Search NASA⌕ Search

SEARCH · Search NASA

Results for “data replication”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 937 records · Page 52

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut.

59 BASIC BIOLOGICAL SCIENCES↗

Developing a Climate-Induced Social Vulnerability Index for Urban Areas: A Case Study of East Tennessee

Census American Community Survey 2008-2012 data are used to construct a spatially explicit Climate-Induced Social Vulnerability Index (CSVI) for the East Tennessee area. This CSVI is a combination of a Social Vulnerability Index (SVI) and a Climate Index. A method is replicated and adapted to derive a custom SVI by Census tract for the counties participating in the East Tennessee Index, and a Climate Index is developed for the same area based on indicators for climate hazards. The resulting datasets are exported as a raster to be integrated and combined within the Urban Climate Adaptation Tool (Urban-CAT) to act as an indicator for communities which may be differentially vulnerable to changes in climate. Results for the SVI are mapped separately from the complete CSVI in this document as results for the latter are in development.

54 ENVIRONMENTAL SCIENCES↗

An Investigation Into Transecting Satellites in Future Space Traffic Management Scenarios

The number of satellites expected to populate the near-Earth space environment is set to dramatically increase in the coming decade as new large constellations are approved and deployed. Current strategies for deploying new batches of these satellites often involve launching into an initial orbit, and then performing apogee raising maneuvers to reach a target altitude. Similarly, end-of-life planning for these constellation satellites can consist of de-orbit burns that lower perigee to permit disposal via re-entry. Both the raising and de-orbiting maneuvers can result in the individual satellites traveling in transecting orbits that have the potential to cross other spacecraft trajectories. While individual large constellations may be able to coexist in separate altitude and inclination bands, having thousands of satellites moving between these bands as new satellites are added and old satellites are removed could pose additional collision risks. Similar concerns have been raised regarding the impact that large numbers of university-class CubeSats might have in terms of their overall collision risk, especially as these satellites typically do not have propulsion systems for active maneuvering. To assess the impact that transecting satellites might have on future space traffic management strategies, this study explored a variety of realistic future scenarios using a high-fidelity simulation tool. The model can simulate the orbit of tens of thousands of resident space objects (RSOs) simultaneously, to include active satellites, debris, rocket bodies, or even future hypothetical satellite constellations, using a realistic force model that incorporates non-spherical gravity, atmospheric drag, and solar radiation pressure, as well as station-keeping. The simulation can be customized to accommodate different methods of calculating the probability of collision, as well as the process for determining probability ellipsoids and screening volumes. This makes it possible to replicate, and compare, different processes used by different spacecraft operators and space situational awareness (SSA) providers. As the model is run forward in time, each conjunction event is recorded, allowing for the analysis of statistics and meta-data related to these events, providing insight into the nature and frequency of potential collisions, such as whether are they active or passive objects, what size are the two objects, and who owns the objects (if known). This information makes it possible to characterize how changes to the status quo affect the number and type of conjunctions that occur, as well as the distributional effects on various types of satellite operators. To assess the general risks that transecting satellites might pose for hypothetical future space object environments, approximately 60,000 new large constellation satellites were considered, in addition to the existing catalog of approximately 7800 known resident space objects (RSOs), over a simulation period of one year. The results indicate that the future space environment will introduce a non-linear increase in conjunction events as the number of RSOs also increase. This will require adjustments to spacecraft fuel budgets in order to conduct the avoidance maneuvers necessary to minimize collision risk, both for existing and new satellites. This increase is due in large part to the higher density of RSOs and the overlap between some constellation orbits. Current catalog objects were shown to require three times more ∆V for collision avoidance (CA) maneuvers in the simulated future environment, and some constellation spacecraft were estimated to devote the majority of their annual ∆V to CA. The impact of small satellites was found to be proportional for the current space environment, and actually decreased in terms of percentage for the future scenario, suggesting that small satellites do not pose an outsized collision risk. Lastly, transecting satellites were found to contribute thousands of additional conjunctions outside of their operational orbit, and may require up to an additional 5% in CA maneuver fuel allocation.

conjunction assessment↗

Review of Grey Box/Black Box Data Contamination Metrics on Open and Commercial Models

