Uncertainty of CERES-maize calibration under different irrigation strategies using pest optimization algorithm

© 2019 by the authors. An important but rarely studied aspect of crop modeling is the uncertainty associated with model calibration and its effect on model prediction. Biomass and grain yield data from a four-year maize experiment (2008–2011) with six irrigation treatments were divided into subsets by either treatments (Calibration-by-Treatment) or years (Calibration-by-Year). These subsets were then used to calibrate crop cultivar parameters in CERES (Crop Environment Resource Synthesis)-Maize implemented within RZWQM2 (Root Zone Water Quality Model 2) using the automatic Parameter ESTimation (PEST) algorithm to explore model calibration uncertainties. After calibration for each subset, PEST also generated 300 cultivar parameter sets by assuming a normal distribution of each parameter within their reported values in the literature, using the Latin hypercube sampling (LHS) method. The parameter sets that produced similar goodness of fit (11–164 depending on subset used for calibration) were then used to predict all the treatments and years of the entire dataset. Our results showed that the selection of calibration datasets greatly affected the calibrated crop parameters and their uncertainty, as well as prediction uncertainty of grain yield and biomass. The high variability in model prediction of grain yield and biomass among the six (Calibration-by-Treatment) or the four (Calibration-by-Year) scenarios indicated that parameter uncertainty should be considered in calibrating CERES-Maize with grain yield and biomass data from different irrigation treatments, and model predictions should be provided with confidence intervals

Soluble Fas might serve as a diagnostic tool for gastric adenocarcinoma

<p>Abstract</p> <p>Background</p> <p>Fas (Apo-1/CD95) and its specific ligand (FasL) are key elements in apoptosis. They have been studied in different malignancies but there are few published studies about the soluble forms of these markers (i.e. sFas/sFasL) in gastric cancer. We have compared the serum levels of sFas/sFasL in gastric adenocarcinoma patients and cases with pre-neoplastic lesions as potential markers for early diagnosis, and investigated their relation with clinicopathological characteristics.</p> <p>Methods</p> <p>Fifty-nine newly-diagnosed cases of gastric adenocarcinoma who had undergone gastrectomy, along with 62 endoscopically- and histologically-confirmed non-cancer individuals were enrolled in this study. sFas/sFasL serum levels were detected by Enzyme Linked Immunosurbent Assay.</p> <p>Results</p> <p>Mean serum sFas level was significantly higher in gastric cancer patients than in control group (305.97 ± 63.71 (pg/ml) vs. 92.98 ± 4.95 (pg/ml), P < 0.001); while the mean serum level of sFasL was lower in patients with gastric adenocarcinoma (0.138 ± 0.04 (pg/ml) vs. 0.150 ± 0.02 (pg/ml), P < 0.001). Mean serum levels of sFas/sFasL were significantly different in both intestinal/diffuse and cardiac/non-cardiac subtypes when compared to the control group (P < 0.001). There was an increase in the serum level of sFas from the first steps of pre-neoplastic lesions to gastric adenocarcinoma (P < 0.001). Patients who had no lymph node involvement (<it>N₀</it>) showed significantly higher serum levels of sFas compared to others (P = 0.044).</p> <p>Conclusions</p> <p>Production of sFas may play a critical role in the carcinogenesis of intestinal-type gastric cancer. sFas serum level may serve as a non-invasive tool for early diagnosis of gastric cancer.</p

An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae

Background: Probabilistic functional gene networks are powerful theoretical frameworks for integrating heterogeneous functional genomics and proteomics data into objective models of cellular systems. Such networks provide syntheses of millions of discrete experimental observations, spanning DNA microarray experiments, physical protein interactions, genetic interactions, and comparative genomics; the resulting networks can then be easily applied to generate testable hypotheses regarding specific gene functions and associations. Methodology/Principal Findings: We report a significantly improved version (v. 2) of a probabilistic functional gene network [1] of the baker's yeast, Saccharomyces cerevisiae. We describe our optimization methods and illustrate their effects in three major areas: the reduction of functional bias in network training reference sets, the application of a probabilistic model for calculating confidences in pair-wise protein physical or genetic interactions, and the introduction of simple thresholds that eliminate many false positive mRNA co-expression relationships. Using the network, we predict and experimentally verify the function of the yeast RNA binding protein Puf6 in 60S ribosomal subunit biogenesis. Conclusions/Significance: YeastNet v. 2, constructed using these optimizations together with additional data, shows significant reduction in bias and improvements in precision and recall, in total covering 102,803 linkages among 5,483 yeast proteins (95% of the validated proteome). YeastNet is available from http://www.yeastnet.org.This work was supported by grants from the N.S.F. (IIS-0325116, EIA-0219061), N.I.H. (GM06779-01,GM076536-01), Welch (F-1515), and a Packard Fellowship (EMM). These agencies were not involved in the design and conduct of the study, in the collection, analysis, and interpretation of the data, or in the preparation, review, or approval of the manuscript.Cellular and Molecular Biolog

Homeostatic regulation of the endoneurial microenvironment during development, aging and in response to trauma, disease and toxic insult

