Results for “Event sequence” — Page 8

DOE OSTI2024

XA21-mediated resistance to Xanthomonas oryzae pv. oryzae is dose dependent

The rice receptor kinase XA21 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae ( Xoo ), the causal agent of rice bacterial blight disease. To investigate the relationship between the expression level of XA21 and resulting resistance, we generated independent HA-XA21 transgenic rice lines accumulating the XA21 immune receptor fused with an HA epitope tag. Whole-genome sequence analysis identified the T-DNA insertion sites in sixteen independent T0 events. Further, through quantification of the HA-XA21 protein and assessment of the resistance to Xoo strain PXO99 in six independent transgenic lines, we observed that XA21-mediated resistance is dose dependent. In contrast, based on the four agronomic traits quantified in these experiments, yield is unlikely to be affected by the expression level of HA-XA21 . These findings extend our knowledge of XA21-mediated defense and contribute to the growing number of well-defined genomic landing pads in the rice genome that can be targeted for gene insertion without compromising yield.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Automated Signal Timing Plan Reconstruction Using High-Resolution Event-Based Controller Data for Digital Twins

Transportation digital twins are essential tools for evaluating emerging technologies such as connected and automated vehicles, adaptive traffic signal control, and mobility optimization strategies. Realistic digital twins require accurate emulation of real-world signal controllers and detailed signal timing plans. However, signal timing plans are often unavailable or difficult to access, forcing researchers and modelers to rely on assumed fixed timings or halt their analysis. To overcome this challenge, we present a method that directly estimates signal timing plan parameters using high-resolution, event-based data from traffic signal controllers. The proposed method extracts key parameters, including cycle length, offset, phase sequence, coordinated phases, phase-specific minimum and maximum green durations, vehicle extensions, and splits under coordination. A rule-based deterministic signal timing reconstruction algorithm based on traffic signal operation rules, such as those outlined in the Signal Timing Manual, is developed and validated. We evaluate this method, which uses high-resolution controller event logs and verified signal timing plans, on 94 signalized intersections in Nashville, Tennessee, demonstrating their ability to generate accurate, simulation-ready signal timing plans for tools such as SUMO and Vissim.

Saroj, Abhilasha [ORNL] (ORCID:0000000191178063)↗

DOE OSTI2021

The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Hyperdiverse tropical rainforests, such as the aseasonal forests in Southeast Asia, are supported by high annual rainfall. Its canopy is dominated by the species-rich tree family of Dipterocarpaceae (Asian dipterocarps), which has both ecological (e.g., supports flora and fauna) and economical (e.g., timber production) importance. Recent ecological studies suggested that rare irregular drought events may be an environmental stress and signal for the tropical trees. We assembled the genome of a widespread but near threatened dipterocarp, Shorea leprosula, and analyzed the transcriptome sequences of ten dipterocarp species representing seven genera. Comparative genomic and molecular dating analyses suggested a whole-genome duplication close to the Cretaceous-Paleogene extinction event followed by the diversification of major dipterocarp lineages (i.e. Dipterocarpoideae). Interestingly, the retained duplicated genes were enriched for genes upregulated by no-irrigation treatment. These findings provide molecular support for the relevance of drought for tropical trees despite the lack of an annual dry season.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Efficient Generalized Boundary Detection Using a Sliding Information Distance

In this work, we present a general machine learning algorithm for boundary detection within general signals based on an efficient, accurate, and robust approximation of the universal normalized information distance. Our approach uses an adaptive sliding information distance (SLID) combined with a wavelet-based approach for peak identification to locate the boundaries. Special emphasis is placed on developing an adaptive formulation of SLID to handle general signals with multiple unknown and/or drifting section lengths. Although specialized algorithms may outperform SLID when domain knowledge is available, these algorithms are limited to specific applications and do not generalize. SLID excels in these cases. We demonstrate the versatility and efficacy of SLID on a variety of signal types, including synthetically generated sequences of tokens, binary executables for reverse engineering applications, and time series of seismic events.

