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At least 541 records · Page 30

Wide-field Hard X-ray Survey with ART-XC

The Astronomical Roentgen Telescope X-ray Concentrator (ART-XC) instrument onboard the Spectrum Röntgen Gamma (SRG) mission began the 4-year all-sky hard X-ray survey since December 2019 and has already completed four scans of the sky. The observations of the ecliptic pole regions will reach exceptional depth thanks to the survey design of overlapping exposure in these regions. We will discuss the progress of the ART-XC survey in the North Ecliptic Pole (NEP) region so far, including the status of the data reduction and analysis pipeline as well as the survey results.

Chien-Ting Chen↗

NASA's Unsteady Pressure-Sensitive Paint Research and Operational Capability Developments

In the last three years, several advancements have been made to produce a new state-of-the-art capability in the field of Aerosciences. NASA’s Aerosciences Evaluations and Test Capabilities (AETC) Portfolio Office has funded a multi-year project to produce the unsteady Pressure-Sensitive Paint (uPSP) technology as an operational capability in key ground test facilities at NASA. The research and development has primarily been conducted at NASA Ames Research Center’s (ARC) Unitary Plan Wind Tunnel (UPWT) 11-by 11-ft Transonic Wind Tunnel (TWT). The NASA ARC UPWT is one of the ground test facilities under NASA AETC’s Portfolio Office. AETC’s goals are to provide the tools to deliver the technology innovations and breakthroughs necessary to address increasingly complex research and development challenges. AETC’s integrated approach will consider the complimentary high-end compute capabilities necessary to advance analysis in conjunction with ground experimental capabilities. The uPSP Capability Challenge Project is a demonstration of several different technologies: 1) the unsteady Pressure-Sensitive Paint (uPSP) technology, and 2) Project: Red Rover, establishing a secure, reliable, fast connection between experimental and computation facilities, leveraging NASA’s computational resources within the High-End Compute Capability (HECC) Project for processing, storing, and sharing data efficiently. This project demonstrates the technical diversity and technical inclusion need to advance the field of Aerosciences. The approach to combine subject matter experts in experimental methods, optical methods, production wind tunnel testing, network engineering, high-end computing, signal processing, grid generation, and visualization while establishing the required infrastructure for subject matter experts to have access to the data while the wind tunnel test is being conducted. The most recent advancements for the uPSP technology have focused on three key areas: development of data products, robust processing pipeline, operational efficiencies and uncertainty quantification.

buffet↗

Effective Defect Detection Using Instance Segmentation for NDI

Ultrasonic testing is a common Non-Destructive Inspection (NDI) method used in aerospace manufacturing. However, the complexity and size of the ultrasonic scans make it challenging to identify defects through visual inspection or machine learning models. Using computer vision techniques to identify defects from ultrasonic scans is an evolving research area. In this study, we used instance segmentation to identify the presence of defects in the ultrasonic scan images of composite panels that are representative of real components manufactured in aerospace. We used two models based on Mask- RCNN (Detectron 2) and YOLO 11 respectively. Additionally, we implemented a simple statistical pre-processing technique that reduces the burden of requiring custom-tailored pre-processing techniques. Our study demonstrates the feasibility and effectiveness of using instance segmentation in the NDI pipeline by significantly reducing data pre-processing time, inspection time, and overall costs.

computer vision techniques↗

Application of unsupervised deep learning to image segmentation and in-situ contact angle measurements in a CO 2 -water-rock system

Rock surface wettability is a critical property that regulates multiphase flows in porous media, which can be quantified using the surface contact angle (CA). X-ray micro-computed tomography (μCT) provides an effective approach to in-situ measurements of surface CAs. However, the CA measurement accuracy depends significantly on the quality of CT image segmentation, which is the clustering of CT pixels into separate phases. Inspired by this, we developed a deep learning (DL)-based CA measurement workflow. Motivated by the recent tremendous progress in unsupervised learning techniques and aiming to avoid expensive manual data annotations, an unsupervised DL pipeline for CT image segmentation was proposed and implemented, which includes unsupervised model training and post-processing. The unsupervised model training was driven by a novel loss function constrained with feature similarity and spatial continuity and implemented by iterative forward and backward paths; the former clustered the pixel-wise feature vectors extracted by convolution neural networks, whereas the latter updated the parameters using gradient descent. An over-segmentation strategy was adopted for model training. The post-processing steps based on agglomerative hierarchical clustering (AHC) were implemented to further merge the over-segmented model output to the desired cluster number, which is intended to improve the efficiency of image segmentation. The developed unsupervised DL pipeline was compared with other commonly-used image segmentation methods using pixel-wise and physics-based evaluation metrics on a synthetic raw-image dataset, which had a known ground truth. The unsupervised DL pipeline showed the best performance. Next, the segmented images were input to an automatic CA measurement tool, and the results were validated by comparisons with manual measurements. The CA values from the manual and automatic measurements showed similar distributions and statistical properties. The automatic measurement demonstrated a wider spectrum because of the much larger number of measurement data points. The primary novelty of the unsupervised DL pipeline developed in this study lies in the novel loss function and the over-segmentation strategy associated with AHC post-processing. Finally, the workflow has been proven an efficient tool for pore-scale wettability characterization, which has a wide range of applications in fundamental studies of multiphase flows in natural porous media, which have critical implications to geological carbon sequestration, hydrocarbon energy recovery, and contaminant transport in groundwater.

