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At least 109 records · Page 6

What Should Health Departments Do with HIV Sequence Data?

Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons, health departments have extensive sequence collections spanning years and even decades of the HIV epidemic. How should these data be used (or not) in public health practice? This is a complex, multi-faceted question that weighs personal risks against public health benefit. The answer is neither straightforward nor universal. However, to make that judgement—of how genetic sequence data should be used in describing and combating the HIV epidemic—we need a clear image of what a phylogenetically enhanced HIV surveillance system can do and what benefit it might provide. In this paper, we present a positive case for how up-to-date analysis of HIV sequence databases managed by health departments can provide unique and actionable information of how HIV is spreading in local communities. We discuss this question broadly, with examples from the US, as it is globally relevant for all health authorities that collect HIV genetic data.

60 APPLIED LIFE SCIENCES↗

Evaluation of the Performance Characteristics of the CGLSS and NLDN Systems Based on Two Years of Ground-Truth Data from Launch Complex 39B, Kennedy Space Center, Florida

From May 2011 through July 2013, the lightning instrumentation at Launch Complex 39B (LC39B) at the Kennedy Space Center, Florida, has obtained high-speed video records and field change waveforms (dE/dt and three-axis dH/dt) for 54 negative polarity return strokes whose strike termination locations and times are known with accuracy of the order of 10 m or less and 1 μs, respectively. A total of 18 strokes terminated directly to the LC39B lighting protection system (LPS), which contains three 181 m towers in a triangular configuration, an overhead catenary wire system on insulating masts, and nine down conductors. An additional 9 strokes terminated on the 106 m lightning protection mast of Launch Complex 39A (LC39A), which is located about 2.7 km southeast of LC39B. The remaining 27 return strokes struck either on the ground or attached to low-elevation grounded objects within about 500 m of the LC39B LPS. Leader/return stroke sequences were imaged at 3200 frames/sec by a network of six Phantom V310 high-speed video cameras. Each of the three towers on LC39B had two high-speed cameras installed at the 147 m level with overlapping fields of view of the center of the pad. The locations of the strike points of 54 return strokes have been compared to time-correlated reports of the Cloud-to-Ground Lightning Surveillance System (CGLSS) and the National Lightning Detection Network (NLDN), and the results of this comparison will be presented and discussed.

Waveforms↗

Automatic Calibration and Health Monitoring of Infrastructure Sensors

Smart transportation infrastructure relies on networks of heterogeneous sensors - cameras, radars, and lidars - continuously monitoring traffic conditions. However, executing the initial spatial calibration of multiple sensors and the subsequent health monitoring presents significant operational challenges. Environmental factors, mechanical vibrations, and gradual drift cause spatial misalignment, degrading fusion performance and tracking accuracy. Traditional calibration approaches require manual intervention with specialized targets or survey equipment, resulting in service interruptions and high maintenance costs. This work presents an automated framework for initial calibration and continuous health monitoring without human intervention or service disruption. Our approach addresses two critical problems: (1) detecting when sensors become miscalibrated during operation, and (2) automatically re-establishing spatial alignment using only operational traffic data. The health monitoring component analyzes measurement innovations - differences between sensor observations and predicted object states - to detect systematic biases indicative of calibration drift. By computing bias magnitude, directional consistency, and rejection rates, the system identifies miscalibrations as small as 0.5 meters. Unlike traditional methods requiring known calibration targets, our diagnostic operates continuously on live traffic observations, enabling early detection before fusion quality degrades. The automatic recalibration algorithm leverages overlapping sensor fields-of-view and temporal correlation of vehicle observations. Using graph-based optimization, the system automatically discovers which sensor pairs observe common regions, estimates pairwise spatial transformations using RANSAC-based robust estimation, and jointly optimizes all sensor poses through bundle adjustment. The framework handles practical deployment challenges, including different sensor sampling rates (1-10 Hz), varying installation positions, unknown orientations, and limited overlap regions (>10%). When approximate sensor positions are available from installation surveys (+/-1m accuracy), the algorithm additionally estimates sensor orientations, refining both position and rotation to sub-meter and sub-degree accuracy. We validate the framework on multi-hour traffic datasets from six heterogeneous sensors with sampling rates ranging from 1 Hz to 10 Hz. Results demonstrate successful calibration even with sparse overlap (<20%) and automatic detection of miscalibrations exceeding 0.8 meters. This work enables a "deploy-and-forget" sensor infrastructure that maintains calibration autonomously, reducing maintenance costs while improving tracking accuracy. The techniques generalize beyond transportation to any multi-sensor monitoring application requiring robust spatial alignment, including smart cities, industrial monitoring, and surveillance systems.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Evaluating disease surveillance strategies for early outbreak detection in contact networks with varying community structure

