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Bayesian estimation of HIV acquisition dates for prevention trials

Accurate timing estimates of when participants acquire HIV in HIV prevention trials are necessary for determining antibody levels at acquisition. The Antibody-Mediated Prevention (AMP) Studies showed that a passively administered broadly neutralizing antibody can prevent the acquisition of HIV from a neutralization-sensitive virus. We developed a pipeline for estimating the date of detectable HIV acquisition (DDA) in AMP Study participants using diagnostic and viral sequence data. Using a Bayesian strategy that combines three streams of data (REN [rev/vpu/env/Δnef] sequence, GP [gag/Δpol] sequence, and diagnostic) where their 95% credible intervals overlap based on pre-specified criteria and decision rules. We evaluated the performance of our AMP pipeline using PacBio viral sequence data from 41 participants across two prospective acute HIV acquisition cohort studies, FRESH and RV217, with twice-weekly sampling. These cohort studies enrolled young women in South Africa and men and women in Kenya and Thailand, respectively, with a high likelihood of HIV acquisition. In evaluating performance, “true DDA” was the center of bounds between last-negative and first-positive RNA diagnostic tests (median time 4 days, range 2–7 days); bias was the mean difference between estimated and true DDA. Using diagnostic data alone yielded timing estimates with a bias of 2.4 days and root mean square error (RMSE) of 7.9 days. These results were improved using sequence + diagnostic data (bias 1.5 days, RMSE 6.9 days), as well as by restricting sequence-based estimation to samples from ≤5 weeks post-DDA (bias 0.2 days, RMSE 7.8 days).

59 BASIC BIOLOGICAL SCIENCES

Flowering Date of Taxonomic Families Predicts Phenological Sensitivity to Temperature: Implications for Forecasting the Effects of Climate Change on Unstudied Taxa

Premise of the study: Numerous long-term studies in seasonal habitats have tracked interannual variation in fi rst fl owering date (FFD) in relation to climate, documenting the effect of warming on the FFD of many species. Despite these efforts, long-term phenological observations are still lacking for many species. If we could forecast responses based on taxonomic affi nity, however, then we could leverage existing data to predict the climate-related phenological shifts of many taxa not yet studied; Methods: We examined phenological time series of 1226 species occurrences (1031 unique species in 119 families) across seven sites in North America and England to determine whether family membership (or family mean FFD) predicts the sensitivity of FFD to standardized interannual changes in temperature and precipitation during seasonal periods before fl owering and whether families differ signifi cantly in the direction of their phenological shifts; Key results: Patterns observed among species within and across sites are mirrored among family means across sites; earlyfl owering families advance their FFD in response to warming more than late-fl owering families. By contrast, we found no consistent relationships among taxa between mean FFD and sensitivity to precipitation as measured here; Conclusions: Family membership can be used to identify taxa of high and low sensitivity to temperature within the seasonal, temperate zone plant communities analyzed here. The high sensitivity of early-fl owering families (and the absence of earlyfl owering families not sensitive to temperature) may refl ect plasticity in fl owering time, which may be adaptive in environments where early-season conditions are highly variable among years.

first flowering date

JWST lensed quasar dark matter survey – II. Strongest gravitational lensing limit on the dark matter free streaming length to date

This is the second in a series of papers in which we use JWST Mid Infrared Instrument multiband imaging to measure the warm dust emission in a sample of 31 multiply imaged quasars, to be used as a probe of the particle nature of dark matter. We present measurements of the relative magnifications of the strongly lensed warm dust emission in a sample of nine systems. The warm dust region is compact and sensitive to perturbations by populations of haloes down to masses $\sim 10^6$ M$_{\odot }$. Using these warm dust flux-ratio measurements in combination with five previous narrow-line flux-ratio measurements, we constrain the halo mass function. In our model, we allow for complex deflector macromodels with flexible third- and fourth-order multipole deviations from ellipticity, and we introduce an improved model of the tidal evolution of subhaloes. We constrain a WDM model and find an upper limit on the half-mode mass of $10^{7.6}\, {\rm M}_\odot$ at posterior odds of 10:1. This corresponds to a lower limit on a thermally produced dark matter particle mass of 6.1 keV. This is the strongest gravitational lensing constraint to date, and comparable to those from independent probes such as the Ly $\alpha$ forest and Milky Way satellite galaxies.