Dataset contamination is a problem where benchmarks and tasks used to evaluate the capabilities of Large Language Models (LLMs) have been incorporated into the training dataset of the models. This gives a false sense of performance that can overestimate how these models will function on truly unseen data. This problem becomes worse with commercial LLMs with larger and non-accessible training data, so techniques have been developed to try to measure the degree to which a model is contaminated with a benchmark’s data. To understand the effectiveness of these techniques, particularly when evaluating contamination on coding tasks, we review trends and categorize techniques by the degree of access to the model that is required. The research literature on this topic has reported mixed effectiveness of these techniques, so we select a set of black box (text access only) and grey box (access to model loss/probabilities required) techniques and apply them to both commercial and non-commercial models. We implement these metrics as part of a framework to test the contamination of Python code in LLMs to see to what extent we can replicate the effectiveness (or ineffectiveness) of these contamination detection techniques. Though we find mixed results in the capabilities of these metrics to identify contamination, we do observe evidence that they can identify contamination (broadly) in fine-tuned models when both a baseline and fine-tuned model is present. Additionally, similarity metrics were able to identify between contaminated and uncontaminated data even in situations where the data is distributionally similar (e.g., drawn from the same set of code projects).

97 MATHEMATICS AND COMPUTING↗

MicroRNA-33 promotes the replicative senescence of mouse embryonic fibroblasts by suppressing CDK6

MicroRNAs are a large class of tiny noncoding RNAs, which have emerged as critical regulators of gene expression, and thus are involved in multiple cellular processes, including cellular senescence. MicroRNA-33 has previously been established to exert crucial effect on cell proliferation, lipid metabolism and cholesterol metabolism. Nonetheless, the association between microRNA-33 and cellular senescence and its underlying molecular mechanism are far to be elucidated. The present study has attempted to probe into the effect of microRNA-33 on MEFs senescence. Our data unveiled that microRNA-33 was dramatically down-regulated in senescent MEFs compared to the young MEFs, and ectopic expression of microRNA-33 promoted MEFs senescence, while knock-down of microRNA-33 exhibited a protective effect against senescence phenotype. Moreover, we verified CDK6 as a direct target of microRNA-33 in mouse. Silencing of CDK6 induced the premature senescence phenotype of MEFs similarly as microRNA-33, while enforced expression of CDK6 significantly reverse the senescence-induction effect of microRNA-33. Taken together, our results suggested that microRNA-33 enhanced the replicative senescence of MEFs potentially by suppressing CDK6 expression. -- Highlights: •MicroRNA-33 was dramatically down-regulated in senescent MEF cells. •Altered expression of microRNA-33 exerted a critical role in MEFs senescence. •MicroRNA-33 promoted the replicative senescence of MEFs via targeting of CDK6.

60 APPLIED LIFE SCIENCES↗

Transient dynamics of terrestrial carbon storage: Mathematical foundation and its applications

Terrestrial ecosystems have absorbed roughly 30% of anthropogenic CO 2 emissions over the past decades, but it is unclear whether this carbon (C) sink will endure into the future. Despite extensive modeling and experimental and observational studies, what fundamentally determines transient dynamics of terrestrial C storage under global change is still not very clear. Here we develop a new framework for understanding transient dynamics of terrestrial C storage through mathematical analysis and numerical experiments. Our analysis indicates that the ultimate force driving ecosystem C storage change is the C storage capacity, which is jointly determined by ecosystem C input (e.g., net primary production, NPP) and residence time. Since both C input and residence time vary with time, the C storage capacity is time-dependent and acts as a moving attractor that actual C storage chases. The rate of change in C storage is proportional to the C storage potential, which is the difference between the current storage and the storage capacity. The C storage capacity represents instantaneous responses of the land C cycle to external forcing, whereas the C storage potential represents the internal capability of the land C cycle to influence the C change trajectory in the next time step. The influence happens through redistribution of net C pool changes in a network of pools with different residence times. Moreover, this and our other studies have demonstrated that one matrix equation can replicate simulations of most land C cycle models (i.e., physical emulators). As a result, simulation outputs of those models can be placed into a three-dimensional (3-D) parameter space to measure their differences. The latter can be decomposed into traceable components to track the origins of model uncertainty. In addition, the physical emulators make data assimilation computationally feasible so that both C flux- and pool-related datasets can be used to better constrain model predictions of land C sequestration. Altogether, this new mathematical framework offers new approaches to understanding, evaluating, diagnosing, and improving land C cycle models.