Disease surveillance systems allow public health agencies to respond to emerging diseases before they become widespread. Developing such systems requires identifying optimal ways to monitor in the context of an epidemic outbreak; this problem is known as sensor selection. Contact networks represent the dynamics of interaction in a population and are used to model how a disease spreads in a population and to explore strategies of sensor selection. We evaluated five sensor selection strategies on their ability to provide an early warning of a COVID-like outbreak in synthetic contact networks encapsulated in four network scenarios. Three of these scenarios assessed different aspects of community structure. The fourth scenario employed a contact network representing the population and interactions of 6.8 million people in New York City, constructed from an agent-based simulation using census and transportation data. This scenario exemplifies how sensor selection strategies may perform in a real-world, urban context. Our findings suggest that the choice of the optimal strategy depends heavily on the community structure of the network. Strategies that select highly connected nodes or maximize network coverage are the optimal surveillance strategy for outbreak detection in many network community structures. However, a naive implementation of these strategies may fail to provide an early warning at all—including in the New York City scenario. Moreover, these methods are impractical for real-world use as they require knowledge of the underlying contact network. Instead, a selection strategy that starts with a set of random nodes and then performs a random walk through a chain of neighbors reliably provides early warnings without requiring prior knowledge of the network. We find this method, called “random chain”, to be the most pragmatic for implementation in a real-world disease surveillance context.

60 APPLIED LIFE SCIENCES↗

Viral Dynamic Models During COVID‐19: Are We Ready for the Next Pandemic?

Mathematical models have been used for about 30 years to improve our understanding of virus-host interaction, in particular during chronic infections. During the COVID-19 pandemic, these models have been used to provide insights into the natural history of acute SARS-CoV-2 infection, optimize antiviral treatment strategies, understand factors associated with transmission, and optimize surveillance systems. The impact of modeling has been accelerated by the availability of unprecedented multidimensional immune data from animal and human systems, which enhanced partnerships between experimentalists and theorists and led to exciting new modeling and statistical developments. In this mini review, we examine the lessons learned from the COVID-19 pandemic and discuss the main insights provided by mathematical models of viral dynamics at the different stages of the outbreak. Although we focus on respiratory infection, we also consider the new areas for development in anticipation of future acute infections from new or reemerging pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

Foodborne illness outbreaks linked to unpasteurised milk and relationship to changes in state laws – United States, 1998–2018

Consumption of unpasteurised milk in the United States has presented a public health challenge for decades because of the increased risk of pathogen transmission causing illness outbreaks. We analysed Foodborne Disease Outbreak Surveillance System data to characterise unpasteurised milk outbreaks. Using Poisson and negative binomial regression, we compared the number of outbreaks and outbreak-associated illnesses between jurisdictions grouped by legal status of unpasteurised milk sale based on a May 2019 survey of state laws. During 2013–2018, 75 outbreaks with 675 illnesses occurred that were linked to unpasteurised milk; of these, 325 illnesses (48%) were among people aged 0–19 years. Of 74 single-state outbreaks, 58 (78%) occurred in states where the sale of unpasteurised milk was expressly allowed. Compared with jurisdictions where retail sales were prohibited (n = 24), those where sales were expressly allowed (n = 27) were estimated to have 3.2 (95% CI 1.4–7.6) times greater number of outbreaks; of these, jurisdictions where sale was allowed in retail stores (n = 14) had 3.6 (95% CI 1.3–9.6) times greater number of outbreaks compared with those where sale was allowed on-farm only (n = 13). This study supports findings of previously published reports indicating that state laws resulting in increased availability of unpasteurised milk are associated with more outbreak-associated illnesses and outbreaks.

