architecture-agnostic theory of how FA works through the lens of information theory: Instead of approximating gradients calculated by BP with the same parameter, FA learns effective representations by embedding target information into neural networks to be trained. We show this through the analysis of FA dynamics in idealized settings and then via a series of experiments. Based on the implications of this theory, we designed three variants of FA and show their comparable performance on several tasks. These variants also account for some phenomena and theories in neuroscience such as predictive coding and representational drift.

Thick target deuteron breakup is a variable-energy accelerator-based source of high-energy neutrons, with applications in fundamental and applied nuclear science and engineering. However, the breakup mechanism remains poorly understood, and data on neutron yields from thick target breakup remains relatively scarce. In this work, the double-differential neutron yields from deuteron breakup have been measured on a thick beryllium target at $\epsilon_d=33$ and 40 MeV, using both time-of-flight and activation techniques. We have also introduced a simple hybrid model for the double-differential deuteron breakup cross section, applicable in the $\epsilon_d=10$--$100$ MeV energy range on light ($Z\leq 6$) targets. This model features four empirical parameters that have been fit to reproduce experimental breakup measurements on beryllium targets, using the method of least-squares. It was shown that these parameters extrapolate well to higher energies, and to other low-Z target materials. We also include optimization of the parameters that modify the Kalbach systematics for compound and pre-equilibrium reactions, in order to better reproduce the experimental data for beryllium targets at large angles.

On the path to exascale the landscape of computer device architectures and corresponding programming models has become much more diverse. While various low-level performance portable programming models are available, support at the application level lacks behind. To address this issue, we present the performance portable block-structured adaptive mesh refinement (AMR) framework Parthenon, derived from the well-tested and widely used Athena++ astrophysical magnetohydrodynamics code, but generalized to serve as the foundation for a variety of downstream multi-physics codes. Parthenon adopts the Kokkos programming model, and provides various levels of abstractions from multi-dimensional variables, to packages defining and separating components, to launching of parallel compute kernels. Parthenon allocates all data in device memory to reduce data movement, supports the logical packing of variables and mesh blocks to reduce kernel launch overhead, and employs one-sided, asynchronous MPI calls to reduce communication overhead in multi-node simulations. Using a hydrodynamics miniapp, we demonstrate weak and strong scaling on various architectures including AMD and NVIDIA GPUs, Intel and AMD x86 CPUs, IBM Power9 CPUs, as well as Fujitsu A64FX CPUs. At the largest scale on Frontier (the first TOP500 exascale machine), the miniapp reaches a total of $1.7\times10^{13}$ zone-cycles/s on 9,216 nodes (73,728 logical GPUs) at ~92% weak scaling parallel efficiency (starting from a single node). In combination with being an open, collaborative project, this makes Parthenon an ideal framework to target exascale simulations in which the downstream developers can focus on their specific application rather than on the complexity of handling massively-parallel, device-accelerated AMR., Comment: 17 pages, 11 figures, accepted for publication in IJHPCA, Codes available at https://github.com/parthenon-hpc-lab

The Wide-field Infrared Transient Explorer (WINTER) is a 1x1 degree infrared survey telescope under development at MIT and Caltech, and slated for commissioning at Palomar Observatory in 2021. WINTER is a seeing-limited infrared time-domain survey and has two main science goals: (1) the discovery of IR kilonovae and r-process materials from binary neutron star mergers and (2) the study of general IR transients, including supernovae, tidal disruption events, and transiting exoplanets around low mass stars. We plan to meet these science goals with technologies that are relatively new to astrophysical research: hybridized InGaAs sensors as an alternative to traditional, but expensive, HgCdTe arrays and an IR-optimized 1-meter COTS telescope. To mitigate risk, optimize development efforts, and ensure that WINTER meets its science objectives, we use model-based systems engineering (MBSE) techniques commonly featured in aerospace engineering projects. Even as ground-based instrumentation projects grow in complexity, they do not often have the budget for a full-time systems engineer. We present one example of systems engineering for the ground-based WINTER project, featuring software tools that allow students or staff to learn the fundamentals of MBSE and capture the results in a formalized software interface. We focus on the top-level science requirements with a detailed example of how the goal of detecting kilonovae flows down to WINTER's optical design. In particular, we discuss new methods for tolerance simulations, eliminating stray light, and maximizing image quality of a fly's-eye design that slices the telescope's focus onto 6 non-buttable, IR detectors. We also include a discussion of safety constraints for a robotic telescope., Comment: Published in SPIE Astronomical Telescopes + Instrumentation 2020, Ground-based and Airborne Instrumentation for Astronomy VIII. 12 pages, 9 figures