The endoneurial microenvironment, delimited by the endothelium of endoneurial vessels and a multi-layered ensheathing perineurium, is a specialized milieu intérieur within which axons, associated Schwann cells and other resident cells of peripheral nerves function. The endothelium and perineurium restricts as well as regulates exchange of material between the endoneurial microenvironment and the surrounding extracellular space and thus is more appropriately described as a blood–nerve interface (BNI) rather than a blood–nerve barrier (BNB). Input to and output from the endoneurial microenvironment occurs via blood–nerve exchange and convective endoneurial fluid flow driven by a proximo-distal hydrostatic pressure gradient. The independent regulation of the endothelial and perineurial components of the BNI during development, aging and in response to trauma is consistent with homeostatic regulation of the endoneurial microenvironment. Pathophysiological alterations of the endoneurium in experimental allergic neuritis (EAN), and diabetic and lead neuropathy are considered to be perturbations of endoneurial homeostasis. The interactions of Schwann cells, axons, macrophages, and mast cells via cell–cell and cell–matrix signaling regulate the permeability of this interface. A greater knowledge of the dynamic nature of tight junctions and the factors that induce and/or modulate these key elements of the BNI will increase our understanding of peripheral nerve disorders as well as stimulate the development of therapeutic strategies to treat these disorders

Direct assimilation of measured soil water content in Root Zone Water Quality Model calibration for deficit-irrigated maize

© 2019 The Authors. Agronomy Journal © 2019 American Society of Agronomy Correct soil water simulation is critical for water balance and plant growth in agricultural systems. Crop production simulation errors have often been attributed to a lack of accuracy in soil water content (SWC) estimates. However, only a few studies have quantified the effects of SWC estimate errors on crop production and evapotranspiration (ET), especially under different irrigation treatments. The objective of this study was to investigate the impacts of direct assimilation of measured SWC during model calibration for deficit irrigated maize (Zea mays L.) on simulated ET, leaf area index (LAI), biomass, and yield. The CERES-Maize model within the Root Zone Water Quality Model (RZWQM) was calibrated using the automatic parameter estimation (PEST) software. Simulation results showed that, using PEST-optimized crop parameters, RZWQM was able to adequately predict crop yield (relative root mean squared error, rRMSE, of 4.8%) and biomass (rRMSE of 7.1%) in response to irrigation levels, in spite of the bias in SWC and ET simulation. However, with the same crop parameters but replacing simulated SWC with measured data, simulations of crop yield and biomass became worse, with higher rRMSE values (14.5% for yield and 21.5% for biomass). This unexpected model performance with SWC assimilation was mainly associated with the water addition and removal from the soil, which was improved only by recalibration of both soil and crop parameters. This study suggested compensating effects between soil and crop parameters during model calibration. Caution should be applied when using measured SWC as model inputs, especially under water stress conditions

Experiences with treating immigrants: a qualitative study in mental health services across 16 European countries

PURPOSE: While there has been systematic research on the experiences of immigrant patients in mental health services within certain European countries, little research has explored the experiences of mental health professionals in the delivery of services to immigrants across Europe. This study sought to explore professionals' experiences of delivering care to immigrants in districts densely populated with immigrants across Europe. METHODS: Forty-eight semi-structured interviews were conducted with mental health care professionals working in 16 European countries. Professionals in each country were recruited from three areas with the highest proportion of immigrants. For the purpose of this study, immigrants were defined as first-generation immigrants born outside the country of current residence, including regular immigrants, irregular immigrants, asylum seekers, refugees and victims of human trafficking. Interviews were transcribed and analysed using thematic analysis. RESULTS: The interviews highlighted specific challenges to treating immigrants in mental health services across all 16 countries including complications with diagnosis, difficulty in developing trust and increased risk of marginalisation. CONCLUSIONS: Although mental health service delivery varies between and within European countries, consistent challenges exist in the experiences of mental health professionals delivering services in communities with high proportions of immigrants. Improvements to practice should include training in reaching appropriate diagnoses, a focus on building trusting relationships and measures to counter marginalisation

New insights into experimental visceral leishmaniasis: Real-time in vivo imaging of Leishmania donovani virulence.

Visceral leishmaniasis is an insidious neglected disease with worldwide distribution. It is caused by parasites from the Leishmania donovani complex, which are able to be transmitted by different species of phlebotomine sand flies and to infect numerous mammal hosts. Despite the high number of people infected or at risk, and the remarkable quantity of studies focusing on this disease, a proper experimental model to efficiently decipher the infectious process of visceral leishmaniasis taking into account the nuances of parasite’s virulence and the duration of the infection is still lacking. Therefore, using golden Syrian hamsters and BALB/c mice, state-of-the-art genetic manipulation applied on a fully virulent L. donovani strain and in vivo imaging approaches, we describe herein three benefits for experimental visceral leishmaniasis: (i) the development of a double transfected bioluminescent (firefly luciferase) and fluorescent (E2-crimson) virulent strain of L. donovani (Ld1S_luci_E2-crimson), favoring a wide range of both in vivo and in vitro investigations, (ii) the establishment of a non-invasive mouse model to evaluate the infectious process during visceral leishmaniasis and the parasite’s virulence in real time, allowing longitudinal studies with the same animals, and (iii) the elaboration of a suitable method to reinstate (and verify anew) the virulence in a population of attenuated parasites, by recovering persistent parasites from chronic infected mice. Consequently, these results open up new perspectives on the study of visceral leishmaniasis, especially in the fields of therapeutics and vaccinology, since the model described herein renders now possible long-lasting follow up studies, with easy and accurate day-by-day verifications of the infection status along with a reduced number of laboratory animals.ClinicalTrials.gov 2013-0047