60 APPLIED LIFE SCIENCES↗

Trends in the administration of COVID-19 vaccines with other vaccines in the United States reported to V-safe during December 14, 2020—May 19, 2023

Introduction COVID-19 vaccines may be administered with other vaccines during the same healthcare visit. COVID-19 monovalent (Fall 2021) and bivalent (Fall 2022) vaccine recommendations coincided with annual seasonal influenza vaccination. Data describing the frequency of the co-administration of COVID-19 vaccines with other vaccines are limited. Methods We used V-safe, a voluntary smartphone-based U.S. safety surveillance system established by the CDC, to describe trends in the administration of COVID-19 vaccines with other vaccines reported to V-safe during December 14, 2020 – May 19, 2023. Results Of the 21 million COVID-19 vaccinations reported to V-safe, 2.2% (459,817) were administered with at least 1 other vaccine. Co-administration most frequently occurred during the first week of October 2023 (27,092; 44.1%). Most reports of co-administration included influenza vaccine (393,003; 85.5%). Co-administration was most frequently reported for registrants aged 6 months-6 years (4,872; 4.4%). Conclusion Reports of co-administration to V-safe peaked during October 2023, when influenza vaccination most often occurs, possibly reflecting increased opportunities for multiple vaccinations and greater acceptability of the co-administration of COVID-19 vaccine with other vaccines, especially influenza vaccine.

60 APPLIED LIFE SCIENCES↗

The impact of adjusting for hysterectomy prevalence on cervical cancer incidence rates and trends among women aged 30 years or older—United States, 2001-2019

Abstract Hysterectomy protects against cervical cancer when the cervix is removed. However, measures of cervical cancer incidence often fail to exclude women with a hysterectomy from the population-at-risk denominator, underestimating and distorting disease burden. In this study, we estimated hysterectomy prevalence from the Behavioral Risk Factor Surveillance System surveys to remove the women who were not at risk of cervical cancer from the denominator and combined these estimates with the US Cancer Statistics data. From these data, we calculated age-specific and age-standardized incidence rates for women aged >30 years from 2001-2019, adjusted for hysterectomy prevalence. We calculated the difference between unadjusted and adjusted incidence rates and examined trends by histology, age, race and ethnicity, and geographic region using joinpoint regression. The hysterectomy-adjusted cervical cancer incidence rate from 2001-2019 was 16.7 per 100 000 women—34.6% higher than the unadjusted rate. After adjustment, incidence rates were higher by approximately 55% among Black women, 56% among those living in the East South Central division, and 90% among women aged 70-79 and ≥80 years. These findings underscore the importance of adjusting for hysterectomy prevalence to avoid underestimating cervical cancer incidence rates and masking disparities by age, race, and geographic region. This article is part of a Special Collection on Gynecological Cancers.

Public, Environmental & Occupational Health↗

Use of nucleic acid amplification testing for rapid detection of Mycobacterium tuberculosis complex among U.S. tuberculosis patients from 2011–2017

Background: Nucleic acid amplification (NAA) tests rapidly detect Mycobacterium tuberculosis complex directly from clinical specimens, providing valuable results for those evaluated for tuberculosis. Methods: We analyzed characteristics of cases with NAA testing performed, compared cases with positive and negative NAA test results, and calculated turnaround time and time to treatment for all verified cases reported to the National Tuberculosis Surveillance System in the United States during 2011–2017. Results: Among 67082 verified tuberculosis cases with NAA testing information, 30820 (45.9%) were reported as not having an NAA test performed; the proportion without NAA testing declined annually, from 60.5% in 2011 to 33.6% in 2017. Of 67082 verified cases, 27912 (41.6%) had positive, 8215 (12.2%) had negative, and 135 (0.2%) had indeterminate NAA test results. Among the 33937 cases with an acid-fast bacilli (AFB) smear-positive result, 24093 (70.9%) had an NAA test performed; 11490 of the 30244 (38.0%) with an AFB smear-negative result had an NAA test performed. Although sputum was the most common specimen type tested, 79.8% (7023/8804) of nonsputum specimen types had a positive NAA test result. Overall, 63.7% of cases with laboratory testing had NAA test results reported <6 days following specimen collection; for 13891 cases not yet on treatment, median time to treatment after the laboratory report date was 2 days. Conclusions: Our analyses demonstrate increased NAA test utilization between 2011 and 2017. However, a large proportion of cases did not have an NAA test performed, reflecting challenges in broader uptake, suggesting an opportunity to expand use of this diagnostic methodology.

