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At least 1,513 records · Page 84

Repurposing a microfluidic formulation device for automated DNA construction

Microfluidic applications have expanded greatly over the past decade. For the most part, however, each microfluidics platform is developed with a specific task in mind, rather than as a general-purpose device with a wide-range of functionality. Here, we show how a microfluidic system, originally developed to investigate protein phase behavior, can be modified and repurposed for another application, namely DNA construction. We added new programable controllers to direct the flow of reagents across the chip. We designed the assembly of a combinatorial Golden Gate DNA library using TeselaGen DESIGN software and used the repurposed microfluidics platform to assemble the designed library from off-chip prepared DNA assembly pieces. Further experiments verified the sequences and function of the on-chip assembled DNA constructs.

59 BASIC BIOLOGICAL SCIENCES↗

Automated Tracking of Shallow Maritime Clouds on Geostationary Imagery to Extract Lifecycle Characteristics

Shallow moist convection is ubiquitous throughout the tropics and represents a key player in boundary layer processes. Satellites have provided many statistics on shallow clouds, such as size, structure, and geographical coverage, from static views of recurring cloud fields. But determining why certain cloud features appear and persist for different periods requires a time-evolving view of their behaviors. Geostationary satellites provide a unique opportunity to follow the time evolution of individual convective features, given their enhanced spatial and temporal sampling. A cloud-tracking tool was developed to identify properties of cloud lifecycle from the NASA Cloud, Aerosol, and Monsoon Processes Philippines Experiment (CAMP2EX) field campaign of 2019. The mission conducted intensive sampling of shallow cumulus in the West Pacific Ocean, in tandem with Rapid Scan imagery from the Advanced Himawari Imager (AHI) on the Japan Meteorological Agency’s (JMA) Himawari-8 satellite. Shallow cumulus was segmented according to thresholds in 0.5-km visible reflectance and with blurring techniques. Despite being limited to daytime hours, the segmentations yielded the best resolution possible for capturing cloud initiation and decay. The tracking procedure is based on a computer vision package that includes Kalman filters for motion prediction, object overlap search, and the Hungarian (or Kuhn-Munkres) matching algorithm for track designation. AHI radiances available within the tracked cloud boundaries are assembled to form individual spectral histories. The resulting catalog provides thousands of cloud histories for domains measuring only a few degrees in latitude and longitude. We present an overview of the cloud-tracking tool, strategies to identify development stages from cloud tracks, and preliminary results that document cumulus lifecycle properties from satellite. The application of AHI 0.5-km reflectance has both strengths and limitations when attempting to track lifecycles of the smallest resolvable clouds. We show that by aggregating cloud tracks from a few case studies of CAMP2EX, we can discern differences in cloud lifetime and development according to ensembles selected from areas of interest. The results demonstrate an ability to quantify lifetimes and assess rates of change in cloud characteristics that are likely controlled by the surrounding environment and meteorology.

Cloud Tracking↗

Automated Tracking of Shallow Maritime Clouds on Geostationary Imagery to Extract Lifecycle Characteristics

Shallow moist convection is ubiquitous throughout the tropics and represents a key player in boundary layer processes. Satellites have provided valuable insight on shallow clouds, such as size, structure, and geographical coverage, from static views of recurring cloud fields. But determining why certain cloud features appear and persist for different periods requires a time-evolving view of their behaviors. Geostationary satellites provide a unique opportunity to follow the time evolution of individual convective features, given their enhanced spatial and temporal sampling. A cloud-tracking tool was developed to identify properties of cloud lifecycle from the NASA Cloud, Aerosol, and Monsoon Processes Philippines Experiment (CAMP2EX) field campaign of 2019. The mission conducted intensive sampling of shallow cumulus in the West Pacific Ocean, in tandem with Rapid Scan imagery from the Advanced Himawari Imager (AHI) on the Japan Meteorological Agency’s (JMA) Himawari-8 satellite. Shallow cumulus were segmented according to thresholds in 0.5-km visible reflectance and with blurring techniques. Despite being limited to daytime hours, the segmentations yielded the best resolution available for capturing cloud initiation, growth, and decay. The tracking procedure is based on a computer vision package that includes Kalman filters for motion prediction, object overlap search, and the Hungarian (or Kuhn-Munkres) matching algorithm for track designation. AHI radiances available within the tracked cloud boundaries are assembled to form individual spectral histories. The resulting catalog provides thousands of cloud histories for domains measuring only a few degrees in latitude and longitude. We present an overview of the cloud-tracking tool and its results for cloud fields sampled throughout CAMP2EX by the airborne P-3. Cloud tracks were selected from about 10 flights to form ensembles, specific groups of tracks occurring in a region with airborne sampling. Cloud lifecycle properties, including duration and maximum area, are calculated for all ensemble members, and analyzed for cloud behavior and P-3 coincidences. By following this strategy, we quantitatively assess the degree of airborne sampling for specific cloud classes defined by the lifecycle calculations. We can summarize which cloud classes had more sampling, the stage of development during sampling, and general differences in character (e.g., isolated congestus vs. cold-pool producer).

