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A genetically encoded biosensor reveals spatiotemporal variation in cellular phosphate content in Brachypodium distachyon mycorrhizal roots
Arbuscular mycorrhizal (AM) symbiosis is accompanied by alterations to root cell metabolism and physiology, and to the pathways of orthophosphate (Pi) entry into the root, which increase with Pi delivery to cortical cells via arbuscules. How AM symbiosis influences the Pi content and Pi response dynamics of cells in the root cortex and epidermis is unknown. Using fluorescence resonance energy transfer (FRET)-based Pi biosensors, here we mapped the relative cytosolic and plastidic Pi content of Brachypodium distachyon mycorrhizal root cells, analyzed responses to extracellular Pi and traced extraradical hyphae-mediated Pi transfer to colonized cells. Colonized cortical cells had a higher cytosolic Pi content relative to noncolonized cortical and epidermal cells, while plastidic Pi content was highest in cells at the infection front. Pi application to the entire mycorrhizal root resulted in transient changes in cytosolic Pi that differed in direction and magnitude depending on cell type and arbuscule status; cells with mature arbuscules showed a substantial transient increase in cytosolic Pi while those with collapsed arbuscules showed a decrease. Directed Pi application to extraradical hyphae resulted in measurable changes in cytosolic Pi of colonized cells 18 h after application. Our experiments reveal that cells within a mycorrhizal root vary in Pi content and Pi response dynamics.
Spatiotemporal analysis of lung immune dynamics in lethal Coccidioides posadasii infection
Coccidioidomycosis, or Valley fever, is a lung disease caused by inhalation of Coccidioides fungi, prevalent in the Southwestern United States, Mexico, and parts of Central and South America. Annually, the United States reports 10,000–20,000 cases, although those numbers are expected to increase as climate change expands the fungal geographic range. While 60% of infections are asymptomatic, 40% symptomatic infections are often misdiagnosed due to similarities with bronchitis or pneumonia. A small subset of infection progress to severe illness, necessitating a better understanding of immune responses during lethal infection. Using single-cell RNA sequencing and spatial transcriptomics, we characterized lung responses during Coccidioides infection. We identified monocyte-derived Spp1-expressing macrophages as potential mediators of tissue remodeling and fibrosis, marked by high expression of profibrotic and proinflammatory transcripts. These macrophages showed elevated TGF-β and IL-6 signaling, pathways involved in fibrosis pathogenesis. Additionally, we observed significant neutrophil infiltration and defective lymphocyte responses, indicating severe adaptive immunity dysregulation in lethal, acute infection. These findings enhance our understanding of Coccidioides infection and suggest new therapeutic targets.
Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale
Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment.
Spatiotemporal Variability of Electric System Reliability Metrics
As urbanization continues to grow, urban density also rises, placing significant stress on critical infrastructure. Cities often face challenges in investing in new infrastructure or upgrading existing ones. One area of infrastructure that has come under strain is the electric grid, leading to prolonged power outages. According to data from the U.S. Energy Information Administration, the average duration of power outages has steadily doubled from 2013 to 2021, primarily due to extreme weather events. The IEEE has developed a series of reliability metrics to assess the reliability of the electric system. However, these metrics are only applied at the utility level, making it challenging to comprehend the variations in these indices at finer spatial resolutions and, consequently, evaluate reliability at the non-utility level. In this study, we leveraged electric outage data collected at 15-minute intervals at the county level to estimate electric system reliability over a six-year period using a novel data analysis approach. Our findings reveal a gradual decline in reliability in the U.S. Southwest compared to national averages. Furthermore, the duration of outages per customer per event has significantly decreased in large portions of California and Florida. These discoveries can be valuable for utility companies as they seek to pinpoint regional anomalies and plan for prioritized remediation efforts.
Intelligent Sampling of Extreme-Scale Turbulence Datasets for Accurate and Efficient Spatiotemporal Model Training
With the end of Moore’s law and Dennard scaling, efficient training increasingly requires rethinking data volume. Can we train better models with significantly less data via intelligent subsampling? To explore this, we develop SICKLE, a sparse intelligent curation framework for efficient learning, featuring a novel maximum entropy (MaxEnt) sampling approach, scalable training, and energy benchmarking. We compare MaxEnt with random and phase-space sampling on large direct numerical simulation (DNS) datasets of turbulence. Evaluating SICKLE at scale on Frontier, we show that subsampling as a preprocessing step can, in many cases, improve model accuracy and substantially lower energy consumption, with observed reductions of up to 38×.
Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models
Abstract Background A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. Results Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp 614 Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro 323 Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. Conclusions These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
Spatiotemporally Registered In-Situ and Ex-Situ Datasets for Laser-based Blown Powder Directed Energy Deposition
This dataset is comprised of in situ sensing data collected during laser-based, blown powder directed energy deposition (DED) of Inconel 718 representing eight different printing conditions: (1) nominal, (2) +15% scan speed, (3) +12% laser power, (4) +42% powder feed rate, (5) +100% jerk limit, (6) +10% layer height, (7) +20% hatch spacing, (8) +20% carrier gas flow. All eight DED builds constructed an identical test coupon geometry consisting of geometric features representative of industrial print requirements (e.g., bulk deposition, thin walls, overhangs). In situ data consists of xyz-coordinates (100 Hz) and on-axis melt pool camera video (60 Hz), both of which have been temporally synchronized to spatially map the melt pool camera data. In addition, post-build X-ray computed tomography (XCT) data for each of the eight test geometries have been spatially registered to the recorded xyz-coordinates, allowing for comparisons between melt pool camera data and flaws identified in the XCT data.
Spatiotemporal refraction of light in an epsilon-near-zero indium tin oxide layer: frequency shifting effects arising from interfaces
When light travels through a medium in which the refractive index is rapidly changing with time, the light will undergo a shift in its frequency. Significant frequency shifting effects have recently been reported for transparent conductive oxides. These observations have been interpreted as emerging from temporal changes to the propagation phase in a bulk medium resulting from temporal variations in the refractive index. It is an effect referred to as temporal refraction. Here, we show that the frequency shift in an epsilon-near-zero layer made of indium tin oxide originates not only from this bulk response but includes a significant effect resulting from temporal changes to the spatial boundary conditions. This boundary effect can lead to a dominant, opposing shift to the bulk effect for certain angles. Hence, this process gives rise to a frequency shift that can be tailored through the angle, decoupling the amplitude and phase modulation.
Spatiotemporal sampling of near-petahertz vortex fields
Measuring the field of visible light with high spatial resolution has been challenging, as many established methods only detect a focus-averaged signal. Here, we introduce a near-field method for optical field sampling that overcomes that limitation by employing the localization of the enhanced near-field of a nanometric needle tip. A probe field perturbs the photoemission from the tip, which is induced by a pump pulse, generating a field-dependent current modulation that can easily be captured with our electronic detection scheme. The approach provides reliable characterization of near-petahertz fields. We show that not only the spiral wavefront of visible femtosecond light pulses carrying orbital angular momentum (OAM) can be resolved but also the field evolution with time in the focal plane. Additionally, our method is polarization sensitive, which makes it applicable to vectorial field reconstruction.
Single-shot spatiotemporal plasma density measurements with a chirped probe pulse
In this work, we present the development and demonstration of a diagnostic for the measurement of the spatial and temporal evolution of plasma density in a single shot. Single-shot Advanced Plasma Probe HolographIc REconstruction (SAPPHIRE) utilizes a chirped probe pulse, a diffractive optical element, a self-referenced interferometer, and an interference bandpass filter to achieve high-fidelity electron density measurements suitable for underdense plasmas that exhibit cylindrical symmetry. The method overcomes limitations in conventional diagnostics, such as reliance on shot-to-shot reproducibility, while capturing plasma dynamics on picosecond timescales with micron-level spatial resolution. The capabilities of SAPPHIRE are demonstrated through measurements of laser-driven plasma channels in helium–nitrogen gas jets. SAPPHIRE demonstrates the formation and expansion of plasma channels in a single shot and the propagation of supersonic ionization fronts while revealing shot-to-shot variations in the plasma profiles. Experimental results are validated against theoretical models and scaling laws, underscoring the robustness and accuracy of this technique. By enabling ultrafast, high-resolution plasma diagnostics in a single exposure, SAPPHIRE represents a transformative advancement in plasma measurement technology.
Spatiotemporal imaging and manipulation of surface plasmons
Abstract Surface plasmon polaritons (SPPs) are travelling surface waves that have shown promise for applications in nanophotonics as they provide a direct route toward photon-mediated electrical signal generation – a central paradigm for speeding up and scaling down photonic elements. SPP waves have also generated fundamental interest due to their high-field strength and sub-wavelength confinement, properties that have enabled the surface-enhanced Raman effect. Over the last decade, photoemission electron microscopy (PEEM) has emerged as a pioneering technique for imaging surface electric fields through ultrashort laser pulse mediated electron emission and has therefore become an indispensable tool for characterizing plasmonic phenomena at interfaces in a variety of materials. PEEM offers nanometer spatial resolution and femtosecond temporal resolution, allowing SPPs to be prepared, monitored, and manipulated on the nanometer-femtosecond scale. Through a brief review of recent reports, we aim to introduce PEEM-based SPP imaging and manipulation modalities and highlight their utility in the context of emerging nanoscale and quantum materials science advancements.
Tethys: A Spatiotemporal Downscaling Model for Global Water Demand
Humans use water for many important tasks, such as drinking, growing food, and cooling power plants. Since future water demands depend on complex global interactions between economic sectors (e.g., demand for wheat in one country causing demand for water to grow that wheat in another country), it is often modeled at coarse spatial and temporal scales as part of models that account for complex, multi-sector system dynamics. However, models that project future water availability typically simulate physical processes at much finer scales. Tethys enables integration between these kinds of models by downscaling region-scale water demand projections using sector-specific proxies and formulas.
