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"Bento, A"
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An open source chemical structure curation pipeline using RDKit
by
Atkinson, Francis
,
Leach, Andrew R.
,
Bellis, Louisa J.
in
ChEMBL
,
Chemistry
,
Chemistry and Materials Science
2020
Background
The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to consistent rules. In order to maintain the quality of the final database and to easily compare and integrate data on the same compound from different sources it is necessary for the chemical structures in the database to be appropriately standardised.
Results
A chemical curation pipeline has been developed using the open source toolkit RDKit. It comprises three components: a
Checker
to test the validity of chemical structures and flag any serious errors; a
Standardizer
which formats compounds according to defined rules and conventions and a
GetParent
component that removes any salts and solvents from the compound to create its parent. This pipeline has been applied to the latest version of the ChEMBL database as well as uncurated datasets from other sources to test the robustness of the process and to identify common issues in database molecular structures.
Conclusion
All the components of the structure pipeline have been made freely available for other researchers to use and adapt for their own use. The code is available in a GitHub repository and it can also be accessed via the ChEMBL Beaker webservices. It has been used successfully to standardise the nearly 2 million compounds in the ChEMBL database and the compound validity checker has been used to identify compounds with the most serious issues so that they can be prioritised for manual curation.
Journal Article
The Effect of Drought on Vegetation Gross Primary Productivity under Different Vegetation Types across China from 2001 to 2020
2022
Climate change has exacerbated the frequency and severity of droughts worldwide. Evaluating the response of gross primary productivity (GPP) to drought is thus beneficial to improving our understanding of the impact of drought on the carbon cycle balance. Although many studies have investigated the relationship between vegetation productivity and dry/wet conditions, the capability of different drought indices of assessing the influence of water deficit is not well understood. Moreover, few studies consider the effects of drought on vegetation with a focus on periods of drought. Here, we investigated the spatial-temporal patterns of GPP, the standardized precipitation evapotranspiration index (SPEI), and the vapor pressure deficit (VPD) in China from 2001 to 2020 and examined the relationship between GPP and water deficit/drought for different vegetation types. The results revealed that SPEI and GPP were positively correlated over approximately 70.7% of the total area, and VPD was negatively correlated with GPP over about 66.2% of the domain. Furthermore, vegetation productivity was more negatively affected by water deficit in summer and autumn. During periods of drought, the greatest negative impact was on deciduous forests and croplands, and woody savannas were the least impacted. This research provides a scientific reference for developing mitigation and adaptation measures to lessen the impact of drought disasters under a changing climate.
Journal Article
An improved global vegetation health index dataset in detecting vegetation drought
2023
Due to global warming, drought events have become more frequent, which resulted in aggravated crop failures, food shortage, larger and more energetic wildfires, and have seriously affected socio-economic development and agricultural production. In this study, a global long-term (1981–2021), high-resolution (4 km) improved vegetation health index (VHI) dataset integrating climate, vegetation and soil moisture was developed. Based on drought records from the Emergency Event Database, we compared the detection efficiency of the VHI before and after its improvement in the occurrence and scope of observed drought events. The global drought detection efficiency of the improved high-resolution VHI dataset reached values as high as 85%, which is 14% higher than the original VHI dataset. The improved VHI dataset was also more sensitive to mild droughts and more accurate regarding the extent of droughts. This improved dataset can play an important role in long-term drought monitoring but also has the potential to assess the impact of drought on the agricultural, forestry, ecological and environmental sectors.
Journal Article
Understanding climate change impacts on drought in China over the 21st century: a multi-model assessment from CMIP6
by
Zhang, Xuesong
,
Miao, Lijuan
,
Xu, Feng
in
704/106/694/2739
,
704/106/694/2786
,
Atmospheric Protection/Air Quality Control/Air Pollution
2024
The future state of drought in China under climate change remains uncertain. This study investigates drought events, focusing on the region of China, using simulations from five global climate models (GCMs) under three Shared Socioeconomic Pathways (SSP1-2.6, SSP3-7.0, and SSP5-8.5) participating in the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3b). The daily Standardized Precipitation Evapotranspiration Index (SPEI) is employed to analyze drought severity, duration, and frequency over three future periods. Evaluation of the GCMs’ simulations against observational data indicates their effectiveness in capturing historical climatic change across China. The rapid increase in CO
2
concentration under high-emission scenarios in the mid- and late-future century (2040–2070 and 2071–2100) substantially influences vegetation behavior via regulation on leaf stomata and canopy structure. This regulation decelerates the increase in potential evapotranspiration, thereby mitigating the sharp rise in future drought occurrences in China. These findings offer valuable insights for policymakers and stakeholders to develop strategies and measures for mitigating and adapting to future drought conditions in China.