dark matter

Dated soil C–N–P profiles, water quality, and chamber fluxes across Ohio and Michigan wetlands (2024–2025)

This dataset includes dated soil core chemistry (bulk density, phosphorus, nitrogen and carbon concentrations), water quality, and chamber flux measurements collected from wetlands in the Midwest United States—12 sites in Ohio, one site in Indiana, one site in Michigan—collected in the spring or summer of 2024 or 2025, all in (.csv) format. These data were generated to examine how wetland restoration, management activities, and time since restoration affect biogeochemical processes, carbon sequestration, nutrient accumulation, water quality, and greenhouse gas emissions. Specifically, these data aim to investigate how restored wetlands differ from natural wetlands in terms of carbon, nitrogen, phosphorus dynamics, as well as carbon dioxide and methane fluxes. Also included are surface and porewater quality parameters and chamber flux measurements across these different wetlands. Sampling was conducted at various sites representing a range of restoration stages, from about 4 years post-restoration up to 105 years post-restoration, and also includes a natural wetland used as a reference in Michigan. These data can be used to determine carbon sequestration rates, nutrient cycling, and to enhance our understanding of biogeochemical responses to wetland restoration in temperate ecosystems. This data package contains (1) a csv file (Water_Quality.csv) containing water quality data (dissolved organic carbon, total dissolved nitrogen, and temperature) organized by location; (2) a csv file (Soil_C_N_P_Seq.csv) containing carbon, nitrogen, and phosphorus concentrations at each soil level and time of each soil level, as well as their sequestration rates; (3) a csv file (CH4_CO2_Flux.csv) including methane and carbon dioxide fluxes that were measured with a chamber; (4) a file-level metadata (FLMD.csv) file that lists each file contained in the dataset with associated metadata; (5) a data dictionary (DD.csv) file that contains terms/column headers used throughout the files along with a definition, units, and data type; and (6) a locations metadata file (Location_metadata.csv).

Earth Science > Atmosphere > Atmospheric Chemistry

Argon-40-argon-39 dating of Apollo sample 15555.

An age of 3.33 (plus or minus 0.05) b.y. was obtained for Apollo 15 sample 15555 by argon-40-argon-39 dating. The age of rock 15555, a basalt from the rim of Hadley Rille, establishes an upper limit to the age of the rille. The basalt flows filling the Hadley Rille section of the Imbrium basin postdate the formation of the basin - as measured by the Apollo 14 samples of the Fra Mauro formation - by at least 500 m.y. Therefore, the mare basalts cannot be simple impact melts but rather must result from some igneous activity on the moon.

Alexander, E. C., Jr.

Helium-uranium dating of corals.

Fanale and Schaeffer (1965) determined He/U ages of corals and other aragonitic fossils, and found that the results generally agreed with independent age estimates. As a more extensive and rigorous test of the reliability of He/U ages of fossil corals, I have determined He/U ages of forty-five independently dated Cenozoic corals. Uranium and thorium isotope compositions and Rn-222 retentivities were also determined as consistency checks. The results indicate that reliable ages are obtained when certain consistency tests are met and specified corrections are made.

Bender, M. L.

Diffusion artifacts in dating by stepwise thermal release of rare gases

It is demonstrated that the age of an isochron of apparent age plateau can be easily altered during a thermal release experiment, and that constant rare gas compositions can be observed which are artifacts of the experimental technique and are not chronologically meaningful. Examples are selected from 40Ar-39Ar dating of lunar samples in which anomalous variations in apparent ages can be ascribed to such experimental artifacts.

Huneke, J. C.