Orientation and Alignment Echoes

We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses

TRANSFORMERS: Robust spatial joins on non-uniform data distributions

Spatial joins are becoming increasingly ubiquitous in many applications, particularly in the scientific domain. While several approaches have been proposed for joining spatial datasets, each of them has a strength for a particular type of density ratio among the joined datasets. More generally, no single proposed method can efficiently join two spatial datasets in a robust manner with respect to their data distributions. Some approaches do well for datasets with contrasting densities while others do better with similar densities. None of them does well when the datasets have locally divergent data distributions. In this paper we develop TRANSFORMERS, an efficient and robust spatial join approach that is indifferent to such variations of distribution among the joined data. TRANSFORMERS achieves this feat by departing from the state-of-the-art through adapting the join strategy and data layout to local density variations among the joined data. It employs a join method based on data-oriented partitioning when joining areas of substantially different local densities, whereas it uses big partitions (as in space-oriented partitioning) when the densities are similar, while seamlessly switching among these two strategies at runtime. We experimentally demonstrate that TRANSFORMERS outperforms state-of-the-art approaches by a factor of between 2 and 8

The ejection of triatomic molecular hydrogen ions H-3(+) produced by the interaction of benzene molecules with ultrafast laser pulses

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An Elisa-Based Platform for Rapid Identification of Structure-Dependent Nucleic Acid-Protein Interactions Detects Novel DNA Triplex Interactors

Unusual nucleic acid structures play vital roles as intermediates in many cellular processes and, in the case of peptide nucleic acid (PNA)-mediated triplexes, are leveraged as tools for therapeutic gene editing. However, due to their transient nature, an understanding of the factors that interact with and process dynamic nucleic acid structures remains limited. Here, we developed snapELISA (structure-specific nucleic acid-binding protein ELISA), a rapid high-throughput platform to interrogate and compare up to 2688 parallel nucleic acid structure-protein interactions in vitro. We applied this system to both triplex-forming oligonucleotide-induced DNA triplexes and DNA-bound PNA heterotriplexes to describe the identification of previously known and novel interactors for both structures. For PNA heterotriplex recognition analyses, snapELISA identified factors implicated in nucleotide excision repair (XPA, XPC), single-strand annealing repair (RAD52), and recombination intermediate structure binding (TOP3A, BLM, MUS81). We went on to validate selected factor localization to genome-targeted PNA structures within clinically relevant loci in human cells. Surprisingly, these results demonstrated XRCC5 localization to PNA triplex-forming sites in the genome, suggesting the presence of a double-strand break intermediate. These results describe a powerful comparative approach for identifying structure-specific nucleic acid interactions and expand our understanding of the mechanisms of triplex structure recognition and repair

On-Line Identification of Autonomous Underwater Vehicles through Global Derivative-Free Optimization

We describe the design and implementation of an on-line identification scheme for Autonomous Underwater Vehicles (AUVs). The proposed method estimates the dynamic parameters of the vehicle based on a global derivative-free optimization algorithm. It is not sensitive to initial conditions, unlike other on-line identification schemes, and does not depend on the differentiability of the model with respect to the parameters. The identification scheme consists of three distinct modules: a) System Excitation, b) Metric Calculator and c) Optimization Algorithm. The System Excitation module sends excitation inputs to the vehicle. The Optimization Algorithm module calculates a candidate parameter vector, which is fed to the Metric Calculator module. The Metric Calculator module evaluates the candidate parameter vector, using a metric based on the residual of the actual and the predicted commands. The predicted commands are calculated utilizing the candidate parameter vector and the vehicle state vector, which is available via a complete navigation module. Then, the metric is directly fed back to the Optimization Algorithm module, and it is used to correct the estimated parameter vector. The procedure continues iteratively until the convergence properties are met. The proposed method is generic, demonstrates quick convergence and does not require a linear formulation of the model with respect to the parameter vector. The applicability and performance of the proposed algorithm is experimentally verified using the AUV Girona 500. © 2013 IEEE

"FAIR-by-Design" Artifacts: Enriching Publications and Software with FAIR Scientific Information at the Time of Creation

