Deep learning estimation of northern hemisphere soil freeze-thaw dynamics using satellite multi-frequency microwave brightness temperature observations.

Satellite microwave sensors are well suited for monitoring landscape freeze-thaw (FT) transitions owing to the strong brightness temperature (TB) or backscatter response to changes in liquid water abundance between predominantly frozen and thawed conditions. The FT retrieval is also a sensitive climate indicator with strong biophysical importance. However, retrieval algorithms can have difficulty distinguishing the FT status of soils from that of overlying features such as snow and vegetation, while variable land conditions can also degrade performance. Here, we applied a deep learning model using a multilayer convolutional neural network driven by AMSR2 and SMAP TB records, and trained on surface (~0-5 cm depth) soil temperature FT observations. Soil FT states were classified for the local morning (6 a.m.) and evening (6 p.m.) conditions corresponding to SMAP descending and ascending orbital overpasses, mapped to a 9 km polar grid spanning a five-year (2016-2020) record and Northern Hemisphere domain. Continuous variable estimates of the probability of frozen or thawed conditions were derived using a model cost function optimized against FT observational training data. Model results derived using combined multi-frequency (1.4, 18.7, 36.5 GHz) TBs produced the highest soil FT accuracy over other models derived using only single sensor or single frequency TB inputs. Moreover, SMAP L-band (1.4 GHz) TBs provided enhanced soil FT information and performance gain over model results derived using only AMSR2 TB inputs. The resulting soil FT classification showed favorable and consistent performance against soil FT observations from ERA5 reanalysis (mean percent accuracy, MPA: 92.7%) and in situ weather stations (MPA: 91.0%). The soil FT accuracy was generally consistent between morning and afternoon predictions and across different land covers and seasons. The model also showed better FT accuracy than ERA5 against regional weather station measurements (91.0% vs. 86.1% MPA). However, model confidence was lower in complex terrain where FT spatial heterogeneity was likely beneath the effective model grain size. Our results provide a high level of precision in mapping soil FT dynamics to improve understanding of complex seasonal transitions and their influence on ecological processes and climate feedbacks, with the potential to inform Earth system model predictions.

Carbon uptake in Eurasian boreal forests dominates the high-latitude net ecosystem carbon budget.

Arctic-boreal landscapes are experiencing profound warming, along with changes in ecosystem moisture status and disturbance from fire. This region is of global importance in terms of carbon feedbacks to climate, yet the sign (sink or source) and magnitude of the Arctic-boreal carbon budget within recent years remains highly uncertain. Here, we provide new estimates of recent (2003-2015) vegetation gross primary productivity (GPP), ecosystem respiration (Reco ), net ecosystem CO2 exchange (NEE; Reco - GPP), and terrestrial methane (CH4 ) emissions for the Arctic-boreal zone using a satellite data-driven process-model for northern ecosystems (TCFM-Arctic), calibrated and evaluated using measurements from >60 tower eddy covariance (EC) sites. We used TCFM-Arctic to obtain daily 1-km2 flux estimates and annual carbon budgets for the pan-Arctic-boreal region. Across the domain, the model indicated an overall average NEE sink of -850 Tg CO2 -C year-1 . Eurasian boreal zones, especially those in Siberia, contributed to a majority of the net sink. In contrast, the tundra biome was relatively carbon neutral (ranging from small sink to source). Regional CH4 emissions from tundra and boreal wetlands (not accounting for aquatic CH4 ) were estimated at 35 Tg CH4 -C year-1 . Accounting for additional emissions from open water aquatic bodies and from fire, using available estimates from the literature, reduced the total regional NEE sink by 21% and shifted many far northern tundra landscapes, and some boreal forests, to a net carbon source. This assessment, based on in situ observations and models, improves our understanding of the high-latitude carbon status and also indicates a continued need for integrated site-to-regional assessments to monitor the vulnerability of these ecosystems to climate change.

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.

BACKGROUND: The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO) in early 2020. RESULTS: As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. CONCLUSION: CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications.

Methane Emission From Global Lakes: New Spatiotemporal Data and Observation-Driven Modeling of Methane Dynamics Indicates Lower Emissions.