54 ENVIRONMENTAL SCIENCES↗

Measurement of top-quark pair production in association with charm quarks in proton–proton collisions at √s = 13 TeV with the ATLAS detector

Inclusive cross-sections or top-quark pair production in association with charm quarks are measured with proton-proton collision data at a center-of-mass energy of 13 TeV corresponding to an integrated luminosity of 140 fb -1 , collected with the ATLAS experiment at LHC between 2015 and 2018. The measurements are performed by requiring one or two charged leptons (electrons and muons), two b-tagged jets, and at least one additional jet in the final state. A custom flavor-tagging algorithm is employed for the simultaneous identification of b-jets and c-jets. In a fiducial phase space that replicates the acceptance of the ATLAS detector, the cross-sections for $t\bar{t}$ + ≥ 2c and $t\bar{t}$ + 1c production are measured to be $1.28^{+0.27}_{-0.24}$ pb and $6.4^{+1.0}_{-0.9}$ pb, respectively. The measurements are primarily limited by uncertainties in the modeling of inclusive $t\bar{t}$ and $t\bar{t}$ + $b\bar{b}$ production, in the calibration of the flavor-tagging algorithm, and by data statistics. Cross-section predictions from various $t\bar{t}$ simulations are largely consistent with the measured cross-section values, though all underpredict the observed values by 0.5 to 2.0 standard deviations. In a phase-space volume without requirements on the $t\bar{t}$ decay products and the jet multiplicity, the cross-section ratios of $t\bar{t}$ + ≥ 2c and $t\bar{t}$ + 1c to total $t\bar{t}$ + jets production are determined to be (1.23 ± 0.25)% and (8.8 ± 1.3)%.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Importance of a Priori Vertical Ozone Profiles for TEMPO Air Quality Retrievals

Ozone (O3) is a toxic pollutant which plays a major role in air quality. Typically, monitoring of surface air quality and O3 mixing ratios is conducted using in situ measurement networks. This is partially due to high-quality information related to air quality being limited from space-borne platforms due to coarse spatial resolution, limited temporal frequency, and minimal sensitivity to lower tropospheric and surface-level O3. The Tropospheric Emissions: Monitoring of Pollution (TEMPO) satellite is designed to address the limitations of current space-based platforms and to improve our ability to monitor North American air quality. TEMPO will provide hourly data of total column and vertical profiles of O3 with high spatial resolution to be used as a near-real-time air quality product. TEMPO O3 retrievals will apply the Smithsonian Astrophysical Observatory profile algorithm developed based on work from GOME (Global Ozone Monitoring Experiment), GOME-2, and OMI (Ozone Monitoring Instrument). This algorithm is suggested to use a priori O3 profile information from a climatological data-base developed from long-term ozone-sonde measurements (tropopause-based (TB-Clim) O3 climatology). This study evaluates the TB-Clim dataset and model simulated O3 profiles, which could potentially serve as a priori O3 profile information in TEMPO retrievals, from near-real-time data assimilation model products (NASA GMAO's (Global Modeling and Assimilation Office) operational GEOS-5 (Goddard Earth Observing System, Version 5) FP (Forecast Products) model and reanalysis data from MERRA2 (Modern-Era Retrospective analysis for Research and Applications, Version 2)) and a full chemical transport model (CTM), GEOS-Chem. In this study, vertical profile products are evaluated with surface (0-2 kilometers) and tropospheric (0-10 kilometers) TOLNet (Tropospheric Ozone Lidar Network) observations and the theoretical impact of individual a priori profile sources on the accuracy of TEMPO O3 retrievals in the troposphere and at the surface are presented. Results indicate that while the TB-Clim climatological dataset can replicate seasonally-averaged tropospheric O3 profiles, model-simulated profiles from a full CTM resulted in more accurate tropospheric and surface-level O3 retrievals from TEMPO when compared to hourly and daily-averaged TOLNet observations. Furthermore, it is shown that when large surface O3 mixing ratios are observed, TEMPO retrieval values at the surface are most accurate when applying CTM a priori profile information compared to all other data products.