Cloud Tracking↗

sas-temper

Modeling remains a considerable challenge for practitioners of SAXS and SANS because the materials being studied are not highly ordered, the length scales being studied are large, and the information content of the data is low. Data analysis is both challenging and time consuming. Novices often rely on the assistance of an expert, such as the instrument scientist who supported them at the facility where the experiment was performed, to analyze their data. The high flux provided by modern facilities makes it possible to study dozens of samples or sample conditions during a single trip. Ultimately, the high throughput of modern instruments limits access to instrument scientists. A bottleneck in the research effort results that reduces facility productivity. Sas-temper seeks to address this problem, as well as the intrinsic difficulties of being confident in non-linear least squared fitting of data, by providing tools that automate much of the manual process of initial data fitting and refinement, as well as by providing tools for characterizing the nature of the parameter space that fits the measured data. The tools provided by sas-temper help small-angle scattering practitioners transition data into results.

Heller, William [Oak Ridge National Lab. (ORNL), O↗

Best practices in software development for robust and reproducible geoscientific models based on insights from the Global Carbon Budget's dynamic vegetation models

Computational models play an increasingly vital role in scientific research by enabling the numerical simulation of complex processes. Such models are also fundamental in geosciences. For instance, they offer critical insights into the impacts of global change on the Earth system today and in the future. Beyond their value as research tools, models are also software products and should therefore adhere to certain established software engineering standards. However, scientists are rarely trained as software developers, which can lead to potential deficiencies in software quality like unreadable, inefficient, or erroneous code. The complexity of models, coupled with their integration into broader workflows, also often makes it challenging to reproduce results, evaluate processes, and build upon them. In this paper, we review the state and current practices of the development processes of the state-of-the-art land surface models used by the Global Carbon Budget. We combine the experience of modelers from the respective research groups with the expertise of software engineers from tech companies to outline key principles and tools for improving software quality in research. We explore four main areas: (1) model testing and validation, (2) scientific, technical, and user documentation, (3) version control, continuous integration, and code review, and (4) the portability and reproducibility of workflows. Our review reveals that while modeling communities are incorporating many best practices, significant room for improvement remains in areas such as automated testing, automated documentation, and reproducibility. Therefore, we here identify and promote essential software engineering practices, including numerous examples of practices from within the community that can serve as guidelines for other models and could help streamline processes across the entire community. We conclude with an open-source example implementation of these principles, demonstrating portable and reproducible data flows, a continuous integration setup, and web-based visualizations. This example may serve as a practical resource for model developers, users, and all scientists engaged in scientific programming.

Gregor, Konstantin [Technical Univ. of Munich (Ger↗

Space science plans for the shuttle era.

Three separate and distinct modes of using the space shuttle system have been identified. These modes include the boost of a spacecraft plus one or more propulsion stages into earth orbit or parking orbit, the establishment and maintenance of automated observatories in space, and the support of exploratory research and instrument development. Studies show that approximately 60% of all planned NASA missions require a shuttle third stage. Illustrations are presented to show how the largest spacecraft, Viking, and its propulsion system, Centaur, and a communications satellite, with an Agena stage to place it into a geostationary orbit, would fit into the shuttle. Results of the NASA Shuttle Sortie Workshop studies are discussed together with prospects of European cooperation in future workshop experiments.

