Publications

From Goals, Waypoints & Paths To Long Term Human Trajectory Forecasting

Human trajectory forecasting is an inherently multi-modal problem. Uncertainty in future trajectories stems from two sources: (a) sources that are known to the agent but unknown to the model, such as long term goals and (b)sources that are unknown to both the agent & the model, such as intent of other agents & irreducible randomness indecisions. We propose to factorize this uncertainty into its epistemic & aleatoric sources. We model the epistemic un-certainty through multimodality in long term goals and the aleatoric uncertainty through multimodality in waypoints& paths. To exemplify this dichotomy, we also propose a novel long term trajectory forecasting setting, with prediction horizons upto a minute, an order of magnitude longer than prior works. Finally, we presentY-net, a scene com-pliant trajectory forecasting network that exploits the pro-posed epistemic & aleatoric structure for diverse trajectory predictions across long prediction horizons.Y-net significantly improves previous state-of-the-art performance on both (a) The well studied short prediction horizon settings on the Stanford Drone & ETH/UCY datasets and (b) The proposed long prediction horizon setting on the re-purposed Stanford Drone & Intersection Drone datasets.

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub .

Accountable Internet Protocol

Dephosphorylation of Tyrosine 393 in Argonaute 2 by Protein Tyrosine Phosphatase 1B Regulates Gene Silencing in Oncogenic RAS-Induced Senescence

Commentary: Carbon Metabolism of the Terrestrial Biosphere: A Multitechnique Approach for Improved Understanding

Understanding terrestrial carbon metabolism is critical because terrestrial ecosystems play a major role in the global carbon cycle. Furthermore, humans have severely disrupted the carbon cycle in ways that will alter the climate system and directly affect terrestrial metabolism. Changes in terrestrial metabolism may well be as important an indicator of global change as the changing temperature signal. Improving our understanding of the carbon cycle at various spatial and temporal scales will require the integration of multiple, complementary and independent methods that are used by different research communities. Tools such as air sampling networks, inverse numerical methods, and satellite data (top-down approaches) allow us to study the strength and location of the global- and continental-scale carbon sources and sinks. Bottom-up studies provide estimates of carbon fluxes at finer spatial scales and examine the mechanisms that control fluxes at the ecosystem, landscape, and regional scales. Bottom-up approaches include comparative and process studies (for example, ecosystem manipulative experiments) that provide the necessary mechanistic information to develop and validate terrestrial biospheric models. An iteration and reiteration of top-down and bottom-up approaches will be necessary to help constrain measurements at various scales. We propose a major international effort to coordinate and lead research programs of global scope of the carbon cycle.

A Facile and Patternable Method for the Surface Modification of Carbon Nanotube Forests Using Perfluoroarylazides

A facile patterning method for the functionalization of vertically aligned carbon nanotubes is described. Modification of the surface of nanotube forests with hydrophilic, hydrophobic, or polymerizable small molecules was achieved via UV-triggered attachment of perfluoroarylazides. Multiple functionalizations of the tube surface can be achieved. Macro- and micropatterning of forest substrates were demonstrated. Superhydrophobic surfaces containing superhydrophilic regions were prepared.

Analysis of Type IIn SN 1998S: Effects of Circumstellar Interaction on Observed Spectra

We present spectral analysis of early observations of the Type IIn supernova 1998S using the general non-local thermodynamic equilibrium atmosphere code PHOENIX. We model both the underlying supernova spectrum and the overlying circumstellar interaction region and produce spectra in good agreement with observations. The early spectra are well fitted by lines produced primarily in the circumstellar region itself, and later spectra are due primarily to the supernova ejecta. Intermediate spectra are affected by both regions. A mass-loss rate of order M ∼ 0.0001-0.001 M ⊙ yr -1 is inferred for a wind speed of 100-1000 km s -1. We discuss how future self-consistent models will better clarify the underlying progenitor structure.