42 ENGINEERING↗

The HEASARC Swift Gamma-Ray Burst Archive: The Pipeline and the Catalog

Since its launch in late 2004, the Swift satellite triggered or observed an average of one gamma-ray burst (GRB) every 3 days, for a total of 771 GRBs by 2012 January. Here, we report the development of a pipeline that semi automatically performs the data-reduction and data-analysis processes for the three instruments on board Swift (BAT, XRT, UVOT). The pipeline is written in Perl, and it uses only HEAsoft tools and can be used to perform the analysis of a majority of the point-like objects (e.g., GRBs, active galactic nuclei, pulsars) observed by Swift. We run the pipeline on the GRBs, and we present a database containing the screened data, the output products, and the results of our ongoing analysis. Furthermore, we created a catalog summarizing some GRB information, collected either by running the pipeline or from the literature. The Perl script, the database, and the catalog are available for downloading and querying at the HEASARC Web site.

BURST ARCHIVE↗

GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics dataand collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretationof the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLabhave begunand will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Samrawit Getachew Gebre↗

GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data, and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Samrawit Gebre↗

WEBINAR, May 6: New Discoveries Using GeneLab

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetry data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

Sylvain V. Costes↗

NASA GeneLab: Open Science for Life in Space

The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 350 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab Sequencing Lab. The GLDS contains rich metadata about each experiment and has integrated radiation dosimetry data from experiments flown on the Space Shuttle, International Space Station, and Free Flying spacecrafts. With the increasing amount and complexity of omics data being generated, GeneLab utilizes community-defined, common models for metadata and terminology so that omics data and results are discoverable and reliably reproducible. GeneLab uses the ISA-Tab specification and semantic model for organizing and representing omics metadata. In addition to metadata standards, data files must be open-source file or common exchange formats to ensure accessibility and usability by all users. To ease data ingestion and transfer, the web-based submission tool allows PIs a user-friendly user interface to curate, organize, and publish their space relevant omics data. In the more recent years, data curation and submission portal has incorporated the FAIR principles making data findable, accessible, interoperable, and reusable. To increase reusability of data, GeneLab has implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 200 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. To train the next generation of scientists, NASA offers training programs such as GeneLab 4 High School (GL4HS) and GeneLab 4 Universities. NLM Curation at a Scale Workshop 2022 | NASA GeneLab (GL4U) to teach students bioinformatics and computational biology methods to analyze omics data. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.

GeneLab↗

The ISO SWS on-line system

The software which is currently being developed for the Short Wavelength Spectrometer (SWS) of the Infrared Space Observatory (ISO) is described. The spectrometer has a wide range of capabilities in the 2-45 micron infrared band. SWS contains two independent gratings, one for the long and one for the short wavelength section of the band. With the gratings a spectral resolution of approximately 1000 to approximately 2500 can be obtained. The instrument also contains two Fabry-Perault's yielding a resolution between approximately 1000 and approximately 20000. Software is currently being developed for the acquisition, calibration, and analysis of SWS data. The software is firstly required to run in a pipeline mode without human interaction, to process data as they are received from the telescope. However, both for testing and calibration of the instrument as well as for evaluation of the planned operating procedures the software should also be suitable for interactive use. Thirdly the same software will be used for long term characterization of the instrument. The software must work properly within the environment designed by the European Space Agency (ESA) for the spacecraft operations. As a result strict constraints are put on I/O devices, throughput etc.