Journal Article
Understanding vegetation phenology responses to easily ignored climate factors in china's mid-high latitudes
2024
Previous studies have primarily focused on the influence of temperature and precipitation on phenology. It is unclear if the easily ignored climate factors with drivers of vegetation growth can effect on vegetation phenology. In this research, we conducted an analysis of the start (SOS) and end (EOS) of the growing seasons in the northern region of China above 30°N from 1982 to 2014, focusing on two-season vegetation phenology. We examined the response of vegetation phenology of different vegetation types to preseason climatic factors, including relative humidity (RH), shortwave radiation (SR), maximum temperature (Tmax), and minimum temperature (Tmin). Our findings reveal that the optimal preseason influencing vegetation phenology length fell within the range of 0–60 days in most areas. Specifically, SOS exhibited a significant negative correlation with Tmax and Tmin in 44.15% and 42.25% of the areas, respectively, while EOS displayed a significant negative correlation with SR in 49.03% of the areas. Additionally, we identified that RH emerged as the dominant climatic factor influencing the phenology of savanna (SA), whereas temperature strongly controlled the SOS of deciduous needleleaf forest (DNF) and deciduous broadleaf forest (DBF). Meanwhile, the EOS of DNF was primarily influenced by Tmax. In conclusion, this study provides valuable insights into how various vegetation types adapt to climate change, offering a scientific basis for implementing effective vegetation adaptation measures.
Journal Article
Enhancing evapotranspiration estimates under climate change: the role of CO2 physiological feedback and CMIP6 scenarios
by
Shui, Wei
,
Qiu, Han
,
Song, Hongquan
in
Carbon dioxide
,
Carbon dioxide concentration
,
Climate and vegetation
2025
The future state of global evapotranspiration (ET) estimation under climate change remains uncertain. Current formulations primarily developed based on the high emission CMIP5 scenario, have been widely used to represent conditions under elevated greenhouse gas pathways. However, these formulations may not adequately capture the enhanced vegetation–climate interactions projected under the lower-emission scenarios of CMIP6. Without updates to account for evolving plant physiological responses to rising CO2, projections may overlook critical feedbacks between atmospheric CO2 concentrations, vegetation behavior, and hydrological processes. To address this, developing CMIP6-specific formulations is essential to leverage its improved datasets and reduce uncertainties in future ET simulations. In this study, we update the Penman-Monteith evapotranspiration (PM-ET) model by incorporating the CO2-vegetation coupling effect. This is achieved using outputs from four Coupled Model Intercomparison Project Phase 6 (CMIP6) global climate models (GCMs) under four Shared Socioeconomic Pathways (SSP1-2.6, SSP2-4.5, SSP3-7.0, SSP5-8.5). Results indicate a sustained historical increase in potential evapotranspiration (Ep). The inclusion of CO2 physiological effects reduces the deviation in projected ET trends by approximately 15 %–20 % compared to CMIP5-based frameworks, accounting for the increase in stomatal resistance driven by CO2 concentrations rising from ∼284 to ∼ 935 ppm. Furthermore, our model predicts an increasing dependence of ET projections on emission scenario, highlighting the growing influence of pathway-specific feedbacks. Overall, our approach demonstrates greater compatibility with CMIP6 simulations, allowing for more accurate representation of ET responses to future CO2 increases. These findings provide valuable insights for advancing the analysis of nonlinear vegetation-atmosphere interactions and hydrological uncertainty under climate and physiological forcings.
Journal Article
The impact of climate change in wheat and barley yields in the Iberian Peninsula
by
Bento, Virgílio A.
,
Russo, Ana
,
Ribeiro, Andreia F. S.
in
704/106
,
704/106/694
,
704/106/694/2739
2021
The impact of climate change on wheat and barley yields in two regions of the Iberian Peninsula is here examined. Regression models are developed by using EURO-CORDEX regional climate model (RCM) simulations, forced by ERA-Interim, with monthly maximum and minimum air temperatures and monthly accumulated precipitation as predictors. Additionally, RCM simulations forced by different global climate models for the historical period (1972–2000) and mid-of-century (2042–2070; under the two emission scenarios RCP4.5 and RCP8.5) are analysed. Results point to different regional responses of wheat and barley. In the southernmost regions, results indicate that the main yield driver is spring maximum temperature, while further north a larger dependence on spring precipitation and early winter maximum temperature is observed. Climate change seems to induce severe yield losses in the southern region, mainly due to an increase in spring maximum temperature. On the contrary, a yield increase is projected in the northern regions, with the main driver being early winter warming that stimulates earlier growth. These results warn on the need to implement sustainable agriculture policies, and on the necessity of regional adaptation strategies.