We report on the position, timing, and energy resolution of a range of plastic scintillator bars and reflector treatments using dual-ended silicon photomultiplier readout. These measurements are motivated by the upcoming construction of an optically segmented single-volume neutron scatter camera, in which neutron elastic scattering off of hydrogen is used to kinematically reconstruct the source direction and energy of an incoming neutron. For this application, interaction position resolutions of about 10 mm and timing resolutions of about 1 ns are necessary to achieve the desired efficiency for fission-energy neutrons. The results presented here indicate that this is achievable with an array of $5\times5\times190~\mathrm{mm}^3$ bars of EJ-204 scintillator wrapped in Teflon tape, read out with SensL's J-series $6\times6~\mathrm{mm}^2$ silicon photomultipliers. With two independent setups, we also explore the systematic variability of the position resolution, and show that, in general, using the difference in the pulse arrival time at the two ends is less susceptible to systematic variation than using the log ratio of the charge amplitude of the two ends. Finally, we measure a bias in the absolute time of interactions as a function of position along the bar: the measured interaction time for events at the center of the bar is $\sim$100 ps later than interactions near the SiPM.

Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identify techniques, the code is designed specifically for non-periodic systems. Application to the small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2-8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a bi-nucleobase CT exciton. The results show that VOTCA-XTP's GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments.

Phase transitions abound in nature and society, and, from species extinction to stock market collapse, their prediction is of widespread importance. In earlier work we showed that Global Transfer Entropy, a general measure of information flow, was found to peak away from the transition on the disordered side for the Ising model, a canonical second-order transition. Here we show that (a) global transfer entropy also peaks on the disordered side of the transition of finite first-order transitions, i.e., those which have finite latent heat and no correlation length divergence, such as ecology dynamics on coral reefs, and (b) analysis of information flow across state boundaries unifies both transition orders. We obtain the first information-theoretic result for the high-order Potts model and the first demonstration of early warning of a first-order transition. The unexpected earlier finding that global transfer entropy peaks on the disordered side of a transition is also found for finite first-order systems, albeit not in the thermodynamic limit. By noting that the interface length of clusters in each phase is the dominant region of information flow, we unify the information theoretic behaviour of first and second-order transitions., Comment: 8 pages, 6 figures

We simulate the Vicsek model utilising topological neighbour interactions and estimate information theoretic quantities as a function of noise, the variability in the extent to which each animal aligns with its neighbours, and the flock direction. We show that these quantities, mutual information and global transfer entropy, are in fact dependent on observation time, and in comparison to the canonical Vicsek model which utilises range-based interactions, the topological variant converges to the long-term limiting behaviour with smaller observation windows. Finally, we show that in contrast to the metric model, which exhibits maximal information flow for the ordered regime, the topological model maintains this maximal information flow beyond the phase transition and into the disordered regime., Comment: 11 pages, 12 figures

We simulate the canonical Vicsek model and estimate the flow of information as a function of noise (the variability in the extent to which each animal aligns with its neighbours). We show that the global transfer entropy for finite flocks not only fails to peak near the phase transition, as demonstrated for the canonical 2D Ising model, but remains constant from the transition to very low noise values. This provides a foundation for future study regarding information flow in more complex models and real-world flocking data., Comment: 10 pages, 6 figures, 1 ancillary file (supplemental materials)