Lakes have been highlighted as one of the largest natural sources of the greenhouse gas methane (CH4) to the atmosphere. However, global estimates of lake CH4 fluxes over the last 20 years exhibit widely different results ranging from 6 to 185 Tg CH4 yr-1, which is to a large extent driven by differences in lake areas and thaw season lengths used. This has generated uncertainty regarding both lake fluxes and the global CH4 budget. This study constrains global lake water CH4 emissions by using new information on lake area and distribution and CH4 fluxes distinguished by major emission pathways; ecoclimatic lake type; satellite-derived ice-free emission period length; and diel- and temperature-related seasonal flux corrections. We produced gridded data sets at 0.25° latitude × 0.25° longitude spatial resolution, representing daily emission estimates over a full annual climatological cycle, appropriate for use in global CH4 budget estimates, climate and Earth System Models, bottom-up biogeochemical models, and top-down inverse model simulations. Global lake CH4 fluxes are 41.6 ± 18.3 Tg CH4 yr-1 with approximately 50% of the flux contributed by tropical/subtropical lakes. Strong temperature-dependent flux seasonality and satellite-derived freeze/thaw dynamics limit emissions at high latitudes. The primary emission pathway for global annual lake fluxes is ebullition (23.4 Tg) followed by diffusion (14.1 Tg), ice-out and spring water-column turnover (3.1 Tg), and fall water-column turnover (1.0 Tg). These results represent a major contribution to reconciling differences between bottom-up and top-town estimates of inland aquatic system emissions in the global CH4 budget.

Uncovering nasopharyngeal carcinoma from chronic rhinosinusitis and healthy subjects using routine medical tests via machine learning.

Nasopharyngeal carcinoma (NPC) is one of the most common types of cancers in South China and Southeast Asia. Clinical data has shown that early detection is essential for improving treatment effectiveness and survival rate. Unfortunately, because the early symptoms of NPC are rather minor and similar to that of diseases such as Chronic Rhinosinusitis (CRS), early detection is a challenge. This paper proposes using machine learning methods to detect NPC using routine medical test data, namely Random Forest (RF), Support Vector Machine (SVM), and Artificial Neural Network (ANN), k-Nearest-Neighbor (KNN) and Logistic Regression (LR). We collected a dataset containing 523 newly diagnosed NPC patients before treatment, 501 newly diagnosed CRS patients before treatment as well as 600 healthy controls. The routine medical test data including age, gender, blood test features, liver function test features, and urine sediment test features. For comparison, we also used data from Epstein-Barr Virus (EBV) antibody tests, which is a specialized test not included among routine medical tests. In our first test, all four methods were tested on classifying NPC vs CRS vs controls; RF gives the best overall performance. Using only routine medical test data, it gives an accuracy of 83.1%, outperforming LR by 12%. In our second test, using only routine medical test data, when classifying NPC vs non-NPC (i.e. CRS or controls), RF achieves an accuracy of 88.2%. In our third test, when classifying NPC vs. controls, RF using only routine test data achieves an accuracy significantly better than RF using only EBV antibody data. Finally, in our last test, RF trained with NPC vs controls, using routine test data only, continued to perform well on an entirely separate dataset. This is a promising result because preliminary NPC detection using routine medical data is easy and inexpensive to implement. We believe this approach will play an important role in the detection and treatment of NPC in the future.

Satellite Flood Inundation Assessment and Forecast Using SMAP and Landsat.

The capability and synergistic use of multisource satellite observations for flood monitoring and forecasts is crucial for improving disaster preparedness and mitigation. Here, surface fractional water cover (FW) retrievals derived from Soil Moisture Active Passive (SMAP) L-band (1.4 GHz) brightness temperatures were used for flood assessment over southeast Africa during the Cyclone Idai event. We then focused on five subcatchments of the Pungwe basin and developed a machine learning based approach with the support of Google Earth Engine for daily (24-h) forecasting of FW and 30-m inundation downscaling and mapping. The Classification and Regression Trees model was selected and trained using retrievals derived from SMAP and Landsat coupled with rainfall forecasts from the NOAA Global Forecast System. Independent validation showed that FW predictions over randomly selected dates are highly correlated (R = 0.87) with the Landsat observations. The forecast results captured the flood temporal dynamics from the Idai event; and the associated 30-m downscaling results showed inundation spatial patterns consistent with independent satellite synthetic aperture radar observations. The data-driven approach provides new capacity for flood monitoring and forecasts leveraging synergistic satellite observations and big data analysis, which is particularly valuable for data sparse regions.

Large loss of CO2 in winter observed across the northern permafrost region.

