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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Development and validation of a 30-day mortality index based on pre-existing medical administrative data from 13,323 COVID-19 patients: The Veterans Health Administration COVID-19 (VACO) Index

Background Available COVID-19 mortality indices are limited to acute inpatient data. Using nationwide medical administrative data available prior to SARS-CoV-2 infection from the US Veterans Health Administration (VA), we developed the VA COVID-19 (VACO) 30-day mortality index and validated the index in two independent, prospective samples. Methods and findings We reviewed SARS-CoV-2 testing results within the VA between February 8 and August 18, 2020. The sample was split into a development cohort (test positive between March 2 and April 15, 2020), an early validation cohort (test positive between April 16 and May 18, 2020), and a late validation cohort (test positive between May 19 and July 19, 2020). Our logistic regression model in the development cohort considered demographics (age, sex, race/ethnicity), and pre-existing medical conditions and the Charlson Comorbidity Index (CCI) derived from ICD-10 diagnosis codes. Weights were fixed to create the VACO Index that was then validated by comparing area under receiver operating characteristic curves (AUC) in the early and late validation cohorts and among important validation cohort subgroups defined by sex, race/ethnicity, and geographic region. We also evaluated calibration curves and the range of predictions generated within age categories. 13,323 individuals tested positive for SARS-CoV-2 (median age: 63 years; 91% male; 42% non-Hispanic Black). We observed 480/3,681 (13%) deaths in development, 253/2,151 (12%) deaths in the early validation cohort, and 403/7,491 (5%) deaths in the late validation cohort. Age, multimorbidity described with CCI, and a history of myocardial infarction or peripheral vascular disease were independently associated with mortality–no other individual comorbid diagnosis provided additional information. The VACO Index discriminated mortality in development (AUC = 0.79, 95% CI: 0.77–0.81), and in early (AUC = 0.81 95% CI: 0.78–0.83) and late (AUC = 0.84, 95% CI: 0.78–0.86) validation. The VACO Index allows personalized estimates of 30-day mortality after COVID-19 infection. For example, among those aged 60–64 years, overall mortality was estimated at 9% (95% CI: 6–11%). The Index further discriminated risk in this age stratum from 4% (95% CI: 3–7%) to 21% (95% CI: 12–31%), depending on sex and comorbid disease. Conclusion Prior to infection, demographics and comorbid conditions can discriminate COVID-19 mortality risk overall and within age strata. The VACO Index reproducibly identified individuals at substantial risk of COVID-19 mortality who might consider continuing social distancing, despite relaxed state and local guidelines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Data for Clumping Index Estimation With 30°-tilted Cameras in Row Crops: Evaluation of Methods and Segment Size Effects

The clumping index (CI) quantifies the spatial distribution of foliage elements and is essential for accurately estimating the plant area index (PAI), canopy radiative transfer, and photosynthesis. Traditionally, the finite-length averaging method (LX), the gap size distribution method (CC), and a combined approach of CC and LX (CLX) have been applied to instruments like TRAC and digital hemispherical photography to estimate CI. However, a comprehensive evaluation of these methods in row crops remains limited, especially regarding the influence of segment size on CI. Meanwhile, digital cameras offer a cost-effective and user-friendly solution for canopy measurements in row crops, yet their application in this context remains underexplored. In this study, we employed a new approach using a 30°-tilted digital camera to estimate CI in corn and soybean fields, applying the LX, CC, and CLX methods. We systematically assessed the performance of these three methods by combining field measurements in real-world fields with simulations using the LESS 3D radiative transfer model. Our results showed that CLX applied to the whole image and 45° segment offered accurate estimation of CI (bias within ±0.1, RMSE < 0.2) and PAI (bias within ±0.4, RMSE < 1) in real-world fields and LESS simulations. The accuracy of the LX method was highly sensitive to segment size, with the best performance observed at the 15° segment (PAI bias within ±0.4). In contrast, the CC method remained stable across different segment sizes, and its performance was generally comparable to that of LX, except at the 15° segment. Across view zenith angles, CI derived from CC generally showed a continuous increase, while those from LX and CLX followed a rising trend at small zenith angles but began to decline at 68°, likely due to an increasing proportion of no-gap segments. Seasonally, LX tended to show decreasing CI during early growth stages but increased as the canopy matured, whereas CC and CLX showed gradually increasing CI before plateauing at peak PAI. The 30°-tilted camera effectively captured CI variations across different angles and growth stages, making it a practical and robust instrument for row crop canopy structure analysis. Applying these CI methods to digital cameras offers a low-cost and accessible CI estimation alternative, improving canopy structure monitoring accuracy in row crops.