Roelfsema, P. R.↗

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function

Computational biology is one of many scientific disciplines ripe for innovation and acceleration with the advent of high-performance computing (HPC). In recent years, the field of machine learning has also seen significant benefits from adopting HPC practices. In this work, we present a novel HPC pipeline that incorporates various machine-learning approaches for structure-based functional annotation of proteins on the scale of whole genomes. Our pipeline makes extensive use of deep learning and provides computational insights into best practices for training advanced deep-learning models for high-throughput data such as proteomics data. We showcase methodologies our pipeline currently supports and detail future tasks for our pipeline to envelop, including large-scale sequence comparison using SAdLSA and prediction of protein tertiary structures using AlphaFold2.

Gao, Mu↗

Quasi-Distributed Fiber Sensor-Based Approach for Pipeline Health Monitoring: Generating and Analyzing Physics-Based Simulation Datasets for Classification

This study presents a framework for detecting mechanical damage in pipelines, focusing on generating simulated data and sampling to emulate distributed acoustic sensing (DAS) system responses. The workflow transforms simulated ultrasonic guided wave (UGW) responses into DAS or quasi-DAS system responses to create a physically robust dataset for pipeline event classification, including welds, clips, and corrosion defects. This investigation examines the effects of sensing systems and noise on classification performance, emphasizing the importance of selecting the appropriate sensing system for a specific application. The framework shows the robustness of different sensor number deployments to experimentally relevant noise levels, demonstrating its applicability in real-world scenarios where noise is present. Overall, this study contributes to the development of a more reliable and effective method for detecting mechanical damage to pipelines by emphasizing the generation and utilization of simulated DAS system responses for pipeline classification efforts. The results on the effects of sensing systems and noise on classification performance further enhance the robustness and reliability of the framework.

36 MATERIALS SCIENCE↗

Implementation and Comparison of Acoustic Travel-Time Measurement Procedures for the Solar Dynamics Observatory-Helioseismic and Magnetic Imager Time-Distance Helioseismology Pipeline

The Helioseismic and Magnetic Imager (HMI) instrument onboard the Solar Dynamics Observatory (SDO) satellite is designed to produce high-resolution Doppler-velocity maps of oscillations at the solar surface with high temporal cadence. To take advantage of these high-quality oscillation data, a time - distance helioseismology pipeline (Zhao et al., Solar Phys. submitted, 2010) has been implemented at the Joint Science Operations Center (JSOC) at Stanford University. The aim of this pipeline is to generate maps of acoustic travel times from oscillations on the solar surface, and to infer subsurface 3D flow velocities and sound-speed perturbations. The wave travel times are measured from cross-covariances of the observed solar oscillation signals. For implementation into the pipeline we have investigated three different travel-time definitions developed in time - distance helioseismology: a Gabor-wavelet fitting (Kosovichev and Duvall, SCORE'96: Solar Convection and Oscillations and Their Relationship, ASSL, Dordrecht, 241, 1997), a minimization relative to a reference cross-covariance function (Gizon and Birch, Astrophys. J. 571, 966, 2002), and a linearized version of the minimization method (Gizon and Birch, Astrophys. J. 614, 472, 2004). Using Doppler-velocity data from the Michelson Doppler Imager (MDI) instrument onboard SOHO, we tested and compared these definitions for the mean and difference traveltime perturbations measured from reciprocal signals. Although all three procedures return similar travel times in a quiet-Sun region, the method of Gizon and Birch (Astrophys. J. 614, 472, 2004) gives travel times that are significantly different from the others in a magnetic (active) region. Thus, for the pipeline implementation we chose the procedures of Kosovichev and Duvall (SCORE'96: Solar Convection and Oscillations and Their Relationship, ASSL, Dordrecht, 241, 1997) and Gizon and Birch (Astrophys. J. 571, 966, 2002). We investigated the relationships among these three travel-time definitions, their sensitivities to fitting parameters, and estimated the random errors that they produce.

HMI↗

Evaluation of existing and proposed computer architectures for future ground-based systems

Parallel processing architectures and techniques used in current supercomputers are described and projections are made of future advances. Presently, the von Neumann sequential processing pattern has been accelerated by having separate I/O processors, interleaved memories, wide memories, independent functional units and pipelining. Recent supercomputers have featured single-input, multiple data stream architectures, which have different processors for performing various operations (vector or pipeline processors). Multiple input, multiple data stream machines have also been developed. Data flow techniques, wherein program instructions are activated only when data are available, are expected to play a large role in future supercomputers, along with increased parallel processor arrays. The enhanced operational speeds are essential for adequately treating data from future spacecraft remote sensing instruments such as the Thematic Mapper.