Naugle, J. E.↗

RIACS

The Research Institute for Advanced Computer Science (RIACS) was established by the Universities Space Research Association (USRA) at the NASA Ames Research Center (ARC) on June 6, 1983. RIACS is privately operated by USRA, a consortium of universities that serves as a bridge between NASA and the academic community. Under a five-year co-operative agreement with NASA, research at RIACS is focused on areas that are strategically enabling to the Ames Research Center's role as NASA's Center of Excellence for Information Technology. The primary mission of RIACS is charted to carry out research and development in computer science. This work is devoted in the main to tasks that are strategically enabling with respect to NASA's bold mission in space exploration and aeronautics. There are three foci for this work: (1) Automated Reasoning. (2) Human-Centered Computing. and (3) High Performance Computing and Networking. RIACS has the additional goal of broadening the base of researcher in these areas of importance to the nation's space and aeronautics enterprises. Through its visiting scientist program, RIACS facilitates the participation of university-based researchers, including both faculty and students, in the research activities of NASA and RIACS. RIACS researchers work in close collaboration with NASA computer scientists on projects such as the Remote Agent Experiment on Deep Space One mission, and Super-Resolution Surface Modeling.

Moore, Robert C.↗

Using Generative Representations to Evolve Robots

Recent research has demonstrated the ability of evolutionary algorithms to automatically design both the physical structure and software controller of real physical robots. One of the challenges for these automated design systems is to improve their ability to scale to the high complexities found in real-world problems. Here we claim that for automated design systems to scale in complexity they must use a representation which allows for the hierarchical creation and reuse of modules, which we call a generative representation. Not only is the ability to reuse modules necessary for functional scalability, but it is also valuable for improving efficiency in testing and construction. We then describe an evolutionary design system with a generative representation capable of hierarchical modularity and demonstrate it for the design of locomoting robots in simulation. Finally, results from our experiments show that evolution with our generative representation produces better robots than those evolved with a non-generative representation.

Hornby, Gregory S.↗

Lightning Jump Algorithm Development for the GOES·R Geostationary Lightning Mapper

Current work on the lightning jump algorithm to be used in GOES‐R Geostationary Lightning Mapper (GLM)'s data stream is multifaceted due to the intricate interplay between the storm tracking, GLM proxy data, and the performance of the lightning jump itself. This work outlines the progress of the last year, where analysis and performance of the lightning jump algorithm with automated storm tracking and GLM proxy data were assessed using over 700 storms from North Alabama. The cases analyzed coincide with previous semi‐objective work performed using total lightning mapping array (LMA) measurements in Schultz et al. (2011). Analysis shows that key components of the algorithm (flash rate and sigma thresholds) have the greatest influence on the performance of the algorithm when validating using severe storm reports. Automated objective analysis using the GLM proxy data has shown probability of detection (POD) values around 60% with false alarm rates (FAR) around 73% using similar methodology to Schultz et al. (2011). However, when applying verification methods similar to those employed by the National Weather Service, POD values increase slightly (69%) and FAR values decrease (63%). The relationship between storm tracking and lightning jump has also been tested in a real‐time framework at NSSL. This system includes fully automated tracking by radar alone, real‐time LMA and radar observations and the lightning jump. Results indicate that the POD is strong at 65%. However, the FAR is significantly higher than in Schultz et al. (2011) (50‐80% depending on various tracking/lightning jump parameters) when using storm reports for verification. Given known issues with Storm Data, the performance of the real‐time jump algorithm is also being tested with high density radar and surface observations from the NSSL Severe Hazards Analysis & Verification Experiment (SHAVE).