Modeling↗
DOE OSTI2020

NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2013

The Global Land-Ocean Temperature Index in Relation to Sunspot Number, the Atlantic Multidecadal Oscillation Index, the Mauna Loa Atmospheric Concentration of CO2, and Anthropogenic Carbon Emissions

Global warming/climate change has been a subject of scientific interest since the early 19th century. In particular, increases in the atmospheric concentration of carbon dioxide (CO2) have long been thought to account for Earth's increased warming, although the lack of a dependable set of observational data was apparent as late as the mid 1950s. However, beginning in the late 1950s, being associated with the International Geophysical Year, the opportunity arose to begin accurate continuous monitoring of the Earth's atmospheric concentration of CO2. Consequently, it is now well established that the atmospheric concentration of CO2, while varying seasonally within any particular year, has steadily increased over time. Associated with this rising trend in the atmospheric concentration of CO2 is a rising trend in the surface-air and sea-surface temperatures (SSTs). This Technical Publication (TP) examines the statistical relationships between 10-year moving averages (10-yma) of the Global Land-Ocean Temperature Index (GLOTI), sunspot number (SSN), the Atlantic Multidecadal Oscillation (AMO) index, and the Mauna Loa CO2 (MLCO2) index for the common interval 1964-2006, where the 10-yma values are used to indicate trends in the data. Scatter plots using the 10-yma values between GLOTI and each of the other parameters are determined, both as single-variate and multivariate fits. Scatter plots are also determined for MLCO2 using single-variate and bivariate (BV) fits, based on the GLOTI alone and the GLOTI in combination with the AMO index. On the basis of the inferred preferential fits for MLCO2, estimates for MLCO2 are determined for the interval 1885-1964, thereby yielding an estimate of the preindustrial level of atmospheric concentration of CO2. Lastly, 10-yma values of MLCO2 are compared against 10-yma estimates of the total carbon emissions (TCE) to determine the likelihood that manmade sources of carbon emissions are indeed responsible for the recent warming now being experienced. (Parametric values used in this TP are those available prior to the end of 2012.)

Wilson, Robert M.↗
NASA NTRS2020

Fluorescence Correction Vegetation Index (FCVI): A physically based reflectance index to separate physiological and non-physiological information in far-red sun-induced chlorophyll fluorescence

Sun-induced chlorophyll fluorescence (SIF) has been used to track vegetation photosynthetic activity for improving estimation of gross primary productivity (GPP) and detecting plant stress. There are both physical and physiological controls of SIF measured at the surface and retrieved from remote sensing including satellite observations. In order to accurately use SIF for monitoring of plant physiology, the effects of physically-based radiation processes related to leaf and canopy structure, notably photosynthetically active radiation (PAR) absorption and SIF scattering and re-absorption, must be characterized. In this study, we investigate both PAR absorption and SIF scattering processes and find that although it is difficult to quantify their effects individually by using just reflectance, the combined effects of the two processes can be well approximated by a reflectance index. This index, referred to as FCVI (Fluorescence Correction Vegetation Index), is defined as the difference between near-infrared (NIR) and broad-band visible (VIS, 400–700 nm) reflectance acquired under identical sun-canopy-observer geometry of the SIF measurements. The development of the index was based on the physical connection between reflectance and far-red SIF, which was revealed by using the spectral invariant theory. The utility of FCVI to correct far-red SIF for PAR absorption and scattering effects, thus improving the link to photosynthesis, was tested with data from: (i) a field experiment for a growing season; and (ii) a numerical experiment which included a number of scenarios generated by a radiative transfer model. For both the observations and simulations, the FCVI provided a promising estimate of the impact of the physically-based radiation processes on far-red SIF of moderately dense canopies (i.e., FCVI ≥ 0.18). Normalizing the TOC far-red SIF by both the incident PAR (iPAR) and the FCVI provided a good estimate of the far-red fluorescence emission efficiency of the canopies examined. This approach enhances our ability to generalize retrievals for vegetation processes as they change through natural growth phases and seasons. Taken together, far-red SIF and FCVI may enable the assessment of the light partitioning of vegetation canopies, an essential step to facilitate the use of far-red SIF for tracking physiological processes.

Peiqi Yang↗
DOE OSTI2021

State Government Revenue Vulnerability Index and Local Government Revenue Vulnerability Index

The State Government Revenue Vulnerability Index (SGRVI) and Local Government Revenue Vulnerability Index (LGRVI) measure the vulnerability of government revenues by estimating monthly changes relative to a January 2020 baseline. Revenues included in both indices include: taxes on products and sales, transportation and housing revenues, individual income taxes, severance taxes and royalties, and property taxes. Local government revenues also include a local revenue from state revenue sharing component. In addition, the main index for the LGRVI for county-level governments includes revenue estimates for sub-county government units, including municipalities, school districts, and special districts. This revenue data is aggregated to produce the indices.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
NASA NTRS1990

Retrospective indexing (RI) - A computer-aided indexing technique

An account is given of a method for data base-updating designated 'computer-aided indexing' (CAI) which has been very efficiently implemented at NASA's Scientific and Technical Information Facility by means of retrospective indexing. Novel terms added to the NASA Thesaurus will therefore proceed directly into both the NASA-RECON aerospace information system and its portion of the ESA-Information Retrieval Service, giving users full access to material thus indexed. If a given term appears in the title of a record, it is given special weight. An illustrative graphic representation of the CAI search strategy is presented.

