Monitoring and modelling of soil–plant interactions: the joint use of ERT, sap flow and eddy covariance data to characterize the volume of an orange tree root zone

Abstract. Mass and energy exchanges between soil, plants and atmosphere control a number of key environmental processes involving hydrology, biota and climate. The understanding of these exchanges also play a critical role for practical purposes e.g. in precision agriculture. In this paper we present a methodology based on coupling innovative data collection and models in order to obtain quantitative estimates of the key parameters of such complex flow system. In particular we propose the use of hydro-geophysical monitoring via "time-lapse" electrical resistivity tomography (ERT) in conjunction with measurements of plant transpiration via sap flow and evapotranspiration (ET) from eddy covariance (EC). This abundance of data is fed to spatially distributed soil models in order to characterize the distribution of active roots. We conducted experiments in an orange orchard in eastern Sicily (Italy), characterized by the typical Mediterranean semi-arid climate. The subsoil dynamics, particularly influenced by irrigation and root uptake, were characterized mainly by the ERT set-up, consisting of 48 buried electrodes on 4 instrumented micro-boreholes (about 1.2 m deep) placed at the corners of a square (with about 1.3 m long sides) surrounding the orange tree, plus 24 mini-electrodes on the surface spaced 0.1 m on a square grid. During the monitoring, we collected repeated ERT and time domain reflectometry (TDR) soil moisture measurements, soil water sampling, sap flow measurements from the orange tree and EC data. We conducted a laboratory calibration of the soil electrical properties as a function of moisture content and porewater electrical conductivity. Irrigation, precipitation, sap flow and ET data are available allowing for knowledge of the system's long-term forcing conditions on the system. This information was used to calibrate a 1-D Richards' equation model representing the dynamics of the volume monitored via 3-D ERT. Information on the soil hydraulic properties was collected from laboratory and field experiments. The successful results of the calibrated modelling exercise allow for the quantification of the soil volume interested by root water uptake (RWU). This volume is much smaller (with a surface area less than 2 m2, and about 40 cm thick) than expected and assumed in the design of classical drip irrigation schemes that prove to be losing at least half of the irrigated water which is not taken up by the plants

A Method for Assessing Drift Potential of a Citrus Herbicide Applicator

The main objective of this study was to evaluate the suitability of the DEIAFA drift test bench system (Dipartimento di Economia e Ingegneria Agraria, Forestale e Ambientale; University of Torino, Italy) for assessing drift potential of a citrus (Citrus sp.) herbicide applicator. The study involved testing the effects of spray drift shield, nozzle type, and ground speed on drift potential of the applications. It was carried out in randomized block design within a split-split-plot experiment with five replications. A computational analysis procedure for evaluation of deposit values, measured along the test bench, was developed to compare the treatments in terms of a drift potential index (DPI). The methodology provided repeatable results. Among the treatments, ground speed was the main factor affecting the DPI. Both nozzle types tested [flat fan extended range nozzle (XR) and wide-angle deflector nozzle (TT)] showed higher DPI at faster speed. Decreasing the ground speed from 6.0 to 3.0 km·h−1 decreased the drift potential on average ≈35%. The performance of XR nozzle was improved by the presence of spray drift shield (27% reduction in DPI). However, the shield did not affect the drift potential of the TT nozzle significantly. The results were significantly affected by the wind velocity normalized by its direction relative to the sprayer travel; therefore, the tests should be carried out in relatively calm wind conditions, as much as possible

Institutions and the uneven geography of the first wave of the COVID-19 pandemic

This paper examines the uneven geography of COVID-19-related excess mortality during the first wave of the pandemic in Europe, before assessing the factors behind the geographical differences in impact. The analysis of 206 regions across 23 European countries reveals a distinct COVID-19 geography. Excess deaths were concentrated in a limited number of regions —expected deaths exceeded 20% in just 16 regions— with more than 40% of the regions considered experiencing no excess mortality during the first six months of 2020. Highly connected regions, in colder and dryer climates, with high air pollution levels, and relatively poorly endowed health systems witnessed the highest incidence of excess mortality. Institutional factors also played an important role. The first wave hit regions with a combination of weak and declining formal institutional quality and fragile informal institutions hardest. Low and declining national government effectiveness, together with a limited capacity to reach out across societal divides, and a frequent tendency to meet with friends and family were powerful drivers of regional excess mortality

Increased heme-oxygenase 1 expression in mesenchymal stem cell-derived adipocytes decreases differentiation and lipid accumulation via upregulation of the canonical Wnt signaling cascade