The existing consensus is that flocks are poised at criticality, entailing long correlation lengths and a maximal value of Shannon mutual information in the large-system limit. We show, by contrast, that for finite flocks in the long observation time limit, mutual information may not only fail to peak at criticality---as observed for other critical systems---but also diverge as noise tends to zero. This result carries implications for other finite-size, out-of-equilibrium systems, where observation times may vary widely compared to time scales of internal system dynamics; thus it may not be assumed that mutual information locates the phase transition., Comment: 9 pages, 4 figures

Information theoretic quantities are extremely useful in discovering relationships between two or more data sets. One popular method---particularly for continuous systems---for estimating these quantities is the nearest neighbour estimators. When system sizes are very large or the systems have periodic boundary conditions issues with performance and correctness surface, however solutions are known for each problem. Here we show that these solutions are inappropriate in systems that simultaneously contain both features and discuss a lesser known alternative solution involving Vantage Point trees that is capable of addressing both issues., Comment: 16 pages, 8 figures

The present study, which takes place in a high-poverty section of a large urban area of the northeastern United States, is based upon the prosocial classroom theoretical model that emphasizes the significance of teachers' social and emotional competence (SEC) and well-being in the development and maintenance of supportive teacher-student relationships, effective classroom management, and social and emotional learning (SEL) program effectiveness. These factors, as well as teachers' classroom management and instructional skills contribute to creating a classroom climate that is conducive to learning and that promotes positive developmental behavioral and academic outcomes among students. Cultivating Awareness and Resilience in Education (CARE) is a mindfulness-based professional development program designed to reduce stress, promote SEC and improve teachers' performance and classroom learning environments. From 8 elementary schools the authors recruited and consented 55 teachers (90.2% female, mean age = 39.41). They had relatively low attrition (7.2%) which was largely balanced across treatment and control conditions, resulting in a diverse sample of 51 teachers (53% white). All were regular lead teachers working in a self-contained classroom setting. The results reported here are from an IES-funded 4-year efficacy and replication study of CARE. The data are from the teacher self-report collected from the first year cohort of the cluster randomized controlled trial. After the teachers completed self-reports they were randomly assigned within schools to receive the CARE intervention or to a wait-list control group. After the treatment group received the CARE program, the same self-report battery was administered to both groups. A figure is appended.

This presentation capitalizes on a three-year, longitudinal, school-randomized trial of the 4Rs Program, a comprehensive, school-based social-emotional and literacy program for elementary schools, to test intervention induced changes in features of classroom climate and key dimensions of teacher affective and pedagogical processes and practices thought to influence children's social-emotional and academic development. Experimental evidence to date suggests the 4Rs Program is effective in improving the quality of classroom climate after one-year of intervention and positively altering the course of children's social-cognitive, emotional, behavioral and academic functioning after two years of intervention. While these results are encouraging, this presentation will extend this work by testing the causal influence of the 4Rs Program on (1) the quality of classroom climate at the end of the second and third years of intervention, and (2) changes in teachers affective and pedagogical processes and practices over three consecutive years of intervention.

The 4Rs Program (Reading, Writing, Respect and Resolution) is a "dual focus" whole school universal intervention designed to promote literacy development and social-emotional learning, that is currently being rigorously evaluated using a school-randomized trial of 18 elementary schools (9 intervention, 9 control) in New York City. The present study aims to estimate the impact of a social-learning and literacy development intervention (4Rs) on highly policy-relevant academic achievement outcomes using administrative data on children from multiple cohorts. In addition, it attempts to discuss the ways in which whole-school analyses using administrative data can complement cohort-specific analysis and inform efforts to improve the experiences of children in schools. The sample includes all 1st through 5th grade children who were present in the 18 study schools in October of 2004 (N=7299). Preliminary findings suggest that the use of administrative data to evaluate whole-school reform efforts has the possibility of complementing high-cost developmental and survey data. Implications for what this type of analysis strategy can bring to the field of prevention science, including the cost-quality tradeoff and how to marry quality administrative data with a whole-school experimental approach to whole-school reform will be discussed. (Contains 1 table.)