Schultz. E.↗

Toward Integrated Operator Interface for Advanced Teleoperation under Time-Delay

This paper briefly describes an Advanced Teleoperator (ATOP) system and its control station where a variety of computer-based operator interface devices and techniques are integrated into a functional setting, accommodating a primary operator and secondary operators. Computer graphics is a key operator interface component in the control station where new types of manual interface devices also are employed. The results of some generic and applications task experiments are summarized, including the performance of a simulated remote satellite servicing task, carried out under four to eight seconds communications time delay, using satellite TV and Internet computer communication links. In conclusion, the paper highlights the lessons learned so far,.

remote control communications delay automation↗

Fostering Geothermal Machine Learning Success: Elevating Big Data Accessibility and Automated Data Standardization in the Geothermal Data Repository: Preprint

The Department of Energy's (DOE) Geothermal Data Repository (GDR) has implemented improvements to both its data lakes and its data standards and automated data pipelines. The GDR data lakes have reduced storage and compute-related barriers to using large geothermal datasets, enabling these large datasets to be accessed by anyone with a modern computer and internet access. More recently, the GDR has been working to further reduce barriers through streamlining the data intake process, educating users on the process and requirements, and aiding users in accessing data from the data lakes. These improvements have augmented the quantity of datasets the GDR is able to accept into its data lakes and have enabled users who are new to cloud tools to access these datasets more easily, overall increasing the accessibility of big geothermal data for use in machine learning and other projects. In addition, the GDR now has built-in data standards and pipelines for drilling data, geospatial data, and distributed acoustic sensing (DAS) data. These standardization efforts aim to enhance the real-world applicability of geothermal machine learning outcomes by improving the quality of training data. Specifically, through standardizing high-value datasets, the GDR is reducing project-specific data curation requirements, thus allowing more time for actual research. By automating this process, the burden of standardization is lifted from the user, ultimately increasing the availability of standardized data.

accessibility↗

Decision blocks: A tool for automating decision making in CLIPS

The human capability of making complex decision is one of the most fascinating facets of human intelligence, especially if vague, judgemental, default or uncertain knowledge is involved. Unfortunately, most existing rule based forward chaining languages are not very suitable to simulate this aspect of human intelligence, because of their lack of support for approximate reasoning techniques needed for this task, and due to the lack of specific constructs to facilitate the coding of frequently reoccurring decision block to provide better support for the design and implementation of rule based decision support systems. A language called BIRBAL, which is defined on the top of CLIPS, for the specification of decision blocks, is introduced. Empirical experiments involving the comparison of the length of CLIPS program with the corresponding BIRBAL program for three different applications are surveyed. The results of these experiments suggest that for decision making intensive applications, a CLIPS program tends to be about three times longer than the corresponding BIRBAL program.

Eick, Christoph F.↗

Simulating excited-state complex ensembles: Fluorescence and solvatochromism in amine-arene exciplexes

Exciplexes are excited-state complexes formed as a result of partial charge transfer from the donor to the acceptor species when one moiety of the donor–acceptor pair is electronically excited. The arene–amine exciplex formed between oligo-(p-phenylene) (OPP) and triethylamine (TEA) is of interest in the catalytic photoreduction of CO2 because it can compete with complete electron transfer to the OPP catalyst. Therefore, formation of the exciplex can hinder the generation of a radical anion OPP·− necessary for subsequent CO2 reduction. We report an implementation of a workflow automating quantum-chemistry calculations that generate and characterize an ensemble of structures to represent this exciplex state. We use FireWorks, Pymatgen, and Custodian Python packages for high-throughput ensemble generation. The workflow includes time-dependent density functional theory optimization, verification of excited-state minima, and exciplex characterization with natural transition orbitals, exciton analysis, excited-state Mulliken charges, and energy decomposition analysis. Fluorescence spectra computed for these ensembles using Boltzmann-weighted contributions of each structure agree better with experiment than our previous calculations based on a single representative exciplex structure [Kron et al., J. Phys. Chem. A 126, 2319–2329 (2022)]. The ensemble description of the exciplex state also reproduces an experimentally observed red shift of the emission spectrum of [OPP-4–TEA]* relative to [OPP-3–TEA]*. The workflow developed here streamlines otherwise labor-intensive calculations that would require significant user involvement and intervention.