Recent warming in the Arctic, which has been amplified during the winter1-3, greatly enhances microbial decomposition of soil organic matter and subsequent release of carbon dioxide (CO2)4. However, the amount of CO2 released in winter is highly uncertain and has not been well represented by ecosystem models or by empirically-based estimates5,6. Here we synthesize regional in situ observations of CO2 flux from arctic and boreal soils to assess current and future winter carbon losses from the northern permafrost domain. We estimate a contemporary loss of 1662 Tg C yr-1 from the permafrost region during the winter season (October through April). This loss is greater than the average growing season carbon uptake for this region estimated from process models (-1032 Tg C yr-1). Extending model predictions to warmer conditions in 2100 indicates that winter CO2 emissions will increase 17% under a moderate mitigation scenario-Representative Concentration Pathway (RCP) 4.5-and 41% under business-as-usual emissions scenario-RCP 8.5. Our results provide a new baseline for winter CO2 emissions from northern terrestrial regions and indicate that enhanced soil CO2 loss due to winter warming may offset growing season carbon uptake under future climatic conditions.

Global Satellite Retrievals of the Near-Surface Atmospheric Vapor Pressure Deficit from AMSR-E and AMSR2.

Near-surface atmospheric Vapor Pressure Deficit (VPD) is a key environmental variable affecting vegetation water stress, evapotranspiration, and atmospheric moisture demand. Although VPD is readily derived from in situ standard weather station measurements, more spatially continuous global observations for regional monitoring of VPD are lacking. Here, we document a new method to estimate daily (both a.m. and p.m.) global land surface VPD at a 25-km resolution using a satellite passive microwave remotely sensed Land Parameter Data Record (LPDR) derived from the Advanced Microwave Scanning Radiometer (AMSR) sensors. The AMSR-derived VPD record shows strong correspondence (correlation coefficient ≥ 0.80, p-value < 0.001) and overall good performance (0.48 kPa ≤ Root Mean Square Error ≤ 0.69 kPa) against independent VPD observations from the Modern-Era Retrospective analysis for Research and Applications, Version 2 (MERRA-2) data. The estimated AMSR VPD retrieval uncertainties vary with land cover type, satellite observation time, and underlying LPDR data quality. These results provide new satellite capabilities for global mapping and monitoring of land surface VPD dynamics from ongoing AMSR2 operations. Overall good accuracy and similar observations from both AMSR2 and AMSR-E allow for the development of climate data records documenting recent (from 2002) VPD trends and potential impacts on vegetation, land surface evaporation, and energy budgets.

Assessing global surface water inundation dynamics using combined satellite information from SMAP, AMSR2 and Landsat.

A method to assess global land surface water (fw) inundation dynamics was developed by exploiting the enhanced fw sensitivity of L-band (1.4 GHz) passive microwave observations from the Soil Moisture Active Passive (SMAP) mission. The L-band fw (fwLBand ) retrievals were derived using SMAP H-polarization brightness temperature (Tb ) observations and predefined L-band reference microwave emissivities for water and land endmembers. Potential soil moisture and vegetation contributions to the microwave signal were represented from overlapping higher frequency Tb observations from AMSR2. The resulting fwLBand global record has high temporal sampling (1-3 days) and 36-km spatial resolution. The fwLBand annual averages corresponded favourably (R=0.85, p-value<0.001) with a 250-m resolution static global water map (MOD44W) aggregated at the same spatial scale, while capturing significant inundation variations worldwide. The monthly fwLBand averages also showed seasonal inundation changes consistent with river discharge records within six major US river basins. An uncertainty analysis indicated generally reliable fwLBand performance for major land cover areas and under low to moderate vegetation cover, but with lower accuracy for detecting water bodies covered by dense vegetation. Finer resolution (30-m) fwLBand results were obtained for three sub-regions in North America using an empirical downscaling approach and ancillary global Water Occurrence Dataset (WOD) derived from the historical Landsat record. The resulting 30-m fwLBand retrievals showed favourable spatial accuracy for water (commission error 31.46%, omission error 30.20%) and land (commission error 0.87%, omission error 0.96%) classifications and seasonal wet and dry periods when compared to independent water maps derived from Landsat-8 imagery. The new fwLBand algorithms and continuing SMAP and AMSR2 operations provide for near real-time, multi-scale monitoring of global surface water inundation dynamics and potential flood risk.