59 BASIC BIOLOGICAL SCIENCES↗

3D-Printed mmWave Quasi-Holographic Antenna for 2-D Beamforming

This paper presents the design and manufacturing of a novel 2D-scanning antenna that integrates a 3D-printed Rotman lens with a quasi-holographic leaky-wave antenna (HLWA). The proposed design achieved beam-scanning capabilities by leveraging the beamforming of the Rotman lens and the high-gain directive properties of the quasi-HLWA. The Rotman lens (RL) enables beam steering in the elevation plane by switching between input ports. The quasi-HLWA, designed using holographic principles, achieves frequency-controlled beam scanning in the azimuth plane. The entire antenna structure was fabricated using additive manufacturing with an Ink1092 substrate and silver ink for the conductive traces. This approach provides greater control over material placement and design freedom compared to traditional methods. A 25° transmission linear substrate taper was used to ensure good impedance matching between the Rotman lens and the quasi-HLWA, allowing greater gain while maintaining a good scanning range. The experimental results validate the 2D scanning capability of the proposed antenna. The antenna system provides coverage from −54° to 54° in the elevation θ plane and −28° to 28° in the azimuth plane ϕ , with a maximum measured gain of 21.3 dBi at 28 GHz with an average radiation efficiency η=60 %. The fabricated prototype was tested, and the performance was in good agreement with the simulated performance.

Rotman lens↗

Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism

Animals and plants interact with microbes by engaging specific surveillance systems, regulatory networks, and response modules that allow for accommodation of mutualists and defense against antagonists. Antimicrobial defense responses are mediated in both animals and plants by innate immunity systems that owe their functional similarities to convergent evolution. Like animals and plants, fungi interact with bacteria. However, the principles governing these relations are only now being discovered. In a study system of host and nonhost fungi interacting with a bacterium isolated from the host, we found that bacteria used a common gene repertoire to engage both partners. In contrast, fungal responses to bacteria differed dramatically between the host and nonhost. These findings suggest that as in animals and plants, the genetic makeup of the fungus determines whether bacterial partners are perceived as mutualists or antagonists and what specific regulatory networks and response modules are initiated during each encounter.

59 BASIC BIOLOGICAL SCIENCES↗

Anomalous And Normal High Performance Computing Datacenter Activities

This code provides annotation and an interface to 10+ hours of video activities in a high performance datacenter with 20+ different types of anomalous activities. The purpose is to enable machine learning for video surveillance systems in high performance computing centers. This is the first code of this type addressing the space of high performance computing datacenters.

Anderson, Matthew↗

Inferring transmission heterogeneity using virus genealogies: estimation and targeted prevention

Spread of HIV typically involves uneven transmission patterns where some individuals spread to a large number of individuals while others to only a few or none. Such transmission heterogeneity can impact how fast and how much an epidemic spreads. Further, more efficient interventions may be achieved by taking such transmission heterogeneity into account. To address these issues, we developed two phylogenetic methods based on virus sequence data: 1) to generally detect if significant transmission heterogeneity is present, and 2) to pinpoint where in a phylogeny high-level spread is occurring. We derive inference procedures to estimate model parameters, including the amount of transmission heterogeneity, in a sampled epidemic. We show that it is possible to detect transmission heterogeneity under a wide range of simulated situations, including incomplete sampling, varying levels of heterogeneity, and including within-host genetic diversity. When evaluating real HIV-1 data from different epidemic scenarios, we found a lower level of transmission heterogeneity in slowly spreading situations and a higher level of heterogeneity in data that included a rapid outbreak, while R0 and Sackin’s index (overall tree shape statistic) were similar in the two scenarios, suggesting that our new method is able to detect transmission heterogeneity in real data. We then show by simulations that targeted prevention, where we pinpoint high-level spread using a coalescence measurement, is efficient when sequence data are collected in an ongoing surveillance system. Such phylogeny-guided prevention is efficient under both single-step contact tracing as well as iterative contact tracing as compared to random intervention.