42 ENGINEERING↗

DOE OSTI2023

Genome-Resolved Metagenomics of Nitrogen Transformations in the Switchgrass Rhizosphere Microbiome on Marginal Lands

Switchgrass (Panicum virgatum L.) remains the preeminent American perennial (C4) bioenergy crop for cellulosic ethanol, that could help displace over a quarter of the US current petroleum consumption. Intriguingly, there is often little response to nitrogen fertilizer once stands are established. The rhizosphere microbiome plays a critical role in nitrogen cycling and overall plant nutrient uptake. We used high-throughput metagenomic sequencing to characterize the switchgrass rhizosphere microbial community before and after a nitrogen fertilization event for established stands on marginal land. We examined community structure and bulk metabolic potential, and resolved 29 individual bacteria genomes via metagenomic de novo assembly. Community structure and diversity were not significantly different before and after fertilization; however, the bulk metabolic potential of carbohydrate-active enzymes was depleted after fertilization. We resolved 29 metagenomic assembled genomes, including some from the ‘most wanted’ soil taxa such as Verrucomicrobia, Candidate phyla UBA10199, Acidobacteria (rare subgroup 23), Dormibacterota, and the very rare Candidatus Eisenbacteria. The Dormibacterota (formally candidate division AD3) we identified have the potential for autotrophic CO utilization, which may impact carbon partitioning and storage. Our study also suggests that the rhizosphere microbiome may be involved in providing associative nitrogen fixation (ANF) via the novel diazotroph Janthinobacterium to switchgrass.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Development of a new control rod drive mechanism design for the ISU AGN-201M reactor

The Aerojet General Nucleonics (AGN) model 201-Modified, known as the AGN-201M reactor, plays an essential role in the educational and research activities at Idaho State University (ISU). The ISU AGN-201M's original Control Rod Drive Mechanism (CRDM) has been in operation for more than fifty years with no large-scale redesigns. The CRDM is required to eject the fuel rods within one second during a SCRAM event (also known as a 'reactor trip') and adjust the control rods' insertion speed, and keeps the rod insertion sequence correct. The existing control rod drive mechanisms meet these criteria but experience a few concerns due to aging. Concerns include complex maintenance and costly repairs for old electromechanical components, rod position feedback errors, and the impediment of the plate during a SCRAM due to binding of the lead screws of the existing mechanism. During a binding event, the drive mechanism becomes locked, preventing the control rod's magnetic plate from moving in or out under the reactor's normal and emergency operating conditions. Although, the binding has no effect on the ability of the rod to exit the core during the SCRAM. To counteract the concerns and issues with the current CRDM, a new design has been proposed using newer components and a simplified design. The new design utilizes more advanced electric and mechanical components that are commercially available. The new CRDM system is divided into four main aspects: (1) control rod movement design (motor, lead screw, guide rods), (2) control rod ejection (springs, electromagnet), (3) control rod position and feedback (position transducer, microswitches), and (4) material selection and structural analysis. The new design aims to reduce the overall complexity and probability of failure to improve the reactor's overall reliability. With proper material selection and improved structural design, the new drives are lighter with little to no change in structural integrity. The new control rod drive mechanism eliminates binding scenarios by using a single lead screw and implementing additional guide rods. An advanced linear position sensor and microswitches replace the existing and aging synchro system for accurate rod position feedback resulting in better reactivity control. The new design meets the reactor's operational limits by having an average reactivity insertion of 0.065% Δk/k per second, which corresponds to a total control rod insertion time of 19.23 s, while the control rod's ejection time remains less than one second during a SCRAM event. The new design ensures the reactor's long-term viability for educational and research activities by increasing the reliability and safety of operation for years to come.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

W$^+$W$^-$ boson pair production in proton-proton collisions at $\sqrt{s} =$ 13 TeV