Chemistry↗

An integrative approach to space-flight physiology using systems analysis and mathematical simulation

An approach was developed to aid in the integration of many of the biomedical findings of space flight, using systems analysis. The mathematical tools used in accomplishing this task include an automated data base, a biostatistical and data analysis system, and a wide variety of mathematical simulation models of physiological systems. A keystone of this effort was the evaluation of physiological hypotheses using the simulation models and the prediction of the consequences of these hypotheses on many physiological quantities, some of which were not amenable to direct measurement. This approach led to improvements in the model, refinements of the hypotheses, a tentative integrated hypothesis for adaptation to weightlessness, and specific recommendations for new flight experiments.

Leonard, J. I.↗

The Language Research Center's Computerized Test System for environmental enrichment and psychological assessment

In the spring of 1987, we undertook to provide environmental enrichment to nonhuman primate subjects in ways that would complement and even contribute to the bio-behaviorial science that justified the monkeys' captivity. Of course, the psychological well-being of captive primates--and indeed all research species-- has been an area of intense research activity since the 1985 amendment of the Animal Welfare Act. This mandate for researchers to ensure the psychological, as well as physical, fitness of experimental animals catalyzed the humane and scientific interests of the research community. The contemporary literature is replete with proposed means both of assaying and of providing enrichment and well-being. Notwithstanding, consensus on either assessment or intervention has yet to be reached. The paradigm we employed was modelled after successful efforts with chimpanzees. An automated test system was constructed in which subjects responded to computer tasks by manipulating a joystick. The tasks, interactive game-like versions of many of the classic testing paradigms of cognitive and comparative psychology, permitted the controlled presentation of stimuli and demands without the required presence of a human experimenter. Despite significant barriers to the success, rhesus monkeys (Macaca mulatta) and a variety of other primate species (including, of course, humans) have mastered the skills necessary for testing in this paradigm. Previous experiments have illustrated the utility of the test system for addressing questions of learning, memory, attention, perception, and motivation. Additional data have been reported to support the contention that the Language Research Center's Computerized Test System (LRC-CTS) serves its other raison d'etre--providing environmental enrichment and assessing psychological well-being. This paper is designed to augment previous descriptions of the technology and the paradigm for scientists and caretakers interested in environmental enrichment and performance assessment with primates.

Non-NASA Center↗

Piloted Well Clear Performance Evaluation of Detect and Avoid Systems with Suggestive Guidance

Regulations to establish operational and performance requirements for unmanned aircraft systems (UAS) are being developed by a consortium of government, industry and academic institutions (RTCA, 2013). Those requirements will apply to the new detect-and-avoid (DAA) systems and other equipment necessary to integrate UAS with the United States (U.S) National Airspace System (NAS) and will be determined according to their contribution to the overall safety case. That safety case requires demonstration that DAA-equipped UAS collectively operating in the NAS meet an airspace safety threshold (AST). Several key gaps must be closed in order to link equipment requirements to an airspace safety case. Foremost among these is calculation of the systems risk ratio, the degree to which a particular system mitigates violation of an aircraft separation standard (FAA, 2013). The risk ratio of a DAA system, in combination with risk ratios of other collision mitigation mechanisms, will determine the overall safety of the airspace measured in terms of the number of collisions per flight hour. It is not known what the effectiveness is of a pilot-in-the-loop DAA system or even what parameters of the DAA system most improve the pilots ability to maintain separation. The relationship between the DAA system design and the overall effectiveness of the DAA system that includes the pilot, expressed as a risk ratio, must be determined before DAA operational and performance requirements can be finalized. Much research has been devoted to integrating UAS into non-segregated airspace (Dalamagkidis, 2009, Ostwald, 2007, Gillian, 2012, Hesselink, 2011, Santiago, 2015, Rorie 2015 and 2016). Several traffic displays intended for use as part of a DAA system have gone through human-in-the-loop simulation and flight-testing. Most of these evaluations were part of development programs to produce a deployable system, so it is unclear how to generalize particular aspects of those designs to general requirements for future traffic displays (Calhoun, 2014). Other displays have undergone testing to collect data that may generalize to new displays, but have not been evaluated in the context of the development of an overall safety case for UAS equipped with DAA systems in the NAS (Bell, 2012). Other research efforts focus on DAA surveillance performance and separation standards. Together with this work, they are expected to facilitate validation of the airspace safety case (Park, 2014 and Johnson, 2015). The contribution of the present work is to quantify the effectiveness of the pilot-automation system to remain well clear as a function of display features and surveillance sensor error. This quantification will help enable selection of a minimum set of DAA design features that meets the AST, a set that may not be unique for all UAS platforms. A second objective is to collect and analyze pilot performance parameters that will improve the modeling of overall DAA system performance in non-human-in-the-loop simulations. Simulating the DAA-equipped UAS in such batch experiments will allow investigation of a much larger number of encounters than is possible in human simulations. This capability is necessary to demonstrate that a particular set of DAA requirements meets the AST under all foreseeable operational conditions.