59 BASIC BIOLOGICAL SCIENCES↗

Hazard Detection Detector Cards

This report presents a comprehensive summary of five advanced anomaly detection tools developed and deployed by Oak Ridge National Laboratory in support of the VA’s Health Information Technology modernization. These detectors—Order Path Tracker, Trend Watcher, Pain Pointer, Performance Monitor, and Patient Record Flag Detector—leverage statistical and machine learning methods to monitor workflow disruptions, detect anomalies in care sequences and volumes, identify bottlenecks, and track system-level performance metrics across VistA and Millennium systems. All detectors have been integrated into the Health Data Analytics Platform (HDAP), with most having completed deployment and testing using live data from targeted stations in cardiology and oncology domains. This work enhances VA’s capacity for proactive system surveillance, promotes patient safety, and informs data-driven operational improvements across the EHR ecosystem.

97 MATHEMATICS AND COMPUTING↗

Infant burn injuries related to water heating for powdered infant formula preparation

Guidance for preparing powdered infant formula (PIF) helps to ensure it meets the nutritional needs of infants and is safe to consume. Among safety concerns is Cronobacter sakazakii contamination which can lead to serious infections and death. PIF preparation guidance varies; there is a lack of consensus on whether there is a need to boil water to inactivate potential Cronobacter and for how long to let the water cool before reconstitution. We sought to quantify the burden of burn injuries among infants related to water heating for PIF preparation. Estimating this burden may help inform preparation recommendations. Burn injuries among infants <18 months of age were identified from 2017 to 2019 National Electronic Injury Surveillance System data collected from sampled hospital emergency departments. Injuries were classified as related to PIF water heating, potentially related to PIF water heating but with undetermined causation, related to other infant feeding aspects, or unrelated to infant formula or breast milk feeding. Unweighted case counts for each injury classification were determined. Across sampled emergency departments, 7 PIF water heating injuries were seen among the 44,395 injuries reported for infants <18 months. No reported PIF water heating injuries were fatal, but 3 required hospitalization. Another 238 injuries potentially related to PIF water heating but with undetermined causation were also seen. Preparation guidance should consider both the potential risk for Cronobacter infection and the potential risk for burns.

60 APPLIED LIFE SCIENCES↗

Robust Wheel Detection for Vehicle Re-Identification

Vehicle re-identification is a demanding and challenging task in automated surveillance systems. The goal of vehicle re-identification is to associate images of the same vehicle to identify re-occurrences of the same vehicle. Robust re-identification of individual vehicles requires reliable and discriminative features extracted from specific parts of the vehicle. In this work, we construct an efficient and robust wheel detector that precisely locates and selects vehicular wheels from vehicle images. The associated hubcap geometry can hence be utilized to extract fundamental signatures from vehicle images and exploit them for vehicle re-identification. Wheels pattern information can yield additional information about vehicles in questions. To that end, we utilized a vehicle imagery dataset that has thousands of side-view vehicle collected under different illumination conditions and elevation angles. The collected dataset was used for training and testing the wheel detector. Experiments show that our approach could detect vehicular wheels accurately for 99.41% of the vehicles in the dataset.

47 OTHER INSTRUMENTATION↗

State-Specific Prevalence of Inactivity, Self-Rated Health Status, and Severe Joint Pain Among Adults With Arthritis — United States, 2019

Arthritis is associated with joint pain, disability, and physical inactivity, potentially resulting in poor quality of life. The Centers for Disease Control and Prevention analyzed 2019 Behavioral Risk Factor Surveillance System data to estimate state-specific arthritis prevalence and, among adults with arthritis, the prevalence of physical inactivity, fair/poor self-rated health status, and severe joint pain. Among adults with arthritis, age-standardized prevalences of physical inactivity, fair/poor health status, and severe joint pain were high in all states and highest in southeastern states. Increased promotion and use of evidence-based public health interventions for arthritis may improve health-promoting behaviors and health outcomes among adults with arthritis.

59 BASIC BIOLOGICAL SCIENCES↗