Over the last two decades, developmental science has made significant progress in understanding children's trajectories toward social-emotional and academic outcomes. At the same time, there has been dramatic growth in the design, implementation, and rigorous evaluation of school-based interventions to promote positive social-emotional development and/or academic achievement. The present study contributes to ongoing scholarship in the school-based prevention of social-emotional, behavioral, and academic problems by reporting three-year longitudinal, experimental impacts of a novel social-emotional learning and literacy development intervention (the 4Rs Program, "Reading, Writing, Respect and Resolution") on a cohort of 3rd grade children's social-emotional, behavioral, and academic functioning after three consecutive years of exposure to the intervention. The findings to date on the impacts of an integrated, social-emotional and literacy program provides clear evidence that this universal intervention has both broad impacts on social-cognitive processes and behaviors in the social-emotional domain, and targeted impacts in the academic domain. This study provides good evidence that universal school-based interventions, delivered to whole populations of children, can result in substantial impacts on children's developmental health and well-being. (Contains 1 figure.)

We consider traffic-update mobile applications that let users learn traffic conditions based on reports from other users. These applications are becoming increasingly popular (e.g., Waze reported 30 million users in 2013) since they aggregate real-time road traffic updates from actual users traveling on the roads. However, the providers of these mobile services have access to such sensitive information as timestamped locations and movements of its users. In this paper, we describe Haze, a protocol for traffic-update applications that supports the creation of traffic statistics from user reports while protecting the privacy of the users. Haze relies on a small subset of users to jointly aggregate encrypted speed and alert data and report the result to the service provider. We use jury-voting protocols based on threshold cryptosystem and differential privacy techniques to hide user data from anyone participating in the protocol while allowing only aggregate information to be extracted and sent to the service provider. We show that Haze is effective in practice by developing a prototype implementation and performing experiments on a real-world dataset of car trajectories.

This report describes one of the largest and longest running school-based violence prevention programs in the country, the Resolving Conflict Creatively Program (RCCP), and discusses the results of a rigorous evaluation of the program's effectiveness conducted by the National Center for Children in Poverty (NCCP) at Columbia University's Joseph L. Mailman School of Public Health. The report is designed to inform policymakers, program developers and managers at the local level, and other opinion leaders and decision makers of effective strategy for directly addressing the problem of violence among children and youth. Founded in 1985, the RCCP now serves approximately 9,000 students in 60 New York City public schools. The program is designed to promote constructive conflict resolution and positive inter-group relations. It is based on the philosophy that aggressive and violent behavior is learned and therefore can be reduced through education. The program is built around a set of core skills: communicating clearly and listening carefully, expressing feelings and dealing with anger, resolving conflicts, fostering cooperation, appreciating diversity, and countering bias. These skills are learned through a curriculum taught by teachers receiving both initial training and ongoing follow-up and support from RCCP staff developers. The RCCP is also implemented through the training of student-based peer mediation groups and school administrators, and by continued outreach to parents. Overall, NCCP's evaluation found that the RCCP had a significant positive impact when teachers taught a high number of lessons from the RCCP curriculum. Among other findings, children receiving a high number of lessons had significantly slower growth in self-reported hostile attributions, aggressive fantasies, and aggressive problem-solving strategies, as well as in teacher-reported aggressive behavior, compared to children receiving a low number of lessons or no lessons at all. (Appendices include related evaluations of the RCCP implementation, NCCP design for the evaluation of the RCCP, and implications of the RCCP evaluation for evaluation research.) (EV)