detect and avoid↗

High School Citizen Scientists Use AI/ML to Predict Intra-Ocular Pressure From Gene Expression Data for Spaceflown Mice

Artificial Intelligence (AI) and Machine Learning (ML) have increasingly become pivotal in biological and biomedical research, largely due to the culture of open data sharing and its associated benefits. The methodologies inherent in AI/ML are particularly adept at identifying and forecasting biological phenotypes from the vast amounts of data generated by next-generation sequencing technologies. These techniques offer substantial promise for advancing research in space biosciences and for the development of automated systems for monitoring space health. Nevertheless, there are crucial aspects to consider when training, validating, and testing machine learning models in both biological research and clinical contexts. It is essential that Open Science principles, including data sharing and the availability of open-source code, are complemented by high-quality, publicly accessible training resources. These resources should focus on best practices and include modules based on real-world scientific cases and data to ensure that future AI/ML practitioners gain practical experience with genuine problems. Addressing this knowledge gap, we have designed, developed, and delivered both interactive and self-paced training programs for citizen scientists worldwide, enabling them to utilize AI/ML for space biology research. This initiative was made possible through generous funding from a Transformation to Open Science Training grant. The interactive training sessions, conducted this summer, utilized AI/ML techniques to analyze data from the Open Science Data Repository, specifically targeting the effects of spaceflight on ocular structure and function. The dataset OSD-583, from the Rodent Research 9 mission, provides experimental data detailing the ocular responses of mice subjected to a 35-day spaceflight, compared with ground control counterparts. Using OSD-583 as observational data, our summer training participants applied AI/ML methods to predict intraocular pressure from RNA-seq data and identify the genes most predictive of the observed responses. Further analysis through pathway enrichment and gene set enrichment revealed that these genes are involved in molecular and cellular processes contributing to retinal degeneration.

James Casaletto↗

ExaWorks software development kit: a robust and scalable collection of interoperable workflows technologies

Scientific discovery increasingly requires executing heterogeneous scientific workflows on high-performance computing (HPC) platforms. Heterogeneous workflows contain different types of tasks (e.g., simulation, analysis, and learning) that need to be mapped, scheduled, and launched on different computing. That requires a software stack that enables users to code their workflows and automate resource management and workflow execution. Currently, there are many workflow technologies with diverse levels of robustness and capabilities, and users face difficult choices of software that can effectively and efficiently support their use cases on HPC machines, especially when considering the latest exascale platforms. We contributed to addressing this issue by developing the ExaWorks Software Development Kit (SDK). The SDK is a curated collection of workflow technologies engineered following current best practices and specifically designed to work on HPC platforms. We present our experience with (1) curating those technologies, (2) integrating them to provide users with new capabilities, (3) developing a continuous integration platform to test the SDK on DOE HPC platforms, (4) designing a dashboard to publish the results of those tests, and (5) devising an innovative documentation platform to help users to use those technologies. Our experience details the requirements and the best practices needed to curate workflow technologies, and it also serves as a blueprint for the capabilities and services that DOE will have to offer to support a variety of scientific heterogeneous workflows on the newly available exascale HPC platforms.

97 MATHEMATICS AND COMPUTING↗