Introduction: Heme oxygenase (HO), a major cytoprotective enzyme, attenuates oxidative stress and obesity. The canonical Wnt signaling cascade plays a pivotal role in the regulation of adipogenesis. The present study examined the interplay between HO-1and the Wnt canonical pathway in the modulation of adipogenesis in mesenchymal stem cell (MSC)-derived adipocytes. Methods: To verify the role of HO-1 in generating small healthy adipocytes, cobalt protoporphyrin (CoPP), inducer of HO-1, was used during adipocyte differentiation. Lipid accumulation was measured by Oil red O staining and lipid droplet size was measured by BODIPY staining. Results: During adipogenesis in vitro, differentiating pre-adipocytes display transient increases in the expression of genes involved in canonical Wnt signaling cascade. Increased levels of HO-1 expression and HO activity resulted in elevated levels of b-catenin, pGSK3b, Wnt10b, Pref-1, and shh along with increased levels of adiponectin (P \u3c 0.05). In addition, induction of HO-1 resulted in a reduction in C/EBPa, PPARg, Peg-1/Mest, aP2, CD36 expression and lipid accumulation (P \u3c 0.05). Suppression of HO-1 gene by siRNA decreased Wnt10b, pGSK3b and b-catenin expression, and increased lipid accumulation. The canonical Wnt responsive genes, IL-8 and SFRP1, were upregulated by CoPP and their expression was decreased by the concurrent administration of tin mesoporphyrin (SnMP), an inhibitor of HO activity. Furthermore, knockdown of Wnt10b gene expression by using siRNA showed increased lipid accumulation, and this effect was not decreased by concurrent treatment with CoPP. Also our results show that blocking the Wnt 10b antagonist, Dickkopf 1 (Dkk-1), by siRNA decreased lipid accumulation and this effect was further enhanced by concurrent administration of CoPP. Conclusions: This is the first study to demonstrate that HO-1 acts upstream of canonical Wnt signaling cascade and decreases lipogenesis and adipocyte differentiation suggesting that the HO-1 mediated increase in Wnt10b can modulate the adipocyte phenotype by regulating the transcriptional factors that play a role in adipogenesis. This is evidenced by a decrease in lipid accumulation and inflammatory cytokine levels, increased adiponectin levels and elevation of the expression of genes of the canonical Wnt signaling cascade

Comparing the use of ERA5 reanalysis dataset and ground-based agrometeorological data under different climates and topography in Italy

Study region: The study region is represented by seven irrigation districts distributed under different climate and topography conditions in Italy. Study focus: This study explores the reliability and consistency of the global ERA5 single levels and ERA5-Land reanalysis datasets in predicting the main agrometeorological estimates commonly used for crop water requirements calculation. In particular, the reanalysis data was compared, variable-by-variable (e.g., solar radiation, R-s; air temperature, T-air; relative humidity, RH; wind speed, u(10); reference evapotranspiration, ET0), with in situ agrometeorological obser-vations obtained from 66 automatic weather stations (2008-2020). In addition, the presence of a climate-dependency on their accuracy was assessed at the different irrigation districts. New hydrological insights for the region: A general good agreement was obtained between observed and reanalysis agrometeorological variables at both daily and seasonal scales. The best perfor-mance was obtained for T-air, followed by RH, R-s, and u(10) for both reanalysis datasets, especially under temperate climate conditions. These performances were translated into slightly higher accuracy of ET0 estimates by ERA5-Land product, confirming the potential of using reanalysis datasets as an alternative data source for retrieving the ET0 and overcoming the unavailability of observed agrometeorological data

A Combined Proteomic and Transcriptomic Signature Is Predictive of Response to Anti-PD-1 Treatment: A Retrospective Study in Metastatic Melanoma Patients

: Resistance biomarkers are needed to identify patients with advanced melanoma obtaining a response to ICI treatment and developing resistance later. We searched a combination of molecular signatures of response to ICIs in patients with metastatic melanoma. In a retrospective study on patients with metastatic melanoma treated with an anti-PD-1 agent carried out at Istituto Nazionale Tumori-IRCCS-Fondazione "G. Pascale", Naples, Italy. We integrated a whole proteome profiling of metastatic tissue with targeted transcriptomics. To assess the prognosis of patients according to groups of low and high risk, we used PFS and OS as outcomes. To identify the proteins and mRNAs gene signatures associated with the patient's response groups, the discriminant analysis for sparse data performed via partial least squares procedure was performed. Tissue samples from 22 patients were analyzed. A combined protein and gene signature associated with poorer response to ICI immunotherapy in terms of PFS and OS was identified. The PFS and OS Kaplan-Meier curves were significantly better for patients with high expression of the protein signature compared to patients with low expression of the protein signature and who were high-risk (Protein: HR = 0.023, 95% CI: 0.003-0.213; p < 0.0001. Gene: HR = 0.053, 95% CI: 0.011-0.260; p < 0.0001). The Kaplan-Meier curves showed that patients with low-risk gene signatures had better PFS (HR = 0 0.221, 95% CI: 0.071-0.68; p = 0.007) and OS (HR = 0.186, 95% CI: 0.05-0.695; p = 0.005). The proteomic and transcriptomic combined analysis was significantly associated with the outcomes of the anti-PD-1 treatment with a better predictive value compared to a single signature. All the patients with low expression of protein and gene signatures had progression within 6 months of treatment (median PFS = 3 months, 95% CI: 2-3), with a significant difference vs. the low-risk group (median PFS = not reached; p < 0.0001), and significantly poorer survival (OS = 9 months, 95% CI: 5-9) compared to patients with high expression of protein and gene signatures (median OS = not reached; p < 0.0001). We propose a combined proteomic and transcriptomic signature, including genes involved in pro-tumorigenic pathways, thereby identifying patients with reduced probability of response to immunotherapy with ICIs for metastatic melanoma