Buchan, Ronald L.↗
NASA NTRS1992

VIEWCACHE: An incremental pointer-base access method for distributed databases. Part 1: The universal index system design document. Part 2: The universal index system low-level design document. Part 3: User's guide. Part 4: Reference manual. Part 5: UIMS test suite

The goal of the Universal Index System (UIS), is to provide an easy-to-use and reliable interface to many different kinds of database systems. The impetus for this system was to simplify database index management for users, thus encouraging the use of indexes. As the idea grew into an actual system design, the concept of increasing database performance by facilitating the use of time-saving techniques at the user level became a theme for the project. This Final Report describes the Design, the Implementation of UIS, and its Language Interfaces. It also includes the User's Guide and the Reference Manual.

Kelley, Steve↗
DOE OSTI2020

Enhanced predictability of Eastern North Pacific Tropical cyclone activity using the ENSO Longitude Index

Past studies have indicated that El Nino-Southern Oscillation (ENSO) plays a major role in the interannual variability of Eastern Pacific hurricane activity. The primary mechanism being the eastward displacement of the warm pool during an El Nino, which carries warm water into that basin thereby creating favorable oceanic conditions. Despite this, the question of whether an accurate knowledge of ENSO enhances seasonal predictabiity of Eastern Pacific hurricanes has not been addressed specifically. In this study, we show that unlike traditional indices of ENSO, the ENSO Longitude Index (ELI) is able to predict Eastern Pacific hurricane activity at significant lead times. By capturing changes in the location of deep convection and associated thermocline processes more accurately, ELI explains the most variability in the upper-ocean heat content in the main development region of the Eastern Pacific basin compared to other ENSO indices. These results have substantial implications for operational seasonal forecasts of Eastern Pacific hurricanes.

Balaguru, Karthik↗
NASA NTRS1988

Relative sensitivity of Normalized Difference Vegetation Index (NDVI) and Microwave Polarization Difference Index (MPDI) for vegetation and desertification monitoring

A simple equation relating the Microwave Polarization Difference Index (MPDI) and the Normalized Difference Vegetation Index (NDVI) is proposed which represents well data obtained from Nimbus 7/SMMR at 37 GHz and NOAA/AVHRR Channels 1 and 2. It is found that there is a limit which is characteristic of a particular type of cover for which both indices are equally sensitive to the variation of vegetation, and below which MPDI is more efficient than NDVI. The results provide insight into the relationship between water content and chlorophyll absorption at pixel size scales.

Becker, Francois↗
NASA NTRS1996

Verification and implementation of microburst day potential index (MDPI) and wind INDEX (WINDEX) forecasting tools at Cape Canaveral Air Station

This report details the research, development, utility, verification and transition on wet microburst forecasting and detection the Applied Meteorology Unit (AMU) did in support of ground and launch operations at Kennedy Space Center (KSC) and Cape Canaveral Air Station (CCAS). The unforecasted wind event on 16 August 1994 of 33.5 ms-1 (65 knots) at the Shuttle Landing Facility raised the issue of wet microburst detection and forecasting. The AMU researched and analyzed the downburst wind event and determined it was a wet microburst event. A program was developed for operational use on the Meteorological Interactive Data Display System (MIDDS) weather system to analyze, compute and display Theta(epsilon) profiles, the microburst day potential index (MDPI), and wind index (WINDEX) maximum wind gust value. Key microburst nowcasting signatures using the WSR-88D data were highlighted. Verification of the data sets indicated that the MDPI has good potential in alerting the duty forecaster to the potential of wet microburst and the WINDEX values computed from the hourly surface data do have potential in showing a trend for the maximum gust potential. WINDEX should help in filling in the temporal hole between the MDPI on the last Cape Canaveral rawinsonde and the nowcasting radar data tools.

Wheeler, Mark↗
NASA NTRS1975

Remote Sensing of Earth Resources (1970 - 1973 supplement): A literature survey with indexes. Section 2: Indexes

Documents related to the identification and evaluation by means of sensors in spacecraft and aircraft of vegetation, minerals, and other natural resources, and the techniques and potentialities of surveying and keeping up-to-date inventories of such riches are cited. These documents were announced in the NASA scientific and technical information system between March 1970 and December 1973.

Source record↗
NASA NTRS2002

Methods for semi-automated indexing for high precision information retrieval

OBJECTIVE: To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. DESIGN: Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. PARTICIPANTS: Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. MEASUREMENTS: Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. RESULTS: Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). SUMMARY: Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy.

Evaluation Studies↗
DOE OSTI2021

An optimized FM-index library for nucleotide and amino acid search

Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

59 BASIC BIOLOGICAL SCIENCES↗