Priori↗

Duck hepatitis B virus covalently closed circular DNA appears to survive hepatocyte mitosis in the growing liver

Nucleos(t)ide analogues that inhibit hepatitis B virus (HBV) DNA replication are typically used as monotherapy for chronically infected patients. Treatment with a nucleos(t)ide analogue eliminates most HBV DNA replication intermediates and produces a gradual decline in levels of covalently closed circular DNA (cccDNA), the template for viral RNA synthesis. It remains uncertain if levels of cccDNA decline primarily through hepatocyte death, or if loss also occurs during hepatocyte mitosis. To determine if cccDNA survives mitosis, growing ducklings infected with duck hepatitis B virus (DHBV) were treated with the nucleoside analogue, Entecavir. Viremia was suppressed at least 10{sup 5}-fold, during a period when average liver mass increased 23-fold. Analysis of the data suggested that if cccDNA synthesis was completely inhibited, at least 49% of cccDNA survived hepatocyte mitosis. However, there was a large duck-to-duck variation in cccDNA levels, suggesting that low level cccDNA synthesis may contribute to this apparent survival through mitosis. - Highlights: • The hepatitis B virus nuclear template is covalently closed circular DNA (cccDNA). • cccDNA was studied during liver growth in duck hepatitis B virus infected ducks. • Virus DNA replication and new cccDNA synthesis were inhibited with Entecavir. • At least 49% of cccDNA appeared to survive hepatocyte mitosis. • Low level virus DNA synthesis may contribute to survival of cccDNA through mitosis.

60 APPLIED LIFE SCIENCES↗

Field testing and validation of a low-cost MPC for demand flexibility for grid-interactive K-12 schools

K-12 school buildings account for the highest energy consumption within the public sector. Implementing advanced HVAC controls in grid-interactive K-12 schools could bring substantial economic advantages and grid flexibility. Our previous study demonstrated that a low-cost model predictive control (MPC) solution, which coordinates multiple packaged units, can enable demand flexibility without major hardware upgrades. However, a significant gap remains between academic pilots and market-ready scalable solutions. This paper extends the previous single-site pilot to a multi-site demonstration involving three school campuses (95 total units) through a commercial technology transfer process. Addressing the challenge of verifying performance with sparse field data, we present a new statistical approach using Bayesian methods to estimate the MPC’s effect on peak demand. Unlike traditional methods, this approach robustly quantifies uncertainty in non-normal, limited datasets. The results confirm the solution’s replicability, achieving a 21.6–38.9% reduction in HVAC peak demand (10.8–22.1% at the site-level) with > 98% probability across diverse locations. Finally, we document critical barriers to scaling software-as-a-service (SaaS) solutions–such as API instability and diverse legacy systems–and offer practical strategies to accelerate the commercial adoption of grid-interactive efficient buildings.

Ham, Sang Woo↗

Primary and secondary battery consumption trends in Sweden 1996–2013: Method development and detailed accounting by battery type

Highlights: • Developed MFA method was validated by the national statistics. • Exponential increase of EEE sales leads to increase in integrated battery consumption. • Digital convergence is likely to be a cause for primary batteries consumption decline. • Factors for estimation of integrated batteries in EE are provided. • Sweden reached the collection rates defined by European Union. - Abstract: In this article, a new method based on Material Flow Accounting is proposed to study detailed material flows in battery consumption that can be replicated for other countries. The method uses regularly available statistics on import, industrial production and export of batteries and battery-containing electric and electronic equipment (EEE). To promote method use by other scholars with no access to such data, several empirically results and their trends over time, for different types of batteries occurrence among the EEE types are provided. The information provided by the method can be used to: identify drivers of battery consumption; study the dynamic behavior of battery flows – due to technology development, policies, consumers behavior and infrastructures. The method is exemplified by the study of battery flows in Sweden for years 1996–2013. The batteries were accounted, both in units and weight, as primary and secondary batteries; loose and integrated; by electrochemical composition and share of battery use between different types of EEE. Results show that, despite a fivefold increase in the consumption of rechargeable batteries, they account for only about 14% of total use of portable batteries. Recent increase in digital convergence has resulted in a sharp decline in the consumption of primary batteries, which has now stabilized at a fairly low level. Conversely, the consumption of integrated batteries has increased sharply. In 2013, 61% of the total weight of batteries sold in Sweden was collected, and for the particular case of alkaline manganese dioxide batteries, the value achieved 74%.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Explosively driven air blast in a conical shock tube