Presentation on the idea of "FAIR-by-Design" Artifacts at the NFDI4Ing Conference 2023. Abstract In several research disciplines, the use and development of software have become an integral part, with researchers reporting in publications the results obtained with software and concepts implemented in software. Consequently, publications and software have become two core artifacts in academia with increasing importance for measuring research impact and reputation. The research community has made great efforts to improve digital access to publications and software. However, even now that these artifacts are available in digital form, researchers still encapsulate the scientific information in static and relatively unstructured documents unsuitable for communication. The next step in the digital transformation of scholarly communication requires a more flexible, fine-grained, context-sensitive, and semantic representation of scientific information to be understandable, processable, and usable by humans and machines. Researchers need support in the form of infrastructures, services, and tools to organize FAIR scientific information from publications and software. Several research disciplines work on initiatives to organize scientific information, e.g., machine learning with “Papers-with-Code”, invasion biology with “Hi-Knowledge”, and biodiversity with “OpenBiodiv”. However, these initiatives are often technically diverse and limited to the respective application domain. For this reason, we from the task area Ellen of NFDI4Ing (and in collaboration with NFDI4DataScience and NFDI4Energy) decided to use the Open Research Knowledge Graph (ORKG), an innovative infrastructure for organizing scientific information from publications and software. The ORKG is a cross-discipline research knowledge graph that offers all research communities an easy-to-use and sustainably governed infrastructure. This infrastructure implements best practices, such as FAIR principles and versioning, with services combining manual crowd-sourcing and (semi-)automated approaches to support researchers in producing, curating, processing, and (re-)using FAIR scientific information from publications and software. As a result, organized scientific information is openly available in the long term and can be understood, processed, and used by humans and machines. Thus, research communities can constantly build, publish, maintain, (re-)use, update, and expand organized scientific information in a long-term and collaborative manner. While the ORKG currently focuses on organizing scientific information from published publications and software, we aim to help researchers create “FAIR-by-Design” artifacts to improve their storage, access, and (re-)use, using the ORKG as exemplary infrastructure. The idea of “FAIR-by-Design” artifacts is that the creators of an artifact describe it with extensive and FAIR information once and in parallel to the time of creation. This FAIR information is embedded directly into the artifact to be available to anyone at any time. Specifically, we developed two tools (SciKGTeX for publications and DataDesc for software) that support researchers in the role of author and developer to enrich their publications and software at the time of writing and development with FAIR scientific information embedded into the respective artifact. SciKGTeX is a LaTeX package to annotate research contributions directly in LaTeX source code. Authors can enrich their publications with structured, machine-actionable, and FAIR scientific information about their research contributions. SciKGTeX embeds the annotated contribution data into the PDF’s XMP metadata so that the FAIR scientific information persists for the lifetime of the artifact. DataDesc is a toolkit that combines different tools to describe software with machine-actionable metadata. Developers can describe Python software and its interfaces with extensive metadata by annotating individual classes and functions directly within the source code. DataDesc converts all metadata into an OpenAPI-compliant YAML file, which various tools can render and process. Regarding the research data management (RDM) lifecycle, both tools target the production phase to support researchers in creating“FAIR-by-Design” artifacts. Creating “FAIR-by-Design” artifacts helps to improve their storage, leading to better access to artifacts and thus laying the foundation for their effective (re-)use. Using the ORKG as exemplary infrastructure, we demonstrate with two proof-of-concepts how infrastructure providers can use the artifacts from SciKGTeX and DataDesc to store the FAIR scientific information in their systems. In the case of SciKGTeX, the ORKG recently added a new upload feature for SciKGTeX annotated PDFs to allow researchers to add the FAIR scientific information of publications quickly and easily. In addition, the ing.grid journal provides a version of their LaTeX template that integrates the SciKGTeX. For DataDesc, we plan such an upload feature and similar use by the community in future work. Researchers only need to create a “FAIR-by-Design” artifact once, and can reuse it on multiple infrastructures to improve their dissemination and discoverability. With improved storage, researchers can more easily discover and access publications and software to determine whether an artifact fulfills their information needs. However, researchers do not have to rely on such infrastructures to find, access, and assess publications or software. When they encounter a “FAIR-by-Design” artifact, it embeds the additional information itself so that they can review the artifact themselves with the same information base. Improved discoverability and accessibility lay the foundation for effective (re-)use as researchers can better understand an artifact. In the case of the ORKG, we can even (re-)use the information from SciKGTeX and DataDesc stored in the ORKG interchangeably. A publication annotated with SciKGTeX can reference a software annotated with DataDesc stored in the ORKG and vice versa. Overall, enabling researchers to create “FAIR-by-Design” artifacts is a promising approach to support the downstream phases of storage, access, and (re-)use in the RDM lifecycle. In our presentation, we want to explain the idea of “FAIR-by-Design” artifacts in more detail using concrete examples based on the two tools and in combination with the ORKG. We believe that the idea of “FAIR-by-Design” artifacts is of interest to the research community. The two tools can inspire other researchers to extend our original approaches and develop new ones to create more “FAIR-by-Design” artifacts by enriching artifacts with FAIR scientific knowledge at the time of creation. Furthermore, we hope to encourage and motivate researchers to use our tools more intensively and thus establish them. In particular, the existing and planned future integration with ORKG and the existing collaboration with the ing.grid journal are motivating incentives for researchers to use SciKGTeX and DataDesc actively.The authors thank the Federal Government, the Heads of Government of the Länder, as well as the Joint Science Conference (GWK), for their funding and support within the NFDI4Ing and NFDI4DataScience consortia. This work was funded by the German Research Foundation (DFG) -project numbers 442146713 and 460234259, by the European Research Council for the project ScienceGRAPH (Grant agreement ID: 819536), and by the TIB - Leibniz Information Centre for Science and Technology