Assessing the Implementation of the Chronic Care Model in Quality Improvement Collaboratives

Objective. To measure organizations' implementation of Chronic Care Model (CCM) interventions for chronic care quality improvement (QI). Data Sources/Study Setting. Monthly reports submitted by 42 organizations participating in three QI collaboratives to improve care for congestive heart failure, diabetes, depression, and asthma, and telephone interviews with key informants in the organizations. Study Design. We qualitatively analyzed the implementation activities of intervention organizations as part of a larger effectiveness evaluation of yearlong collaboratives. Key study variables included measures of implementation intensity (quantity and depth of implementation activities) as well as fidelity to the CCM. Data Collection/Extraction Methods. We developed a CCM‐based scheme to code sites' intervention activities and criteria to rate their depth or likelihood of impact. Principal Findings. The sites averaged more than 30 different change efforts each to implement the CCM. The depth ratings for these changes, however, were more modest, ranging from 17 percent to 76 percent of the highest rating possible. The participating organizations significantly differed in the intensity of their implementation efforts ( p <.001 in both quantity and depth ratings). Fidelity to the CCM was high. Conclusions. Collaborative participants were able, with some important variation, to implement large numbers of diverse QI change strategies, with high CCM fidelity and modest depth of implementation. QI collaboratives are a useful method to foster change in real world settings.

The morphing of decay powered to interaction powered Type II supernova ejecta at nebular times

There is significant astronomical interest around the intense mass loss that appears to take place in some massive stars immediately before core collapse. However, because it occurs too late, it has a negligible impact on the star’s evolution or the final yields. These properties are then influenced instead by the longer term, quasi-steady, and relatively weak mass loss taking place during H and He burning. Late-time observations of core-collapse supernovae (SNe) interacting with the progenitor wind are one means of constraining this secular mass loss. Here, we present radiative transfer calculations for a Type II SN from a standard red-supergiant (RSG) star explosion. At first, a reference model was computed without interaction power. A second model was then taken to assume a constant interaction power of 10 40 erg s −1 associated with a typical RSG progenitor wind mass-loss rate of 10 −6 M ⊙ yr −1 . We focused on the phase between 350 and 1000 d after explosion. We find that without interaction power, the ejecta are powered through radioactive decay, whose exponential decline produces an ever-fading SN. Instead, with a constant interaction power of 10 40 erg s −1 , the spectrum morphs from decay powered at 350 d, with narrow lines forming in the inner metal-rich ejecta, to interaction powered at 1000 d, with broad boxy lines forming in the outer H-rich ejecta. Intermediate times are characterized by a hybrid and complex spectrum made of overlapping narrow and broad lines. While interaction boosts primarily the flux in the ultraviolet, which remains largely unobserved today, a knee in the R -band light curve or a U -band boost are clear signatures of interaction at late times. The model predictions offer a favorable comparison with a number of Type II SNe, including SN 2004et or SN 2017eaw at 500–1000 d after explosion.

Carbon Quantum Dots: In vitro and in vivo Studies on Biocompatibility and Biointeractions for Optical Imaging

Xiumei Tian1 ,* Ao Zeng1 ,* Ziying Liu,1 Cunjing Zheng,2 Yuezi Wei,1 Peiheng Yang,1 Minru Zhang,1 Fanwen Yang,1 Fukang Xie1 1School of Basic Medical Sciences, Affiliated Stomatology Hospital, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China; 2Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, People’s Republic of China*These authors contributed equally to this workCorrespondence: Fukang Xie Tel +86 20 136 4231 6682Email 378141679@qq.comFanwen Yang Tel +86 20 135 0308 0690Fax +86 20 3710 3509Email yangfanwen@163.comBackground: Understanding the biocompatibility and biointeractions of nano-carbon quantum dots (nano-CQDs) in vitro and in vivo is important for assessing their potential risk to human health. In the previous research, the physical properties of CQDs synthesized by the laser ablation in liquid (LAL) method were analyzed in detail; however, possible bioapplications were not considered.Materials and Methods: CQDs were prepared by LAL and characterized by atomic force microscopy, fluorescence lifetime, absorption spectrum, Fourier-transform infrared spectroscopy, and dynamic light scattering. Their biocompatibility was evaluated in vitro using assays for cytotoxicity, apoptosis, and biodistribution and in vivo using immunotoxicity and the relative expression of genes. Cells were measured in vitro using fluorescence-lifetime imaging microscopy to analyze the biointeractions between CQDs and intracellular proteins.Results: There were no significant differences in biocompatibility between the CQDs and the negative control. The intracellular interactions had no impact on the optical imaging of CQDs upon intake by cells. Optical imaging of zebrafish showed the green fluorescence was well dispersed.Conclusion: We have demonstrated that the CQDs have an excellent biocompatibility and can be used as efficient optical nanoprobes for cell tracking and biomedical labeling except for L929 and PC-3M cells.Keywords: nanoprobe, immunotoxicity, biodistribution, biointeraction, optical imaging