Explosively driven shock tubes present challenges in terms of safety concerns and expensive upkeep of test facilities but provide more realistic approximations to the air blast resulting from free-field detonations than those provided by gas-driven shock tubes. Likewise, the geometry of conical shock tubes can naturally approximate a sector cut from a spherically symmetric blast, leading to a better agreement with the blast profiles of free-field detonations when compared to those provided by shock tubes employing constant cross sections. The work presented in this article documents the design, fabrication, and testing of an explosively driven conical shock tube whose goal was to closely replicate the blast profile seen from a larger, free-field detonation. By constraining the blast through a finite area, large blasts (which can add significant damage and safety constraints) can be simulated using smaller explosive charges. The experimental data presented herein show that a close approximation to the free-field air blast profile due to a 1.5 lb charge of C4 at 76 in. can be achieved by using a 0.032 lb charge in a 76-in.-long conical shock tube (which translates to an amplification factor of nearly 50). Modeling and simulation tools were used extensively in designing this shock tube to minimize expensive fabrication costs.

42 ENGINEERING↗

A Representative Democracy to Reduce Interdependency in a Multimodel Ensemble

The collection of Earth system models available in the archive of phase 5 of CMIP (CMIP5) represents, at least to some degree, a sample of uncertainty of future climate evolution. The presence of duplicated code as well as shared forcing and validation data in the multiple models in the archive raises at least three potential problems: biases in the mean and variance, the overestimation of sample size, and the potential for spurious correlations to emerge in the archive because of model replication. Analytical evidence is presented to demonstrate that the distribution of models in the CMIP5 archive is not consistent with a random sample, and a weighting scheme is proposed to reduce some aspects of model codependency in the ensemble. A method is proposed for selecting diverse and skillful subsets of models in the archive, which could be used for impact studies in cases where physically consistent joint projections of multiple variables (and their temporal and spatial characteristics) are required.

54 ENVIRONMENTAL SCIENCES↗

Survey of Use Cases and Scenarios on the Open Energy Data Initiative Solar Systems Integration (OEDI SI) Platform

The Open Energy Data Initiative Solar Systems Integration (OEDI SI) Data and Modeling Platform offers a comprehensive set of use cases tailored for power systems analysis. Each use case is centered around a specific power system analysis problem, supported by composite input data and reference algorithms. These composite input datasets are meticulously assembled using OEDI SI's data preprocessing tools, which integrate raw data from various sources. The primary objectives of the OEDI SI Platform include facilitating access to composite input data through widely accepted input/output formats and verified results. This accessibility enables power system network researchers and developers to validate their algorithms and showcase their applications' capabilities to the broader community. Moreover, the platform strives to promote reproducible, robust, replicable, and generalizable solar systems integration research.

14 SOLAR ENERGY↗

Thermal Protection System P50 Cork Char Response Characterization to Ascent Flight Shear and Heating Environments

NASA’s Space Launch System (SLS) experienced deflagration of the acreage of the Core Stage base heat shield during the Green Run hot-fire test campaigns and Artemis I flight. The burning products from the base heat shield during Green Run hot-fire test operation led to concerns in aerothermal environments and thermal protection system (TPS) performance prior to Artemis I flight. Updated design thermal environments accounting for cork combustion were developed using Green Run measurements and assessed prior to Artemis I, resulting in increased TPS thickness for the base heat shield. This work documents a highly controlled ground test within the NASA Marshall Space Flight Center’s Propulsion Test Branch Hot Gas Facility (HGF) and investigates the P50 cork TPS response due to sensitivity changes in radiative heat rates and surface shear stress. Prior to testing at the HGF, most of the P50 cork panels had a thick layer of char due to the cork combustion process replicated in a thermal vacuum chamber. SLS ascent shear stress and heating rate profile were simulated within the HGF by running the combustion-driven wind tunnel at off-nominal conditions and Mach numbers below 1. This test data provided insight into aerothermal measurements from Artemis I flight as well as informing updated base heating design environments for Artemis II. An in-depth understanding of the TPS P50 cork char response and observations is presented for launch vehicle flight ascent environments.