Emergency Medicine Research Directors and Research Programs: Characteristics and Factors Associated with Productivity

: Background: Periodic surveys of research directors (RDs) in emergency medicine (EM) are useful to assess the specialty's development and evolution of the RD role. Objectives: To assess associations between characteristics and research productivity of RDs and EM programs. Methods: A survey of EM RDs was developed using the nominal group technique and pilot tested. RDs or surrogate respondents at programs certified by the Accreditation Council for Graduate Medical Education were contacted by e-mail in early 2005. The survey assessed programs' research infrastructure and productivity, as well as RD characteristics, responsibilities, and career satisfaction. Three measures of research productivity were empirically defined: research publications, grant awards, and grant revenue. Results: Responses were received from 86% of 123 EM programs. Productivity was associated with the presence of nonclinical faculty, dedicated research coordinators, and reduced clinical hours for research faculty. Programs with an RD did not have greater research productivity, using any measure, than those without an RD. The majority of RDs cited pursuing their own studies, obtaining funding, research mentoring, and research administration to be major responsibilities. The majority characterized internal research funding, grant development support, and support from other faculty as inadequate. Most RDs are satisfied with their careers and expect to remain in the position for three or more years. Conclusions: Research productivity of EM residency programs is associated with the presence of dedicated research faculty and staff and with reduced clinical demands for research faculty. Despite perceiving deficiencies in important resources, most RDs are professionally satisfied.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72908/1/j.aem.2006.01.027.pd

PAH under XUV excitation: an ultrafast XUV- photochemistry experiment for astrophysics

International audienceUnderstanding processes induced by XUV excitation of Polycyclic Aromatic Hydrocarbons (PAHs) is at the heart of molecular astrophysics, which aims at understanding molecular evolution in interstellar media. We used ultrashort XUV pulses to produce highly excited PAHs cations. The photo-induced dynamics is probed using a pump-probe XUV-IR spectroscopy. By studying PAH from small (naphthalene) to large (hexabenzocoronene) PAHs, we show that the dynamic is governed by the large density of states, in which many-body quantum effects are dominant

Fractional Echoes

We report the observation of fractional echoes in a double-pulse excited nonlinear system. Unlike standard echoes which appear periodically at delays which are integer multiple of the delay between the two exciting pulses, the fractional echoes appear at rational fractions of this delay. We discuss the mechanism leading to this phenomenon, and provide the first experimental demonstration of fractional echoes by measuring third harmonic generation in a thermal gas of CO2 molecules excited by a pair of femtosecond laser pulses