Impact of cemiplimab treatment duration on clinical outcomes in advanced cutaneous squamous cell carcinoma

: Treatment duration with checkpoint inhibitors must be optimized to prevent unjustified toxicity, but evidence for the management of cutaneous squamous cell carcinoma is lacking. A retrospective study was performed to evaluate the survival of patients with cutaneous squamous cell carcinoma (CSCC) who discontinued cemiplimab due to different causes and without progression. Among 95 patients with CSCC who received cemiplimab, 22 (23%) patients discontinued immunotherapy due to causes other than progression, such as comorbidities, toxicity, complete response or lack of compliance (group that discontinued before censoring [DBC]), then 73 patients had standard treatment scheduled (STS). The overall survival was 25.2 months (95% CI: 8.9-29.4) in STS group and 28.3 months (95% CI: 12.7-28.3) in the DBC group; deaths for all causes were 11/22 (50%) in the DBC group and 34/73 (46.6%) in the STS group (p = 0.32). 10/22 (45.4%) subjects died due to CSCC in the DBC after discontinuation and 34/73 (46.6%) in the STS group, and the difference between groups was not significant (p = 0.230). Duration of treatment was significantly lower in subjects with stable disease versus those with complete or partial response (16.9, 30.6 and 34.9 months, respectively; p = 0.004). Among the 22 STS patients, 12 received cemiplimab for less than 12 months (10 [83%] died) and 10 for at least 12 months (1 [10%] died). Our observation, finding no outcome difference between DBC and STS groups, suggests that ICI treatment after one year might expose patients to further treatment related events without efficacy advantages

Comparing the use of ERA5 reanalysis dataset and ground-based agrometeorological data under different climates and topography in Italy

Study region: The study region is represented by seven irrigation districts distributed under different climate and topography conditions in Italy. Study focus: This study explores the reliability and consistency of the global ERA5 single levels and ERA5-Land reanalysis datasets in predicting the main agrometeorological estimates commonly used for crop water requirements calculation. In particular, the reanalysis data was compared, variable-by-variable (e.g., solar radiation, R-s; air temperature, T-air; relative humidity, RH; wind speed, u(10); reference evapotranspiration, ET0), with in situ agrometeorological obser-vations obtained from 66 automatic weather stations (2008-2020). In addition, the presence of a climate-dependency on their accuracy was assessed at the different irrigation districts. New hydrological insights for the region: A general good agreement was obtained between observed and reanalysis agrometeorological variables at both daily and seasonal scales. The best perfor-mance was obtained for T-air, followed by RH, R-s, and u(10) for both reanalysis datasets, especially under temperate climate conditions. These performances were translated into slightly higher accuracy of ET0 estimates by ERA5-Land product, confirming the potential of using reanalysis datasets as an alternative data source for retrieving the ET0 and overcoming the unavailability of observed agrometeorological data

Gene-expression signature predicts autoimmune toxicity in metastatic melanoma

Objectives To identify predictive gene-expression signatures for immune-related adverse events (irAEs) in patients with melanoma treated with anti-PD-1 inhibitors, in the adjuvant therapy (AT) and first-line therapy (FLT). Methods This retrospective study analyzed baseline whole-blood gene expression profile from 161 patients with resected stage III or unresectable stage III-IV melanoma treated with anti-PD-1 inhibitors. RNA was extracted from baseline peripheral blood samples and profiled using the NanoString nCounter PanCancer IO 360 panel. Gene-expression signatures were identified and validated using cross-validated sparse partial least squares modeling and principal component analysis, then correlated with toxicity occurrence. Results A total of 223 and 186 irAEs were observed in the AT and FLT groups, respectively, including arthralgia, colitis, and headache. Distinct gene-expression signatures significantly predicted toxicity occurrence, with variation across therapy settings. Arthralgia was predicted by immune-related and apoptotic gene signatures (eg, SMAD5, FASLG in FLT; ICOS, TGFB2 in AT), while colitis was linked to inflammatory and adhesion-related pathways. In the AT group, headache was associated with genes involved in interferon and adhesion signaling. Across both cohorts, specific signatures predicted overall irAE risk and timing. No events were observed in patients with low-risk signatures over the follow-up period. In the FLT cohort, arthralgia and cutaneous toxicities were positively associated with ORR, while arthralgia, asthenia, colitis, fatigue, and skin-related toxicities correlated with improved disease control rate. No significant association between irAEs and relapse risk was observed in the adjuvant cohort. Conclusions Whole-blood gene-expression profiling enables early identification of patients at high risk for irAEs during anti-PD-1 therapy. These predictive biomarkers may guide personalized toxicity monitoring in melanoma treatment