Big-Data-Driven Geo-Spatiotemporal Correlation Analysis between Precursor Pollen and Influenza and its Implication to Novel Coronavirus Outbreak
Although studies of many respiratory viruses and pollens are often framed by both seasonal and health related perspectives, pollen has yet to be extensively examined as an important covariate to seasonal respiratory viruses (SRVs) in any context, including a causal one. This study contributes to those goals through an investigation of SRVs and pollen counts at selected regions across the Western Hemisphere. Two complementary decadal-scaled geospatial profiles were developed. One laterally spanned the US and was anchored by detailed pollen information for Albuquerque, New Mexico. The other straddled the equator to include Fortaleza, Brazil. We found that the geospatial and climatological patterns of pollen advancement and decline across the US every year presented a statistically significant correlation to the subsequent emergence and decline of SRVs. Other significant covariates included winds, temperatures, and atmospheric moisture. Our study indicates that areas of the US with lower geostrophic wind baselines are typically areas of persistently higher and earlier influenza like illness (ILI) cases. In addition to that continental- scaled contrast, many sites indicated seasonal highs of geostrophic winds and ILI which were closely aligned. These observations suggest extensive scale-dependent connectivity of viruses to geostrophic circulation. Pollen emergence and its own scale-dependent circulation may contribute to the geospatial and seasonal patterns of ILI. We explore some uncertainties associated with this investigation, and consider the possibility that in a temperate climate, following a Spring pollen emergence, a resulting increase in pollen triggered human Immunoglobulin E (IgE) antibodies may suppress ILIs for several months.
Spatiotemporal Analyses of Groundwater and Shoreline Cr(VI) Concentrations in the 100 Areas at Hanford
Cleanup efforts have been ongoing since the late 1990s to remediate contaminated waste sites and groundwater in the 100 Areas at the U.S. Department of Energy (DOE) Hanford Site. One of the primary contaminants of concern is hexavalent chromium (Cr(VI)), which was used as a corrosion inhibitor in cooling water for nuclear reactors that formerly operated along the shoreline of the Columbia River. Cleanup efforts have included 1) removal, treatment (as needed), and disposal of contaminated sediments; 2) in situ redox manipulation as a permeable reactive barrier; 3) pump-and-treat; 4) soil flushing; and 5) monitored natural attenuation. DOE’s annual groundwater monitoring reports document the significant reductions in Cr(VI) plume areas that have occurred over the past 10 years or more as a result of these cleanup efforts. The Record of Decision for the 100-HR-3 operable unit specified a cleanup level (CUL) for Cr(VI) in groundwater of 48 µg/L to protect human receptors, and a surface water CUL of 10 µg/L to protect aquatic organisms in the Columbia River. The Record of Decision did not specify point-of-compliance locations for the surface water CUL. Data for 2019 from the six groundwater operable units (OUs) in the 100 Areas indicate that the 48 μg/L groundwater CUL has been achieved in 100% of the wells in the 100-BC and 100-NR OUs, and in 89- 97% of the wells in the other OUs (100-KR, 100-HR-D, 100-HR-H, 100-FR). Data for 2019 indicate that 100% of the aquifer tubes monitored for Cr(VI) in the 100 Areas have concentrations below the 48 μg/L groundwater CUL. However, the 10 μg/L standard has not yet been consistently achieved for both inland groundwater monitoring wells and shoreline aquifer tubes. This report describes a series of data analyses performed to identify consistent relationships, if any, between inland well and shoreline Cr(VI) concentrations within the 100 Areas. To this end, select monitoring data for Cr(VI) measured in groundwater and aquifer tubes at the 100 Areas were analyzed for a 10-year period—2010 to 2019. Relationships between inland groundwater plumes and surface-water points of discharge in and along the Columbia River were examined through several analyses that included inland well and aquifer tube concentrations as a function of distance from the shoreline, evaluation of cumulative probability plots, trend analysis, correlation analysis, cluster analysis, and identification of plume trajectories for each of the 100 Areas. The analyses did not identify consistent relationships between inland groundwater Cr(VI) concentrations and shoreline concentrations within the 100 Areas due to several confounding factors influencing groundwater flow directions and Cr(VI) concentrations. The proximity of groundwater Cr(VI) plumes to the river, and the highly dynamic nature of the river, influence the transport behavior of the plumes and create challenges for quantifying attenuation of Cr(VI) between the inland monitoring wells and shoreline concentrations. Other factors contributing to temporal and spatial Cr(VI) concentrations, as supported by some of the data analyses, include the presence of vadose zone sources, variable sorption behavior, and complexities associated with Cr(VI) mass transfer between the upper and lower aquifers and their interactions with the river. Hence, monitoring to assess compliance with target CULs will need to be determined for each area individually since several factors influence Cr(VI) concentrations in the 100 Areas.
AI-Based Approach for Advancing the Understanding of Spatiotemporal Drought Characteristics
Focal Area (3): Our proposal will focus on insight gleaned from observed and simulated complex data by using artificial intelligence (AI), big data analytics, and other advanced methods.