Schulbach, C.↗

Learning epistatic polygenic phenotypes with Boolean interactions

Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1 , a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.

59 BASIC BIOLOGICAL SCIENCES↗

NASA GeneLab RNASeq Consensus Pipeline: A Nextflow Implementation

The NASA GeneLab project (genelab.nasa.gov) seeks to accelerate space biology research through cataloging and democratizing omics data. Since raw omics data is largely inaccessible to non-bioinformaticians, GeneLab works with the scientific community to develop standard processing pipelines to generate and publish processed data. Unlike raw data, processed data has greater immediate value to a wide range of users with varying technical backgrounds and computational capabilities. Standardizing processing workflows is essential to match the pace of raw data generation, ensure reproducibility, and enable standardized processed data for comparison across datasets. Previously, GeneLab developed a standardized pipeline for processing RNAseq data, referred to as the ‘GeneLab RNAseq Consensus Pipeline (RCP)’, in collaboration with GeneLab’s Analysis Working Groups. The work presented here is a Nextflow implementation of GeneLab’s RCP that automates and accelerates data processing of RNASeq datasets hosted on GeneLab. In addition to the core data processing, the workflow also includes staging of GeneLab raw data and a robust verification and validation (V&V) program that runs after each processing step to identify errors in real-time, stop additional downstream computation, and preserve computational resources. The workflow, including the staging and V&V functionality, is open source for others to reuse and modify at https://github.com/nasa/GeneLab_Data_Processing/tree/master/RNAseq.

Jonathan Dejesus Oribello↗

NASA GeneLab RNASeq Consensus Pipeline: A Nextflow Implementation

The NASA GeneLab project (genelab.nasa.gov) seeks to accelerate space biology research through cataloging and democratizing omics data. Since raw omics data is largely inaccessible to non-bioinformaticians, GeneLab works with the scientific community to develop standard processing pipelines to generate and publish processed data. Unlike raw data, processed data has greater immediate value to a wide range of users with varying technical backgrounds and computational capabilities. Standardizing processing workflows is essential to match the pace of raw data generation, ensure reproducibility, and enable standardized processed data for comparison across datasets. Previously, GeneLab developed a standardized pipeline for processing RNAseq data, referred to as the ‘GeneLab RNAseq Consensus Pipeline (RCP)’, in collaboration with GeneLab’s Analysis Working Groups. The work presented here is a Nextflow implementation of GeneLab’s RCP that automates and accelerates data processing of RNASeq datasets hosted on GeneLab. In addition to the core data processing, the workflow also includes staging of GeneLab raw data and a robust verification and validation (V&V) program that runs after each processing step to identify errors in real-time, stop additional downstream computation, and preserve computational resources. The workflow, including the staging and V&V functionality, is open source for others to reuse and modify at https://github.com/nasa/GeneLab_Data_Processing/tree/master/RNAseq.

Jonathan D Oribello↗

EV-ELM (Electric Vehicle Policies with the Energy Language Model) [SWR-25-156]

Electric Vehicle Policies with the Energy Language Model (EV-ELM) leverages previous work using Large Language Models (LLMs) to find, download, and parse policy information related to energy infrastructure. In this application, we use LLMs to find policy documents related to the permitting and installation of electric vehicle charging infrastructure. This software contains the code to find, download, and parse these documents, while a related data record in the Open Energy Data Initiative (OEDI) will include the resulting output dataset that can be used for downstream analysis. The EV-ELM repository contains code for the EV-ELM project, which focuses on retrieving and processing EV permitting processes using large language models. The project is composed of two pipelines: (1) a web scraping pipeline for discovering and downloading EV permitting documents, and (2) a document parsing and extraction pipeline that processes the downloaded files to produce structured data. The web scraping pipeline is designed to extract relevant information from various websites, while the document parsing pipeline processes and analyzes the extracted documents to derive meaningful insights. Both pipelines depend on the NLR elm repository, which provides essential tools and functionalities for handling and processing the data. The web scraping pipeline is a modified version of the ordinance_gpt example within the elm repository. It has been adapted to fit the specific requirements of the EV-ELM project, ensuring that it effectively captures and processes the necessary information related to EV permitting.

Olson, Reid [National Laboratory of the Rockies (N↗