Journal Article
Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure
2023
We conduct a large-scale meta-analysis of heart failure genome-wide association studies (GWAS) consisting of over 90,000 heart failure cases and more than 1 million control individuals of European ancestry to uncover novel genetic determinants for heart failure. Using the GWAS results and blood protein quantitative loci, we perform Mendelian randomization and colocalization analyses on human proteins to provide putative causal evidence for the role of druggable proteins in the genesis of heart failure. We identify 39 genome-wide significant heart failure risk variants, of which 18 are previously unreported. Using a combination of Mendelian randomization proteomics and genetic cis-only colocalization analyses, we identify 10 additional putatively causal genes for heart failure. Findings from GWAS and Mendelian randomization-proteomics identify seven (
CAMK2D
,
PRKD1
,
PRKD3
,
MAPK3
,
TNFSF12
,
APOC3
and
NAE1
) proteins as potential targets for interventions to be used in primary prevention of heart failure.
Here, the authors perform a large-scale meta-analysis of genome-wide association studies and cis-MR proteomics to identify protein biomarkers and drug targets for heart failure.
Journal Article
Meteosat Land Surface Temperature Climate Data Record: Achievable Accuracy and Potential Uncertainties
2015
The European Organization for the Exploitation of Meteorological Satellites’ (EUMETSAT) Meteosat satellites provide the unique opportunity to compile a 30+ year land surface temperature (LST) climate data record. Since the Meteosat instrument on-board Meteosat 2–7 is equipped with a single thermal channel, single-channel LST retrieval algorithms are used to ensure consistency across Meteosat satellites. The present study compares the performance of two single-channel LST retrieval algorithms: (1) A physical radiative transfer-based mono-window (PMW); and (2) a statistical mono-window model (SMW). The performance of the single-channel algorithms is assessed using a database of synthetic radiances for a wide range of atmospheric profiles and surface variables. The two single-channel algorithms are evaluated against the commonly-used generalized split-window (GSW) model. The three algorithms are verified against more than 60,000 LST ground observations with dry to very moist atmospheres (total column water vapor (TCWV) 1–56 mm). Except for very moist atmospheres (TCWV > 45 mm), results show that Meteosat single-channel retrievals match those of the GSW algorithm by 0.1–0.5 K. This study also outlines that it is possible to put realistic uncertainties on Meteosat single-channel LSTs, except for very moist atmospheres: simulated theoretical uncertainties are within 0.3–1.0 K of the in situ root mean square differences for TCWV < 45 mm.
Journal Article
High-resolution downscaling of CMIP6 Earth system and global climate models using deep learning for Iberia
by
Bento, Virgílio A
,
Lemos, Gil
,
Johannsen, Frederico
in
Artificial intelligence
,
Artificial neural networks
,
Climate change
2024
Deep learning (DL) methods have recently garnered attention from the climate change community for being an innovative approach to downscaling climate variables from Earth system and global climate models (ESGCMs) with horizontal resolutions still too coarse to represent regional- to local-scale phenomena. In the context of the Coupled Model Intercomparison Project phase 6 (CMIP6), ESGCM simulations were conducted for the Sixth Assessment Report (AR6) of the Intergovernmental Panel on Climate Change (IPCC) at resolutions ranging from 0.70 to 3.75∘. Here, four convolutional neural network (CNN) architectures were evaluated for their ability to downscale, to a resolution of 0.1∘, seven CMIP6 ESGCMs over the Iberian Peninsula – a known climate change hotspot, due to its increased vulnerability to projected future warming and drying conditions. The study is divided into three stages: (1) evaluating the performance of the four CNN architectures in predicting mean, minimum, and maximum temperatures, as well as daily precipitation, trained using ERA5 data and compared with the Iberia01 observational dataset; (2) downscaling the CMIP6 ESGCMs using the trained CNN architectures and further evaluating the ensemble against Iberia01; and (3) constructing a multi-model ensemble of CNN-based downscaled projections for temperature and precipitation over the Iberian Peninsula at 0.1∘ resolution throughout the 21st century under four Shared Socioeconomic Pathway (SSP) scenarios. Upon validation and satisfactory performance evaluation, the DL downscaled projections demonstrate overall agreement with the CMIP6 ESGCM ensemble in magnitude for temperature projections and sign for the projected temperature and precipitation changes. Moreover, the advantages of using a high-resolution DL downscaled ensemble of ESGCM climate projections are evident, offering substantial added value in representing regional climate change over Iberia. Notably, a clear warming trend is observed in Iberia, consistent with previous studies in this area, with projected temperature increases ranging from 2 to 6 ∘C, depending on the climate scenario. Regarding precipitation, robust projected decreases are observed in western and southwestern Iberia, particularly after 2040. These results may offer a new tool for providing regional climate change information for adaptation strategies based on CMIP6 ESGCMs prior to the next phase of the European branch of the Coordinated Regional Climate Downscaling Experiment (EURO-CORDEX) experiments.
Journal Article