A measurement of the W+W- boson pair production cross section in proton-proton collisions at s=13 TeV is presented. The data used in this study are collected with the CMS detector at the CERN LHC and correspond to an integrated luminosity of 35.9 fb-1. The W+W- candidate events are selected by requiring two oppositely charged leptons (electrons or muons). Two methods for reducing background contributions are employed. In the first one, a sequence of requirements on kinematic quantities is applied allowing a measurement of the total production cross section, 117.6±6.8 pb, which agrees well with the theoretical prediction. Fiducial cross sections are also reported for events with zero or one jet, and the change in the zero-jet fiducial cross section with the jet transverse momentum threshold is measured. Normalized differential cross sections are reported within the fiducial region. A second method for suppressing background contributions employs two random forest classifiers. The analysis based on this method includes a measurement of the total production cross section and also a measurement of the normalized jet multiplicity distribution in W+W- events. Finally, a dilepton invariant mass distribution is used to probe for physics beyond the standard model in the context of an effective field theory, and constraints on the presence of dimension-6 operators are derived.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Cross-platform analysis of public responses to the 2019 Ridgecrest earthquake sequence on Twitter and Reddit

Online social networks (OSNs) have become a powerful tool to study collective human responses to extreme events such as earthquakes. Most previous research concentrated on a single platform and utilized users’ behaviors on a single platform to study people’s general responses. In this study, we explore the characteristics of people’s behaviors on different OSNs and conduct a cross-platform analysis of public responses to earthquakes. Our findings support the Uses and Gratification theory that users on Reddit and Twitter are engaging with platforms that they may feel best reflect their sense of self. Using the 2019 Ridgecrest earthquakes as our study cases, we collected 510,579 tweets and 45,770 Reddit posts (including 1437 submissions and 44,333 comments) to answer the following research questions: (1) What were the similarities and differences between public responses on Twitter and Reddit? (2) Considering the different mechanisms of Twitter and Reddit, what unique information of public responses can we learn from Reddit as compared with Twitter? By answering these research questions, we aim to bridge the gap of cross-platform public responses research towards natural hazards. Our study evinces that the users on the two different platforms have both different topics of interest and different sentiments towards the same earthquake, which indicates the necessity of investigating cross-platform OSNs to reveal a more comprehensive picture of people’s general public responses towards certain disasters. Our analysis also finds that r/conspiracy subreddit is one of the major venues where people discuss the 2019 Ridgecrest earthquakes on Reddit and different misinformation/conspiracies spread on Twitter and Reddit platforms (e.g., “Big one is coming” on Twitter and “Nuclear test” on Reddit).

58 GEOSCIENCES↗

DOE OSTI2022

Jets from main sequence and white dwarf companions during common envelope evolution

ABSTRACT It has long been speculated that jet feedback from accretion on to the companion during a common envelope (CE) event could affect the orbital evolution and envelope unbinding process. We present global 3D hydrodynamical simulations of CE evolution (CEE) that include a jet subgrid model and compare them with an otherwise identical model without a jet. Our binary consists of a 2-M⊙ red giant branch primary and a 1- or 0.5-M⊙ main sequence (MS) or white dwarf (WD) secondary companion modelled as a point particle. We run the simulations for 10 orbits (40 d). Our jet model adds mass at a constant rate $\dot{M}_\mathrm{j}$ of the order of the Eddington rate, with maximum velocity vj of the order of the escape speed, to two spherical sectors with the jet axis perpendicular to the orbital plane. We explore the influence of the jet on orbital evolution, envelope morphology and envelope unbinding, and assess the dependence of the results on the jet mass-loss rate, launch speed, companion mass, opening angle, and accretion rate. In line with our theoretical estimates, jets are choked around the time of first periastron passage and remain choked thereafter. Subsequent to choking, but not before, jets efficiently transfer energy to bound envelope material. This leads to increases in unbound mass of up to $\sim 10{{\ \rm per\ cent}}$, as compared to the simulations without jets. We also estimate the cumulative effects of jets over a full CE phase, finding that jets launched by MS and WD companions are unlikely to dominate envelope unbinding.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Assessment of the Phase-to-Ground Fault Apparent Admittance Method with Phase/Ground Boundaries to Detect Types of Electrical Faults for Protective Relays Using Signature Library and Simulated Events