CCDC 1536867: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

The SENSE study: Post intervention effects of a randomized controlled trial of a cognitive–behavioral and mindfulness-based group sleep improvement intervention among at-risk adolescents.

The SENSE study provides evidence that a multicomponent group sleep intervention that includes cognitive-behavioral and mindfulness-based therapies can reduce sleep initiation problems and related daytime dysfunction, along with concomitant anxiety symptoms, among at-risk adolescents. (PsycINFO Database Record

Pt-based nanoparticles: Synthesis and imaging by high pressure-STM

HP-STM is an efficient method to study structural changes of the catalyst under different gas mixtures. The particles have to be homogeneously distributed over the region of analysis. Colloidal synthesis is a reliable way to produce monodisperse NP’s with narrow size distribution, but the disadvantages of this synthesis are:• the capping agent has to be removed without damaging the substrate by avoiding aggregation of the nanoparticles• the deposition process (dip coating or Langmuir-Blodgett deposition) induces unavoidable dirt on surfaceWe were able to image PtCo nanoparticles with good resolution.

Torsional Coupling and Earthquake Response of Simple Elastic and Inelastic Systems

The effects are analyzed of torsional coupling on the earthquake response of simple one-story structures in elastic and inelastic ranges of behavior. The structures considered are symmetrical about one principal axis of resistance, resulting in coupling only between lateral displacement along the perpendicular axis and the torsional displacement. Torsional coupling arising only from eccentricity between centers of mass and elastic resistance is considered. Systems with several resisting elements are idealized by a single element model. Response of such a model to a selected earthquake ground motion are presented for a range of the basic structural parameters. The response quantities presented include maximum lateral and torsional deformations of the system as well as maximum deformations of individual columns. The response in the inelastic range of behavior is effected by torsional coupling to generally a lesser degree than elastic response.

CCDC 1911861: Experimental Crystal Structure Determination

General models for rational cameras and the case of two-slit projections

The rational camera model recently introduced in [19] provides a general methodology for studying abstract nonlinear imaging systems and their multi-view geometry. This paper builds on this framework to study "physical realizations" of rational cameras. More precisely, we give an explicit account of the mapping between between physical visual rays and image points (missing in the original description), which allows us to give simple analytical expressions for direct and inverse projections. We also consider "primitive" camera models, that are orbits under the action of various projective transformations, and lead to a general notion of intrinsic parameters. The methodology is general, but it is illustrated concretely by an in-depth study of two-slit cameras, that we model using pairs of linear projections. This simple analytical form allows us to describe models for the corresponding primitive cameras, to introduce intrinsic parameters with a clear geometric meaning, and to define an epipolar tensor characterizing two-view correspondences. In turn, this leads to new algorithms for structure from motion and self-calibration.

CCDC 2078735: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Crystal Structure, Dissolution, and Deposition of a 5 nm Functionalized Metal−Organic Great Rhombicuboctahedron

A metal-organic great rhombicuboctahedron (termed MOP-18) was functionalized with extended alkyl chains and crystallized. It has 12 rigid square-shaped Cu2(CO2)4 paddle-wheel building units and 24 5-dodecoxybenzene-1,3-dicarboxylate links. MOP-18 is soluble in a variety of organic solvents, such as tetrahydrofuran, chloroform, and toluene, which enabled its assembly on graphite substrate and its observation by scanning tunneling microscopy.