aerothermodynamics↗

MULTIPHYSICS-MODELING OF FIRE-INDUCED URANIUM AEROSOL FORMATION – A-POSTERIORI BENCHMARKING OF EXPERIMENTS

The formulation and solution of a model that properly described the temperature profiles of uranium in fire conditions was prepared, verified and validated, to support a-posteriori benchmarking of historical experiments. Data from the multi-physics model combined with data regression from the experiments provides a useful tool for exploring sources of potential bias in historical experiments. The approaches used are augmented by visual observations and photographic evidence allowing for correlations between various phenomena, independent of whether or not that specific phenomena are part of the validated model. In this manner, the validated model is a tool for a-posteriori benchmarking, and not a model designed to replicate the experimental output exactly for any specific experiment. For experiments like the Clark (2015) experiments, this integrated model (including chemistry) demonstrated that the largest bias was associated in the metallurgy of the coupons. The model developed does serve as a basis for defending which of the historical alloys tested are the most appropriate for any other alloy being considered (e.g., one that has not yet been tested). The model identifies key reactions that impact uranium chemistry and can significantly bias experimental results. Through use of the model and energy balances, data from historical experiments by Elder and Tinkle (1980) were regressed and benchmarked. This study identifies that all uranium alloys are not equal and that there are distinct differences between the dominant alloys representing distinct metallurgical phases.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Say where you sample: Increasing site selection transparency in urban ecology

Urban ecological studies have the potential to extend our understanding of socio-ecological systems beyond that of an individual city or region. Cross-comparative empirical work and synthesis are imperative to develop a general urban ecological theory. This can be achieved only if studies are replicable and generalizable. Transparency in methods reporting facilitates generalizability and replicability by documenting the decisions scientists make during the various steps of research design; this is particularly true for sampling design and selection because of their impact on both internal and external validity and the potential to unintentionally introduce bias. Three interdependent aspects of sample design are study sample selection (e.g., specific organisms, soils, or water), sample specification (measurement of specific variable of interest), and site selection (locations sampled). Of these, documentation of site selection—the where component of sample design—is underrepresented in the urban ecology literature. Using a stratified random sample of 158 papers from 12 major urban ecology journals, we investigated how researchers selected study sites in urban ecosystems and evaluated whether their site selection methods were transparent. We extracted data from these papers using a 50-question, theory-based questionnaire and a multiple-reviewer approach. Our sample represented almost 45 years of urban ecology research across 40 different countries. We found that more than 80% of the papers read were not transparent in their site selection methodology. We do not believe site selection methods are replicable for 70% of the papers read. Key weaknesses include incomplete descriptions of populations and sampling frames, urban gradients, sample selection methods, and property access. Low transparency in reporting the where methodology limits urban ecologists’ ability to assess the internal and external validity of studies’ findings and to replicate published studies; it also limits the generalizability of existing studies. The challenges of low transparency are particularly relevant in urban ecology, a field where standard protocols for site selection and delineation are still being developed. These limitations interfere with the fields’ ability to build theory and inform policy. We conclude by offering a set of recommendations to increase transparency, replicability, and generalizability.

54 ENVIRONMENTAL SCIENCES↗

The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle

Chromatin modifications are epigenetic regulatory features with major roles in various cellular events, yet they remain understudied in algae. Here, we interrogated the genome-wide distribution pattern of mono- and trimethylated histone H3 lysine 4 (H3K4) using chromatin-immunoprecipitation followed by deep-sequencing (ChIP-seq) during key phases of the Chlamydomonas cell cycle: early G 1 phase, Zeitgeber Time 1 (ZT1), when cells initiate biomass accumulation, S/M phase (ZT13) when cells are replicating DNA and undergoing mitosis, and late G 0 phase (ZT23) when they are quiescent. Tri-methylated H3K4 was predominantly enriched at transcription start sites of the majority of protein coding genes (85%). The likelihood of a gene being marked by H3K4me3 correlated with it being transcribed at some point during the life cycle but not necessarily by continuous active transcription, as exemplified by early zygotic genes, which may remain transcriptionally dormant for thousands of generations between sexual cycles. The exceptions to this rule were around 120 loci, some of which encode non-poly-adenylated transcripts, such as small nuclear RNAs and replication-dependent histones that had H3K4me3 peaks only when they were being transcribed. Mono-methylated H3K4 was the default state for the vast majority of histones that were bound outside of transcription start sites and terminator regions of genes. A small fraction of the genome that was depleted of any H3 lysine 4 methylation was enriched for DNA cytosine methylation and the genes within these DNA methylation islands were poorly expressed. Besides marking protein coding genes, H3K4me3 ChIP-seq data served also as a annotation tool for validation of hundreds of long non-coding RNA genes.

59 BASIC BIOLOGICAL SCIENCES↗