Protective relays in electric power grids recognize the types of electrical faults in a few seconds. The most common detection method to detect the types of electrical faults is based on measuring the angle between the zero and negative sequence currents. However, it is not completely accurate because the phase to phase ground and phase to ground electrical faults could have the same detection conditions. Therefore, engineers need to plot the events after an electrical fault to observe the nature of the incidents in detail. In this study, the phase to ground fault apparent (PGFA) admittance method with phase/ground boundaries identified the types of electrical faults located in distribution power lines and feeders. This method was based on measuring the PGFA admittance magnitudes for the faulted and non-faulted phases, resulting in greater than zero and near zero, respectively. The PGFA admittance algorithm was built with MATLAB/ Simulink software and tested with signature library and grid simulation events. The PGFA method with phase/ground boundaries was evaluated with the confusion matrix. The measured and predicted values matched in more than 90% of the tests, and the PGFA admittance method with phase/ground boundaries presented an accuracy of 94.3% and a precision of 100%.

Piesciorovsky, Emilio↗

DOE OSTI2021

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

DOE OSTI2021

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

DOE OSTI2021

WA-Omic_LA.1.0 - Quantitative Lipidomics, Metabolomics, and Sequencing (16S/ITS) Publication Data DOI Package

Corresponding Data Publication: "Rapid remodeling of the soil lipidome in response to a drying-rewetting event." This study reveals specific changes in lipids and metabolites that are indicative of stress adaptation, substrate use, and cellular recovery during soil drying and subsequent rewetting. Drought induced nutrient limitation was reflected in the lipidome and polar metabalome, both of which rapidly shifted (within hours) upon rewet. Reduced nutrient access in dry soil caused the replacement of glycerophospholipids with phosphorus-free lipids and impeded resource-expensive osmolyte accumulation. Elevated levels of ceramides and lipids with long chain polyunsaturated fatty acids, in dry soil suggests that lipids play an important role in fungal drought tolerance. Increasing abundance of bacterial glycerophospholipids and triacylglycerols with fatty acids typical of bacteria and polar metabolites suggest metabolic recovery in representative bacteria once the environmental conditions are conducive for growth. These results underscore the importance of the soil lipidome as a robust indicator of microbial community responses, especially at the short time scales of cell-environment reactions. Data package contents reported here are the first version and contain pre- and post-processed data acquisition and subsequent downstream analysis files using various data source instrument method techniques and Mass Spectroscopy (MS) EMSL capabilities. This publication data package DOI is a comprehensive high-throughput multi-omics data lifecycle collection containing processed data method metadata. Support files include additional data download “Read Me” file containing data descriptor information and data source application ontologies (see data dictionary). Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. For increased data availability and interoperability, GC-MS/LC-MS mass spectrometry datasets (Thermo .raw ) were deposited at the MassIVE database repository under the related data accession MSV000086931 and can be accessed by using the API. Statistical data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location.

Amplicon sequencing 16S ITS LC-MS/MS lipidomics mu↗

DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Heating events in the nascent solar system recorded by rare earth element isotopic fractionation in refractory inclusions

Equilibrium condensation of solar gas is often invoked to explain the abundance of refractory elements in planets and meteorites. This is partly motivated, by the observation that the depletions in both the least and most refractory rare earth elements (REEs) in meteoritic group II calcium-aluminum–rich inclusions (CAIs) can be reproduced by thermodynamic models of solar nebula condensation. We measured the isotopic compositions of Ce, Nd, Sm, Eu, Gd, Dy, Er, and Yb in eight CAIs to test this scenario. Contrary to expectation for equilibrium condensation, we find light isotope enrichment for the most refractory REEs and more subdued isotopic variations for the least refractory REEs. This suggests that group II CAIs formed by a two-stage process involving fast evaporation of preexisting materials, followed by near-equilibrium recondensation. The calculated time scales are consistent with heating in events akin to FU Orionis– or EX Lupi–type outbursts of eruptive pre–main-sequence stars.

58 GEOSCIENCES↗

DOE OSTI2021

Three-dimensional paganica fault morphology obtained from hypocenter clustering (L'Aquila 2009 seismic sequence, Central Italy)

In seismic modelling, fault planes are normally assumed to be flat due to the lack of data which can constrain fault morphology. However, incorporating 3D fault morphology is important for modelling several phenomena, for example calculating mainshock induced stress changes. Here we utilize a data-analytical method to unveil the 3D rupture morphology of faults using unsupervised clustering techniques applied to earthquake hypocenters in seismic sequences. We apply this method to the 2009 L'Aquila seismic sequence which involved a M W 6.1 mainshock on April 6th. We use a dataset of about 50,000 relocated events, mostly microearthquakes, reaching magnitude of completeness equal to 0.7. Clustering distinguishes the earthquakes as occurring in three main clusters along with other minor fault segments. We then represent the morphology of the main Paganica fault system (responsible for the largest mainshock) using splines. This method shows promise as a step toward robustly and quickly obtaining 3D rupture morphologies where earthquake sequences have been monitored. The 3D model is presented interactively online, and the processing is presented in an interactive Jupyter Notebook (https://bit.ly/2MnCFdj).

58 GEOSCIENCES↗

DOE OSTI2020

Stress-Drop and Source Scaling of the 2019 Ridgecrest, California, Earthquake Sequence

Stress drop, while difficult to measure reliably and at scale, is a key source parameter for understanding the earthquake rupture process and its relationship to strong ground motion. Here, we use a P-wave spectral decomposition approach, designed for large and densely sampled datasets, to measure earthquake stress drop in the region surrounding the 2019 Ridgecrest, California, earthquake sequence. With more than 11,000 measurements of earthquake stress drop in the 20-yr time period from 2000 through 2019, this dataset provides an opportunity to understand how coseismic stress changes and how other geophysical factors relate to the distribution of stress drop and its evolution in space and time. We observe a mild but persistent deviation from self-similar scaling, with larger events having systematically higher stress drops, though this trend depends on the assumption of an omega-square source spectral model. Earthquake stress drop increases with hypocentral depth in this study region, and the Ridgecrest aftershocks tend to have higher stress drops than the pre-event seismicity. This is in part due to their deeper hypocenters. Coherent spatial patterns of stress drop in the aftershock sequence correlate with the slip distribution of the M 7.1 mainshock, whose northwest rupture tip terminated in a long-lived zone of enervated stress drop. Although physical interpretation of these results is complicated by the trade-offs between the timing, depth, and location of these earthquakes, the observations provide new insight into the physics of the earthquake source in an area of renewed seismic activity in southern California.

58 GEOSCIENCES↗

DOE OSTI2022

Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification

To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of time someone has been infected with HIV. To train our model, we used five biomarkers based on real data from serological assays, HIV sequence data, and target cell counts in longitudinally followed, untreated patients with known infection times. The biomarkers were modeled with a mixed effects framework to allow for patient specific variation and general trends, and fit to patient data using Markov Chain Monte Carlo (MCMC) methods. Subsequently, the density of the unobserved infection time conditional on observed biomarkers were obtained by integrating out the random effects from the model fit. This probabilistic information about infection times was incorporated into the likelihood function for the transmission history and phylogenetic tree reconstruction, informed by the HIV sequence data. To critically test our methodology, we developed a coalescent-based simulation framework that generates phylogenies and biomarkers given a specific or general transmission history. Testing on many epidemiological scenarios showed that biomarker augmented phylogenetics can reach 90% accuracy under idealized situations. Under realistic within-host HIV-1 evolution, involving substantial within-host diversification and frequent transmission of multiple lineages, the average accuracy was at about 50% in transmission clusters involving 5–50 hosts. Realistic biomarker data added on average 16 percentage points over using the phylogeny alone. Using more biomarkers improved the performance. Shorter temporal spacing between transmission events and increased transmission heterogeneity reduced reconstruction accuracy, but larger clusters were not harder to get right. More sequence data per infected host also improved accuracy. We show that the method is robust to incomplete sampling and that adding biomarkers improves reconstructions of real HIV-1 transmission histories. The technology presented here could allow for better prevention programs by providing data for locally informed and tailored strategies.

60 APPLIED LIFE SCIENCES↗